RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. Radiation Biology Ontology 2024-02-29 editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO:0000112 uberon example_of_usage true example_of_usage example of usage example of usage definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor term editor alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator An entity primarily responsible for making the content of the resource. Creator Creator creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. http://purl.org/dc/elements/1.1/description uberon dc-description true dc-description An account of the content of the resource. Description Description description Typically, a Title will be a name by which the resource is formally known. http://purl.org/dc/elements/1.1/title uberon dc-title true dc-title A name given to the resource. Title Title title Mark Miller 2018-05-11T13:47:29Z http://purl.org/dc/terms/license uberon dcterms-license true dcterms-license license created by created_by creation date has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. An alternative label for a given entity such as a commonly used abbreviation or synonym. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has_obo_namespace has_related_synonym in_subset label label http://www.w3.org/2000/01/rdf-schema#seeAlso spatial uberon seeAlso true seeAlso see also is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of http://www.ebi.ac.uk/efo/part_of BFO:0000050 part of external quality spatial uberon part_of part_of EFO_0000822 part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part http://www.ebi.ac.uk/efo/has_part BFO:0000051 chebi_ontology external quality spatial uberon has_part false has_part has part has part has_part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes BFO:0000057 has participant preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external uberon preceded_by preceded_by preceded by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in https://wiki.geneontology.org/Occurs_in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000067 uberon contains_process contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process contains process x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000096 rostral_to spatial uberon anterior_to anterior_to anterior to x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 spatial uberon dorsal_to dorsal_to dorsal to x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:0000099 caudal to spatial uberon posterior_to posterior_to posterior to x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm caudal to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 spatial uberon ventral_to ventral_to ventral to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 spatial uberon deep_to deep_to deep to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:cjm Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 spatial uberon superficial_to superficial_to superficial to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:0000120 NCIT:C25229 spatial uberon in_left_side_of in_left_side_of in left side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:PATO_mtg_2009 X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:0000121 NCIT:C25228 spatial uberon in_right_side_of in_right_side_of in right side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:PATO_mtg_2009 X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion. BSPO:0000122 spatial uberon in_posterior_side_of in_posterior_side_of in posterior side of X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion. BSPO:PATO_mtg_2009 X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion. BSPO:0000123 spatial uberon in_anterior_side_of in_anterior_side_of in anterior side of X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion. BSPO:PATO_mtg_2009 x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:0000124 spatial uberon in_proximal_side_of in_proximal_side_of in proximal side of x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:PATO_mtg_2009 x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:0000125 spatial uberon in_distal_side_of in_distal_side_of in distal side of x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:PATO_mtg_2009 X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure BSPO:0000126 spatial uberon in_lateral_side_of in_lateral_side_of in lateral side of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure UBERON:cjm X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y BSPO:0001106 spatial uberon proximalmost_part_of proximalmost_part_of proximalmost part of X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y https://orcid.org/0000-0002-6601-2165 x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 spatial uberon immediately_deep_to immediately_deep_to immediately deep to x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:curators X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y BSPO:0001108 spatial uberon distalmost_part_of distalmost_part_of distalmost part of X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y https://orcid.org/0000-0002-6601-2165 X intersects median plane of iff X crosses the midine plane of Y. BSPO:0005001 spatial uberon intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects midsagittal plane of x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:0015014 spatial uberon immediately_superficial_to immediately_superficial_to immediately superficial to x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:curators X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. BSPO:0015101 spatial uberon in_dorsal_side_of in_dorsal_side_of in dorsal side of X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. BSPO:cjm http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part concretizes intended to realize realizes A duck swimming in a pond is partially surrounded by air and partially surrounded by water. x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x Definition modified from 'surrounded by'. partially_surrounded_by A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. derives from part of Afforestation results in the expansion of a forest. A process, p, results in the expansion of a material entity, m, if the spatial extent of m is increased as a result of participating in p. results in expansion of A relation between a process and a disposition such that the existence of the disposition is caused by the execution of the process. Consider ceding to RO 2018-11-03T20:58:13Z generates GOREL:0002003 external results_in_distribution_of results_in_distribution_of results in distribution of results_in_distribution_of GOREL:0002004 external results_in_fission_of results_in_fission_of results in fission of results_in_fission_of hasAncestryStatus has measurement unit label This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot http://www.ebi.ac.uk/efo/has_input OBI:0000293 has specified input has_input has_specified_input has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters http://www.ebi.ac.uk/efo/is_input_of is specified input of is_input_of is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot OBI:0000299 has specified output has_output has_specified_output has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified output of is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in http://www.ebi.ac.uk/efo/EFO_0000829 RO:0000052 inheres_in characteristic_of inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in inheres in inheres_in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 external bearer_of bearer_of has_characteristic bearer of bearer of has characteristic has characteristic https://github.com/oborel/obo-relations/pull/284 participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation Participates in is a primitive instance-level relation between a continuant and a process in which it participates. For example a scanner participates in a scanning process at some specific time. a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 external uberon participates_in participates_in participates in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the A continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant has_participant has participant has participant has_participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of RO:0000079 function_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of RO:0000080 quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of RO:0000081 role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function RO:0000085 has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality http://www.ebi.ac.uk/efo/has_quality RO:0000086 uberon has_quality has_quality has quality has quality has_quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 chebi_ontology has_role false false has_role has role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence RO:0000091 has_disposition has disposition inverse of has disposition RO:0000092 disposition_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of RO:0001015 uberon location_of location_of location of location of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 uberon located_in located_in located in located in https://wiki.geneontology.org/Located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of surface of RO:0002000 2D_boundary_of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary RO:0002002 uberon has_boundary has_2D_boundary has_boundary has 2D boundary has 2D boundary http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 uberon innervated_by innervated_by innervated_by innervated_by X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland RO:0002007 uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z RO:0002013 external has_regulatory_component_activity has_regulatory_component_activity has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z RO:0002014 external has_negative_regulatory_component_activity has_negative_regulatory_component_activity By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z RO:0002017 has_component_activity A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z RO:0002018 has_component_process has component process A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. 2017-07-20T17:19:37Z RO:0002021 occurs_across occurs across dos 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z RO:0002025 has_effector_activity This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland <= RO:0002081 before_or_simultaneous_with Primitive instance level timing relation between events before or simultaneous with x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 uberon simultaneous_with simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with simultaneous with David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland RO:0002086 ends_after X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of RO:0002087 external uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately preceded by David Osumi-Sutherland ends_at_start_of meets RO:0002090 external immediately_precedes immediately_precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes immediately precedes David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) RO:0002100 has_soma_location has soma location Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002103 uberon synapsed_by synapsed_by synapsed by synapsed by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) RO:0002104 has_plasma_membrane_part has plasma membrane part Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002120 synapsed_to N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) synapsed to x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 external spatial uberon overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps true x overlaps y iff they have some part in common. BSPO:cjm Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002134 uberon innervates innervates innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) RO:0002150 uberon continuous_with continuous_with continuous with continuous with FMA:85972 lactation SubClassOf 'only in taxon' some 'Mammalia' x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria RO:0002160 uberon only_in_taxon only_in_taxon only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. RO:0002176 uberon connects connects connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 uberon attaches_to_part_of attached_to_part_of attaches_to_part_of attached to part of attached to part of true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure RO:0002178 uberon supplies supplies supplies supplies Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure RO:0002179 uberon drains drains drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 external uberon has_component qualifier has_component qualifier For use in recording has_part with a cardinality constraint. placeholder relation to indicate normality/abnormality. has component has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt RO:0002207 has developmental precursor uberon directly_develops_from directly_develops_from TODO - add child relations from DOS directly develops from directly develops from inverse of directly develops from developmental precursor of RO:0002210 directly_develops_into directly develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates regulates (processual) Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external uberon capable_of capable_of capable of capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO:0002216 external uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x Chris Mungall RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded by A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall RO:0002220 spatial uberon adjacent_to adjacent_to adjacent to adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 external uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of develops from part of x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 uberon develops_in develops_in develops in develops in inverse of ends with Chris Mungall RO:0002229 uberon ends ends ends ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by RO:0002230 external uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y starts with process that occurs in RO:0002231 has_start_location has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in RO:0002232 has_end_location has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes RO:0002233 external has_input has_input has input has input https://wiki.geneontology.org/Has_input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces RO:0002234 external has_output has_output has output has output https://wiki.geneontology.org/Has_output In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. RO:0002252 uberon connecting_branch_of connecting_branch_of connecting branch of inverse of connecting branch of RO:0002253 has_connecting_branch has connecting branch Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 developmentally_contributes_to developmentally contributes to t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 uberon developmentally_induced_by developmentally_induced_by developmentally induced by developmentally induced by Inverse of developmentally induced by RO:0002257 developmentally_induces developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. RO:0002263 acts_upstream_of acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. RO:0002264 affects acts_upstream_of_or_within acts upstream of or within https://wiki.geneontology.org/Acts_upstream_of_or_within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally replaces Inverse of developmentally preceded by Chris Mungall RO:0002286 developmentally_succeeded_by developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall RO:0002287 part_of_developmental_precursor_of part of developmental precursor of p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall RO:0002295 external results_in_developmental_progression_of results_in_developmental_progression_of results in developmental progression of results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. http://www.geneontology.org/GO.doc.development.shtml RO:0002296 results_in_development_of results in development of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of results_in_formation_of results in formation of results in formation of an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. GOC:mtg_berkeley_2013 RO:0002298 results_in_morphogenesis_of results in morphogenesis of an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. GOC:mtg_berkeley_2013 RO:0002299 results_in_maturation_of results in maturation of Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. Pier Buttigieg adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. has habitat has habitat p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm RO:0002304 external causally_upstream_of,_positive_effect causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. cjm RO:0002305 external causally_upstream_of,_negative_effect causally_upstream_of,_negative_effect holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of characteristic of part of inheres in part of true an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity GOC:mtg_berkeley_2013 RO:0002315 results_in_acquisition_of_features_of results in acquisition of features of A relationship that holds via some environmental process Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. RO:0002327 enables enables https://wiki.geneontology.org/Enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 part_of_structure_that_is_capable_of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of RO:0002331 involved_in involved in https://wiki.geneontology.org/Involved_in inverse of enables Chris Mungall RO:0002333 enabled_by enabled by https://wiki.geneontology.org/Enabled_by inverse of regulates Chris Mungall regulated by (processual) RO:0002334 external regulated_by regulated_by regulated by regulated by inverse of negatively regulates Chris Mungall RO:0002335 external negatively_regulated_by negatively_regulated_by negatively regulated by negatively regulated by inverse of positively regulates Chris Mungall RO:0002336 external positively_regulated_by positively_regulated_by positively regulated by positively regulated by A relationship that holds via some process of localization Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to related via localization to This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. RO:0002338 has_target_start_location has target start location This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. RO:0002339 has_target_end_location has target end location Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l RO:0002341 results_in_transport_along results in transport along Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. RO:0002342 results_in_transport_across results in transport across 'pollen tube growth' results_in growth_of some 'pollen tube' RO:0002343 results_in_growth_of results in growth of 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) RO:0002344 results_in_transport_to_from_or_in results in transport to from or in An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO RO:0002350 member_of member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member has member inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of input of inverse of has output Chris Mungall RO:0002353 external uberon output_of output_of output of output of Chris Mungall RO:0002354 formed_as_result_of formed as result of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attached_to attaches_to attached to attached to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin has muscle origin has muscle origin We need to import uberon muscle to create a stricter domain constraint m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) RO:0002373 uberon has_muscle_insertion has_muscle_insertion has muscle insertion has muscle insertion We need to import uberon muscle into RO to use as a stricter domain constraint A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) RO:0002375 in_branching_relationship_with in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 uberon tributary_of tributary_of tributary of tributary of http://en.wikipedia.org/wiki/Tributary A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios RO:0002379 spatially_coextensive_with spatially coextensive with In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y RO:0002380 uberon branching_part_of branching_part_of branching part of branching part of FMA:85994 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall RO:0002384 has_developmental_potential_involving has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into inverse of upstream of Chris Mungall RO:0002404 external causally_downstream_of causally_downstream_of causally downstream of causally downstream of Chris Mungall RO:0002405 external immediately_causally_downstream_of immediately_causally_downstream_of immediately causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. Chris Mungall indirectly activates RO:0002407 indirectly_positively_regulates indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. Chris Mungall indirectly inhibits RO:0002409 indirectly_negatively_regulates indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates This relation groups causal relations between material entities and causal relations between processes relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall RO:0002411 external causally_upstream_of causally_upstream_of causally upstream of causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall RO:0002412 external immediately_causally_upstream_of immediately_causally_upstream_of immediately causally upstream of immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) RO:0002418 external affects causally_upstream_of_or_within causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within Chris Mungall RO:0002427 external causally_downstream_of_or_within causally_downstream_of_or_within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall RO:0002428 involved_in_regulation_of involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall RO:0002429 involved_in_positive_regulation_of involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall RO:0002430 involved_in_negative_regulation_of involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in RO:0002432 enables activity in is_active_in is active in https://wiki.geneontology.org/Is_active_in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with interacts_with interacts with http://purl.obolibrary.org/obo/MI_0914 http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with RO:0002436 molecularly_interacts_with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. RO:0002447 phosphorylates phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré RO:0002448 molecularly controls directly_regulates_activity_of directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits RO:0002449 molecularly decreases activity of directly_negatively_regulates_activity_of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates RO:0002450 molecularly increases activity of directly_positively_regulates_activity_of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall RO:0002479 has_part_that_occurs_in has part that occurs in true Chris Mungall is kinase activity See notes for inverse relation RO:0002485 receives_input_from receives input from This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. RO:0002486 sends_output_to sends output to Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. RO:0002487 relation_between_physical_entity_and_a_process_or_stage relation between physical entity and a process or stage x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). RO:0002488 uberon existence_starts_during existence_starts_during existence starts during x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). RO:0002489 uberon existence_starts_with existence_starts_with existence starts with x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) RO:0002490 existence_overlaps The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) RO:0002491 exists during uberon existence_starts_and_ends_during existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. https://orcid.org/0000-0002-6601-2165 x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). RO:0002493 uberon existence_ends_with existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall RO:0002494 uberon transformation_of transformation_of transformation of x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall RO:0002495 uberon immediate_transformation_of immediate_transformation_of immediate transformation of x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process RO:0002500 causal_agent_in_process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002501 causal_relation_between_processes causal relation between processes Chris Mungall depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002506 causal_relation_between_entities causal relation between entities s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 uberon has_skeleton has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. Chris Mungall causally influenced by (entity-centric) RO:0002559 causally_influenced_by causally influenced by Chris Mungall interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) RO:0002566 causally_influences causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. RO:0002567 biomechanically_related_to biomechanically related to m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Wikipedia:Antagonist_(muscle) RO:0002568 uberon has_muscle_antagonist has_muscle_antagonist has muscle antagonist inverse of branching part of RO:0002569 uberon has_branching_part has_branching_part has branching part x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 uberon conduit_for conduit_for conduit for x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity RO:0002572 uberon luminal_space_of luminal_space_of luminal space of inverse of has skeleton RO:0002576 uberon skeleton_of skeleton_of skeleton of Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) RO:0002578 external directly_regulates directly_regulates directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p RO:0002586 results_in_breakdown_of results in breakdown of RO:0002588 external results_in_assembly_of results_in_assembly_of results in assembly of RO:0002590 external results_in_disassembly_of results_in_disassembly_of results in disassembly of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 external results_in_organization_of results_in_organization_of results in organization of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall RO:0002595 causal_relation_between_material_entity_and_a_process causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. RO:0002596 capable_of_regulating capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. RO:0002597 capable_of_negatively_regulating capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. RO:0002598 capable_of_positively_regulating capable of positively regulating Inverse of 'causal agent in process' RO:0002608 external process_has_causal_agent process_has_causal_agent process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) RO:0002629 external directly_positively_regulates directly_positively_regulates directly positively regulates https://wiki.geneontology.org/Directly_positively_regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) RO:0002630 external directly_negatively_regulates directly_negatively_regulates directly negatively regulates https://wiki.geneontology.org/Directly_negatively_regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel RO:0003000 uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel RO:0003001 uberon produced_by produced_by produced by produced by p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. 2018-12-13T11:26:17Z RO:0004007 external has_primary_input_or_output has_primary_input_or_output has primary input or output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. 2018-12-13T11:26:32Z RO:0004008 external has_primary_output has_primary_output has primary output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:cjm GOC:dph GOC:kva GOC:pt PMID:27812932 p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. 2018-12-13T11:26:56Z RO:0004009 has_primary_input has primary input p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. cjm 2017-12-26T19:45:49Z realized in response to stimulus Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z RO:0004031 enables_subfunction enables subfunction cjm 2018-01-26T23:49:30Z RO:0004032 acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect cjm 2018-01-26T23:49:51Z RO:0004033 acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z RO:0004034 acts_upstream_of,_positive_effect acts upstream of, positive effect https://wiki.geneontology.org/Acts_upstream_of,_positive_effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z RO:0004035 acts_upstream_of,_negative_effect acts upstream of, negative effect https://wiki.geneontology.org/Acts_upstream_of,_negative_effect cjm 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect cjm 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. Austin Meier Chris Mungall David Osumi-Sutherland Marie Angelique Laporte triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process triggered by process RO:cjm The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré RO:0011002 regulates_activity_of regulates activity of p acts on population of c iff c' is a collection, has members of type c, and p has participant c 2020-06-08T17:21:33Z RO:0012003 acts_on_population_of acts on population of 2021-02-26T07:28:29Z RO:0012008 results_in_fusion_of results in fusion of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. pg 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates indirectly regulates q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. RO:0015006 different_in_magnitude_relative_to different in magnitude relative to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. RO:0015007 increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased in magnitude relative to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. RO:0015011 has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has cross section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. https://orcid.org/0000-0002-6601-2165 A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. https://orcid.org/0000-0001-9625-1899 https://orcid.org/0000-0003-2620-0345 A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. RO:0019000 gene_ontology regulates_characteristic regulates_characteristic regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. RO:0019001 gene_ontology positively_regulates_characteristic positively_regulates_characteristic positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. RO:0019002 gene_ontology negatively_regulates_characteristic negatively_regulates_characteristic negatively regulates characteristic p has anatomical participant c iff p has participant c, and c is an anatomical entity 2018-09-26T01:08:58Z RO:0040036 external results_in_changes_to_anatomical_or_cellular_structure results_in_changes_to_anatomical_or_cellular_structure results in changes to anatomical or cellular structure chebi_ontology has_parent_hydride false false has parent hydride chebi_ontology is_conjugate_acid_of true false is conjugate acid of chebi_ontology is_conjugate_base_of true false is conjugate base of chebi_ontology is_substituent_group_from false false is substituent group from chebi_ontology is_tautomer_of true is tautomer of x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into extends_fibers_into X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y https://orcid.org/0000-0002-7073-9172 Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s. add to RO uberon indirectly_supplies indirectly_supplies uberon layer_part_of layer part of x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. uberon capable_of_has_part site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of has atomic number Number of protons in an atomic nucleus We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning has atomic number has number of atomic nuclei has measurement value has specified numeric value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified numeric value has specified value A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value The atomic mass (ma or m) is the mass of an atom. The protons and neutrons of the nucleus account for nearly all of the total mass of atoms, with the electrons and nuclear binding energy making minor contributions. has atomic mass mass number A planned process that has specified output a software product and that involves the creation of source code. Mathias Brochhausen William R. Hogan http://en.wikipedia.org/wiki/Software_development A planned process resulting in a software product involving the creation of source code. software development creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000002 continuant continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. processual entity (BFO) An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a chair a heart a heart a leg a leg a molecule a molecule a spatial region a spatial region an atom an atom an orchestra. an orchestra. an organism an organism the bottom right portion of a human torso the bottom right portion of a human torso the interior of your mouth the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl anatomical entity (BFO) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000004 A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) James Malone (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] http://www.ebi.ac.uk/efo/EFO_0001433 true An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. http://www.ifomis.org/bfo/1.1/span#ProcessualEntity NCIt:C29862 SNOMEDCT:415178003 BFO:0000015 An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease. an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease. BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. James Malone modified from original b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disease property http://www.ebi.ac.uk/efo/EFO_0001438 true A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C. http://www.ifomis.org/bfo/1.1/snap#Disposition NCIt:C41205 BFO:0000016 disposition disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. https://orcid.org/0000-0001-8815-0078 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000017 realizable realizable entity realizable_entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] quality Quality quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril A quality is an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee James Malone a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] http://www.ebi.ac.uk/efo/EFO_0001436 true A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property). http://www.ifomis.org/bfo/1.1/snap#Quality NCIt:C25283 SNOMEDCT:263496004 quality quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. James Malone Sirarat Sarntivijai (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] sample characteristic http://www.ebi.ac.uk/efo/EFO_0001443 true A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant BFO:0000020 SpecificallyDependentContinuant specifically dependent continuant BFO:0000020 A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. characteristic material property specifically dependent continuant specifically dependent continuant https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 We should name the inverse in COB and avoid the confusing inverse(..) construct b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. James Malone b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] http://www.ebi.ac.uk/efo/EFO_0001440 true A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts. http://www.ifomis.org/bfo/1.1/snap#Role MeSH:D012380 NCIt:C48835 BFO:0000023 role role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat object fiat object part object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] site object gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000031 A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] material MaterialEntity material entity A heart, a human, a fly, a microarray. a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. James Malone A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] sample factor http://www.ebi.ac.uk/efo/EFO_0001434 true An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. http://www.ifomis.org/bfo/1.1/snap#MaterialEntity material type BFO:0000040 material entity material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) Material anatomical entity that is a member of an individual species or is a viral or viroid particle. organism or virus Melissa Haendel 9/18/11 organism or virus or viroid Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. -1 0.000548579903 0.0 KEGG:C05359 PMID:21614077 Wikipedia:Electron electron chebi_ontology Elektron beta beta(-) beta-particle e e(-) e- negatron CHEBI:10545 electron PMID:21614077 Europe PMC electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. chebi_ontology dicarboxylic acids and derivatives CHEBI:131927 dicarboxylic acids and O-substituted derivatives dicarboxylic acids and derivatives ChEBI A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3. -1 (C14H20NO11)n.H2O chebi_ontology hyaluronan hyaluronate polyanion CHEBI:132153 hyaluronate hyaluronan UniProt hyaluronate polyanion ChEBI Any steroid that has beta-configuration at position 5. chebi_ontology 5beta steroids 5beta-steroid 5beta-steroids CHEBI:136889 5beta steroid 5beta steroids ChEBI 5beta-steroid ChEBI 5beta-steroids ChEBI An atom of an element that exhibits properties that are between those of metals and nonmetals, or that has a mixture of them. The term generally includes boron, silicon, germanium, arsenic, antimony, and tellurium, while carbon, aluminium, selenium, polonium, and astatine are less commonly included. Wikipedia:Metalloid chebi_ontology metalloid metalloids CHEBI:137980 metalloid atom metalloid ChEBI metalloids ChEBI A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water. Wikipedia:Mineral_acid chebi_ontology inorganic acids mineral acid mineral acids CHEBI:138103 inorganic acid inorganic acids ChEBI mineral acid ChEBI mineral acids ChEBI Any member of a group of hydroxy steroids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration, while in lower vertebrates, some bile acids, known as allo-bile acids, have 5alpha-configuration. chebi_ontology CHEBI:138366 bile acids Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology gas molecular entities gaseous molecular entities gaseous molecular entity CHEBI:138675 gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI -1 CH2NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M 60.03212 60.00910 NC([O-])=O Beilstein:3903503 CAS:302-11-4 Gmelin:239604 carbamate chebi_ontology Carbamat Karbamat carbamate ion carbamic acid, ion(1-) CHEBI:13941 carbamate Beilstein:3903503 Beilstein CAS:302-11-4 ChemIDplus Gmelin:239604 Gmelin carbamate IUPAC carbamate UniProt Carbamat ChEBI Karbamat ChEBI carbamate ion ChemIDplus carbamic acid, ion(1-) ChemIDplus An antigenic epitope recognized by an anti-bilirubin monoclonal antibody designated 24G7. A substructure of bilirubin IXalpha, it is the region containing the oxo group at C-1, the methyl group at C-2, C-(4, 5, 6, 9), and N-21 and -22. 0 C7H6N2O 134.136 134.04801 C(=CC(NC(=*)*)=*)(NC(C(C)=*)=O)* chebi_ontology CHEBI:142163 24G7 epitope electron donor A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. CHEBI:13699 CHEBI:2377 KEGG:C00028 KEGG:C16722 Acceptor chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur CHEBI:15339 acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter. +1 C7H16NO2 InChI=1S/C7H16NO2/c1-7(9)10-6-5-8(2,3)4/h5-6H2,1-4H3/q+1 OIPILFWXSMYKGL-UHFFFAOYSA-N 146.20748 146.11756 CC(=O)OCC[N+](C)(C)C CHEBI:12686 CHEBI:13715 CHEBI:22197 CHEBI:2416 CHEBI:40559 Beilstein:1764436 CAS:51-84-3 DrugBank:DB03128 Drug_Central:65 Gmelin:326108 KEGG:C01996 LINCS:LSM-5888 PDBeChem:ACH PMID:14764638 PMID:15014918 PMID:15231705 PMID:15361288 PMID:18050502 PMID:18407448 PMID:19255787 PMID:20963497 PMID:21130809 PMID:21246223 PMID:21545631 PMID:21601579 Wikipedia:Acetylcholine 2-acetyloxy-N,N,N-trimethylethanaminium ACETYLCHOLINE Acetylcholine acetylcholine chebi_ontology ACh Azetylcholin O-Acetylcholine choline acetate CHEBI:15355 acetylcholine Beilstein:1764436 ChemIDplus CAS:51-84-3 ChemIDplus CAS:51-84-3 KEGG COMPOUND Drug_Central:65 DrugCentral Gmelin:326108 Gmelin PMID:14764638 Europe PMC PMID:15014918 Europe PMC PMID:15231705 Europe PMC PMID:15361288 Europe PMC PMID:18050502 Europe PMC PMID:18407448 Europe PMC PMID:19255787 Europe PMC PMID:20963497 Europe PMC PMID:21130809 Europe PMC PMID:21246223 Europe PMC PMID:21545631 Europe PMC PMID:21601579 Europe PMC 2-acetyloxy-N,N,N-trimethylethanaminium IUPAC ACETYLCHOLINE PDBeChem Acetylcholine KEGG_COMPOUND acetylcholine UniProt ACh ChemIDplus Azetylcholin ChEBI O-Acetylcholine KEGG_COMPOUND choline acetate ChemIDplus A simple monocarboxylic acid containing two carbons. 0 C2H4O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) QTBSBXVTEAMEQO-UHFFFAOYSA-N 60.05200 60.02113 CC(O)=O CHEBI:22169 CHEBI:2387 CHEBI:40486 Beilstein:506007 CAS:64-19-7 Drug_Central:4211 Gmelin:1380 HMDB:HMDB0000042 KEGG:C00033 KEGG:D00010 KNApSAcK:C00001176 LIPID_MAPS_instance:LMFA01010002 MetaCyc:ACET PDBeChem:ACT PDBeChem:ACY PMID:12005138 PMID:15107950 PMID:16630552 PMID:16774200 PMID:17190852 PMID:19416101 PMID:19469536 PMID:22153255 PMID:22173419 PPDB:1333 Reaxys:506007 Wikipedia:Acetic_acid ACETIC ACID Acetic acid acetic acid chebi_ontology AcOH CH3-COOH CH3CO2H E 260 E-260 E260 Essigsaeure Ethanoic acid Ethylic acid HOAc INS No. 260 MeCO2H MeCOOH Methanecarboxylic acid acide acetique ethoic acid CHEBI:15366 acetic acid Beilstein:506007 Beilstein CAS:64-19-7 ChemIDplus CAS:64-19-7 KEGG COMPOUND CAS:64-19-7 NIST Chemistry WebBook Drug_Central:4211 DrugCentral Gmelin:1380 Gmelin LIPID_MAPS_instance:LMFA01010002 LIPID MAPS PMID:12005138 Europe PMC PMID:15107950 Europe PMC PMID:16630552 Europe PMC PMID:16774200 Europe PMC PMID:17190852 Europe PMC PMID:19416101 Europe PMC PMID:19469536 Europe PMC PMID:22153255 Europe PMC PMID:22173419 Europe PMC Reaxys:506007 Reaxys ACETIC ACID PDBeChem Acetic acid KEGG_COMPOUND acetic acid IUPAC AcOH ChEBI CH3-COOH IUPAC CH3CO2H ChEBI E 260 ChEBI E-260 ChEBI E260 ChEBI Essigsaeure ChEBI Ethanoic acid KEGG_COMPOUND Ethylic acid ChemIDplus HOAc ChEBI INS No. 260 ChEBI MeCO2H ChEBI MeCOOH ChEBI Methanecarboxylic acid ChemIDplus acide acetique ChemIDplus ethoic acid ChEBI water The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes). +1 H InChI=1S/p+1 GPRLSGONYQIRFK-UHFFFAOYSA-N 1.00794 1.008 [H+] CHEBI:10744 CHEBI:13357 CHEBI:5584 KEGG:C00080 Hydron hydrogen(1+) hydron chebi_ontology H(+) H+ CHEBI:15378 hydron Hydron KEGG_COMPOUND hydrogen(1+) IUPAC hydron IUPAC H(+) UniProt H+ KEGG_COMPOUND 0 O2 InChI=1S/O2/c1-2 MYMOFIZGZYHOMD-UHFFFAOYSA-N 31.998 31.98983 O=O CHEBI:10745 CHEBI:13416 CHEBI:23833 CHEBI:25366 CHEBI:30491 CHEBI:44742 CHEBI:7860 CAS:7782-44-7 Gmelin:485 HMDB:HMDB0001377 KEGG:C00007 KEGG:D00003 MetaCyc:OXYGEN-MOLECULE MolBase:750 PDBeChem:OXY PMID:10906528 PMID:16977326 PMID:18210929 PMID:18638417 PMID:19840863 PMID:7710549 PMID:9463773 Wikipedia:Oxygen dioxygen chebi_ontology Disauerstoff E 948 E-948 E948 O2 OXYGEN MOLECULE Oxygen [OO] dioxygene molecular oxygen CHEBI:15379 dioxygen CAS:7782-44-7 ChemIDplus CAS:7782-44-7 KEGG COMPOUND CAS:7782-44-7 NIST Chemistry WebBook Gmelin:485 Gmelin PMID:10906528 Europe PMC PMID:16977326 Europe PMC PMID:18210929 Europe PMC PMID:18638417 Europe PMC PMID:19840863 Europe PMC PMID:7710549 Europe PMC PMID:9463773 Europe PMC dioxygen IUPAC Disauerstoff ChEBI E 948 ChEBI E-948 ChEBI E948 ChEBI O2 IUPAC O2 KEGG_COMPOUND O2 UniProt OXYGEN MOLECULE PDBeChem Oxygen KEGG_COMPOUND [OO] MolBase dioxygene ChEBI molecular oxygen ChEBI A trace radioisotope of argon with atomic mass of 38.964313 and a half-life of 269 years. 0 [39Ar] InChI=1S/Ar/i1-1 XKRFYHLGVUSROY-BJUDXGSMSA-N 38.964 38.96431 [Ar] CAS:25729-41-3 PMID:16429279 PMID:17781454 PMID:17791262 PMID:28017500 PMID:28755564 PMID:30487580 chebi_ontology (39)18Ar (39)Ar (39)Ar radioisotope Ar-39 Ar-39 radioisotope argon 39 argon, isotope of mass 39 argon-39 CHEBI:155827 argon-39 atom CAS:25729-41-3 ChemIDplus PMID:16429279 Europe PMC PMID:17781454 Europe PMC PMID:17791262 Europe PMC PMID:28017500 Europe PMC PMID:28755564 Europe PMC PMID:30487580 Europe PMC (39)18Ar ChEBI (39)Ar ChemIDplus (39)Ar radioisotope ChEBI Ar-39 ChEBI Ar-39 radioisotope ChEBI argon 39 ChEBI argon, isotope of mass 39 ChemIDplus argon-39 ChEBI Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals. 0 C2H4O2(CH2O)n CHEBI:13755 CHEBI:22305 CHEBI:2561 KEGG:C01370 Wikipedia:Aldose Aldose chebi_ontology aldoses an aldose CHEBI:15693 aldose Aldose KEGG_COMPOUND aldoses ChEBI an aldose UniProt A peptide containing ten or more amino acid residues. C4H6N2O3R2(C2H2NOR)n CHEBI:14860 CHEBI:8314 KEGG:C00403 Polypeptide polypeptides chebi_ontology Polypeptid polipeptido CHEBI:15841 polypeptide Polypeptide KEGG_COMPOUND polypeptides IUPAC Polypeptid ChEBI polipeptido ChEBI A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. 0 (C5H8O6PR)n.C10H17O10PR2 CHEBI:13672 CHEBI:14859 CHEBI:8312 KEGG:C00419 Polynucleotide chebi_ontology polynucleotides CHEBI:15986 polynucleotide Polynucleotide KEGG_COMPOUND polynucleotides ChEBI An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. 0 H3N InChI=1S/H3N/h1H3 QGZKDVFQNNGYKY-UHFFFAOYSA-N 17.03056 17.02655 [H]N([H])[H] CHEBI:13405 CHEBI:13406 CHEBI:13407 CHEBI:13771 CHEBI:22533 CHEBI:44269 CHEBI:44284 CHEBI:44404 CHEBI:7434 Beilstein:3587154 CAS:7664-41-7 Drug_Central:4625 Gmelin:79 HMDB:HMDB0000051 KEGG:C00014 KEGG:D02916 KNApSAcK:C00007267 MetaCyc:AMMONIA MolBase:930 PDBeChem:NH3 PMID:110589 PMID:11139349 PMID:11540049 PMID:11746427 PMID:11783653 PMID:13753780 PMID:14663195 PMID:15092448 PMID:15094021 PMID:15554424 PMID:15969015 PMID:16008360 PMID:16050680 PMID:16348008 PMID:16349403 PMID:16614889 PMID:16664306 PMID:16842901 PMID:17025297 PMID:17439666 PMID:17569513 PMID:17737668 PMID:18670398 PMID:22002069 PMID:22081570 PMID:22088435 PMID:22100291 PMID:22130175 PMID:22150211 PMID:22240068 PMID:22290316 PMID:22342082 PMID:22385337 PMID:22443779 PMID:22560242 Reaxys:3587154 Wikipedia:Ammonia AMMONIA Ammonia ammonia azane chebi_ontology Ammoniak NH3 R-717 [NH3] ammoniac amoniaco spirit of hartshorn CHEBI:16134 ammonia Beilstein:3587154 Beilstein CAS:7664-41-7 ChemIDplus CAS:7664-41-7 KEGG COMPOUND CAS:7664-41-7 NIST Chemistry WebBook Drug_Central:4625 DrugCentral Gmelin:79 Gmelin PMID:110589 Europe PMC PMID:11139349 Europe PMC PMID:11540049 Europe PMC PMID:11746427 Europe PMC PMID:11783653 Europe PMC PMID:13753780 Europe PMC PMID:14663195 Europe PMC PMID:15092448 Europe PMC PMID:15094021 Europe PMC PMID:15554424 Europe PMC PMID:15969015 Europe PMC PMID:16008360 Europe PMC PMID:16050680 Europe PMC PMID:16348008 Europe PMC PMID:16349403 Europe PMC PMID:16614889 Europe PMC PMID:16664306 Europe PMC PMID:16842901 Europe PMC PMID:17025297 Europe PMC PMID:17439666 Europe PMC PMID:17569513 Europe PMC PMID:17737668 Europe PMC PMID:18670398 Europe PMC PMID:22002069 Europe PMC PMID:22081570 Europe PMC PMID:22088435 Europe PMC PMID:22100291 Europe PMC PMID:22130175 Europe PMC PMID:22150211 Europe PMC PMID:22240068 Europe PMC PMID:22290316 Europe PMC PMID:22342082 Europe PMC PMID:22385337 Europe PMC PMID:22443779 Europe PMC PMID:22560242 Europe PMC Reaxys:3587154 Reaxys AMMONIA PDBeChem Ammonia KEGG_COMPOUND ammonia IUPAC azane IUPAC Ammoniak ChemIDplus NH3 IUPAC NH3 KEGG_COMPOUND NH3 UniProt R-717 ChEBI [NH3] MolBase ammoniac ChEBI amoniaco ChEBI spirit of hartshorn ChemIDplus A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid. -2 O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2 QAOWNCQODCNURD-UHFFFAOYSA-L 96.06360 95.95283 [O-]S([O-])(=O)=O CHEBI:15135 CHEBI:45687 CHEBI:9335 Beilstein:3648446 CAS:14808-79-8 Gmelin:2120 HMDB:HMDB0001448 KEGG:C00059 KEGG:D05963 MetaCyc:SULFATE PDBeChem:SO4 PMID:11200094 PMID:11452993 PMID:11581495 PMID:11798107 PMID:12166931 PMID:12668033 PMID:14597181 PMID:15093386 PMID:15984785 PMID:16186560 PMID:16345535 PMID:16347366 PMID:16348007 PMID:16483812 PMID:16534979 PMID:16656509 PMID:16742508 PMID:16742518 PMID:17120760 PMID:17420092 PMID:17439666 PMID:17709180 PMID:18398178 PMID:18815700 PMID:18846414 PMID:19047345 PMID:19244483 PMID:19544990 PMID:19628332 PMID:19812358 PMID:30398859 Reaxys:3648446 Wikipedia:Sulfate Sulfate sulfate tetraoxidosulfate(2-) tetraoxosulfate(2-) tetraoxosulfate(VI) chebi_ontology SO4(2-) SULFATE ION Sulfate anion(2-) Sulfate dianion Sulfate(2-) Sulfuric acid ion(2-) [SO4](2-) sulphate sulphate ion CHEBI:16189 sulfate Beilstein:3648446 Beilstein CAS:14808-79-8 ChemIDplus CAS:14808-79-8 NIST Chemistry WebBook Gmelin:2120 Gmelin PMID:11200094 Europe PMC PMID:11452993 Europe PMC PMID:11581495 Europe PMC PMID:11798107 Europe PMC PMID:12166931 Europe PMC PMID:12668033 Europe PMC PMID:14597181 Europe PMC PMID:15093386 Europe PMC PMID:15984785 Europe PMC PMID:16186560 Europe PMC PMID:16345535 Europe PMC PMID:16347366 Europe PMC PMID:16348007 Europe PMC PMID:16483812 Europe PMC PMID:16534979 Europe PMC PMID:16656509 Europe PMC PMID:16742508 Europe PMC PMID:16742518 Europe PMC PMID:17120760 Europe PMC PMID:17420092 Europe PMC PMID:17439666 Europe PMC PMID:17709180 Europe PMC PMID:18398178 Europe PMC PMID:18815700 Europe PMC PMID:18846414 Europe PMC PMID:19047345 Europe PMC PMID:19244483 Europe PMC PMID:19544990 Europe PMC PMID:19628332 Europe PMC PMID:19812358 Europe PMC PMID:30398859 Europe PMC Reaxys:3648446 Reaxys Sulfate KEGG_COMPOUND sulfate IUPAC sulfate UniProt tetraoxidosulfate(2-) IUPAC tetraoxosulfate(2-) IUPAC tetraoxosulfate(VI) IUPAC SO4(2-) IUPAC SULFATE ION PDBeChem Sulfate anion(2-) HMDB Sulfate dianion HMDB Sulfate(2-) HMDB Sulfuric acid ion(2-) HMDB [SO4](2-) IUPAC sulphate ChEBI sulphate ion ChEBI A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells. 0 (C14H21NO12)n CHEBI:14412 CHEBI:24622 CHEBI:24623 CHEBI:5772 Beilstein:8538277 CAS:9004-61-9 HMDB:HMDB0010366 KEGG:C00518 KEGG:D08043 KEGG:G10505 PMID:11122186 PMID:18056362 PMID:18290544 Reaxys:8187837 Wikipedia:Hyaluronan Hyaluronic acid chebi_ontology Hyaluronsaeure [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n acide hyaluronique acido hialuronico hyaluronan CHEBI:16336 hyaluronic acid Beilstein:8538277 Beilstein CAS:9004-61-9 ChemIDplus CAS:9004-61-9 KEGG COMPOUND PMID:11122186 Europe PMC PMID:18056362 Europe PMC PMID:18290544 Europe PMC Reaxys:8187837 Reaxys Hyaluronic acid KEGG_COMPOUND Hyaluronsaeure ChEBI [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n ChEBI [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n KEGG_COMPOUND acide hyaluronique ChEBI acido hialuronico ChEBI hyaluronan ChEBI carbon dioxide A naturally occurring polypeptide synthesized at the ribosome. CHEBI:8526 KEGG:C00017 chebi_ontology Protein a protein polypeptide chain protein polypeptide chains CHEBI:16541 protein polypeptide chain Protein KEGG_COMPOUND a protein UniProt polypeptide chain ChEBI protein polypeptide chains ChEBI Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. CHEBI:15131 CHEBI:23008 CHEBI:9318 Wikipedia:Carbohydrate carbohydrate carbohydrates chebi_ontology Kohlenhydrat Kohlenhydrate a carbohydrate carbohidrato carbohidratos glucide glucides glucido glucidos hydrates de carbone saccharide saccharides saccharidum CHEBI:16646 carbohydrate carbohydrate IUPAC carbohydrates IUPAC Kohlenhydrat ChEBI Kohlenhydrate ChEBI a carbohydrate UniProt carbohidrato IUPAC carbohidratos IUPAC glucide ChEBI glucides ChEBI glucido ChEBI glucidos ChEBI hydrates de carbone ChEBI saccharide IUPAC saccharides IUPAC saccharidum ChEBI Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. 0 (C2H2NOR)nC2H3NOR CHEBI:14753 CHEBI:25906 CHEBI:7990 KEGG:C00012 Peptide peptides chebi_ontology Peptid peptido peptidos CHEBI:16670 peptide Peptide KEGG_COMPOUND peptides IUPAC Peptid ChEBI peptido ChEBI peptidos ChEBI +1 C8H12NO3 InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/p+1 SFLSHLFXELFNJZ-UHFFFAOYSA-O 170.187 170.08117 C1=CC(=CC(=C1O)O)C(C[NH3+])O chebi_ontology noradrenaline CHEBI:166902 noradrenaline(1+) noradrenaline UniProt Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001. chebi_ontology glycans CHEBI:167559 glycan glycans ChEBI An aminoalkylindole consisting of indole having a 2-aminoethyl group at the 3-position. 0 C10H12N2 InChI=1S/C10H12N2/c11-6-5-8-7-12-10-4-2-1-3-9(8)10/h1-4,7,12H,5-6,11H2 APJYDQYYACXCRM-UHFFFAOYSA-N 160.21570 160.10005 NCCc1c[nH]c2ccccc12 CHEBI:15274 CHEBI:27161 CHEBI:46157 CHEBI:9767 Beilstein:125513 CAS:61-54-1 DrugBank:DB08653 Gmelin:603448 HMDB:HMDB0000303 KEGG:C00398 KNApSAcK:C00001434 MetaCyc:TRYPTAMINE PDBeChem:TSS PMID:16126914 PMID:22770225 PMID:24345948 PMID:24558969 Reaxys:125513 Wikipedia:Tryptamine 2-(1H-indol-3-yl)ethanamine Tryptamine chebi_ontology 1H-indole-3-ethanamine 2-(1H-INDOL-3-YL)ETHANAMINE 2-(3-indolyl)ethylamine 3-(2-Aminoethyl)indole CHEBI:16765 tryptamine Beilstein:125513 Beilstein CAS:61-54-1 ChemIDplus CAS:61-54-1 KEGG COMPOUND CAS:61-54-1 NIST Chemistry WebBook Gmelin:603448 Gmelin PMID:16126914 Europe PMC PMID:22770225 Europe PMC PMID:24345948 Europe PMC PMID:24558969 Europe PMC Reaxys:125513 Reaxys 2-(1H-indol-3-yl)ethanamine IUPAC Tryptamine KEGG_COMPOUND 1H-indole-3-ethanamine NIST_Chemistry_WebBook 2-(1H-INDOL-3-YL)ETHANAMINE PDBeChem 2-(3-indolyl)ethylamine ChemIDplus 3-(2-Aminoethyl)indole KEGG_COMPOUND A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. 0 C33H36N4O6 InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14- BPYKTIZUTYGOLE-IFADSCNNSA-N 584.673 584.26348 CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(CC2=C(CCC(O)=O)C(C)=C(N2)\C=C2/NC(=O)C(C=C)=C2C)N1 CHEBI:13898 CHEBI:22870 CHEBI:3099 Beilstein:74376 CAS:635-65-4 Gmelin:411033 HMDB:HMDB0000054 KEGG:C00486 KNApSAcK:C00029828 MetaCyc:BILIRUBIN PDBeChem:BLR PMID:12799017 PMID:18442622 PMID:23763371 PMID:23768684 PMID:30224965 PMID:8605219 PMID:9587403 Reaxys:74376 Wikipedia:Bilirubin 3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid bilirubin chebi_ontology 1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid 2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid 8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione Bilirubin bilirubin(Z,Z) bilirubin-IXalpha CHEBI:16990 bilirubin IXalpha Beilstein:74376 Beilstein CAS:635-65-4 ChemIDplus CAS:635-65-4 KEGG COMPOUND Gmelin:411033 Gmelin PMID:12799017 Europe PMC PMID:18442622 Europe PMC PMID:23763371 Europe PMC PMID:23768684 Europe PMC PMID:30224965 Europe PMC PMID:8605219 Europe PMC PMID:9587403 Europe PMC Reaxys:74376 Reaxys 3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid IUPAC bilirubin IUPAC 1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid ChemIDplus 2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid ChemIDplus 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid IUPAC 8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione JCBN Bilirubin KEGG_COMPOUND bilirubin(Z,Z) ChEBI bilirubin-IXalpha ChEBI High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:13302 CHEBI:21123 CHEBI:33698 CHEBI:4291 CAS:9007-49-2 KEGG:C00039 Deoxyribonucleic acid deoxyribonucleic acids chebi_ontology (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m DNA DNAn DNAn+1 DNS Desoxyribonukleinsaeure deoxyribonucleic acids desoxyribose nucleic acid thymus nucleic acid CHEBI:16991 deoxyribonucleic acid CAS:9007-49-2 ChemIDplus CAS:9007-49-2 KEGG COMPOUND Deoxyribonucleic acid KEGG_COMPOUND deoxyribonucleic acids IUPAC (Deoxyribonucleotide)m KEGG_COMPOUND (Deoxyribonucleotide)n KEGG_COMPOUND (Deoxyribonucleotide)n+m KEGG_COMPOUND DNA IUPAC DNA KEGG_COMPOUND DNA UniProt DNAn KEGG_COMPOUND DNAn+1 KEGG_COMPOUND DNS ChEBI Desoxyribonukleinsaeure ChEBI deoxyribonucleic acids ChEBI desoxyribose nucleic acid ChemIDplus thymus nucleic acid ChEBI A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H). 0 COR2 28.010 27.99491 [*]C([*])=O CHEBI:13427 CHEBI:13646 CHEBI:24974 CHEBI:6127 CHEBI:8742 KEGG:C01450 Wikipedia:Ketone Ketone ketones chebi_ontology Keton R-CO-R' a ketone cetone ketones CHEBI:17087 ketone Ketone KEGG_COMPOUND ketones IUPAC Keton ChEBI R-CO-R' KEGG_COMPOUND a ketone UniProt cetone ChEBI ketones ChEBI A compound in which a carbohydrate component is covalently bound to a protein component. CHEBI:14349 CHEBI:5481 CHEBI:5493 KEGG:C00326 Glycoprotein glycoproteins chebi_ontology Glykoprotein Glykoproteine a glycoprotein glicoproteina glicoproteinas glycoproteine glycoproteines CHEBI:17089 glycoprotein Glycoprotein KEGG_COMPOUND glycoproteins IUPAC Glykoprotein ChEBI Glykoproteine ChEBI a glycoprotein UniProt glicoproteina ChEBI glicoproteinas ChEBI glycoproteine ChEBI glycoproteines ChEBI An aldohexose used as a source of energy and metabolic intermediate. 0 C6H12O6 180.15588 180.06339 CHEBI:14313 CHEBI:24277 CHEBI:33929 CHEBI:5418 CAS:50-99-7 KEGG:C00293 Wikipedia:Glucose Glucose gluco-hexose glucose chebi_ontology DL-glucose Glc Glukose CHEBI:17234 glucose CAS:50-99-7 KEGG COMPOUND Glucose KEGG_COMPOUND gluco-hexose IUPAC glucose IUPAC DL-glucose ChEBI Glc JCBN Glukose ChEBI The carbon oxoanion resulting from the removal of a proton from carbonic acid. -1 CHO3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1 BVKZGUZCCUSVTD-UHFFFAOYSA-M 61.01684 60.99312 OC([O-])=O CHEBI:13363 CHEBI:22863 CHEBI:40961 CHEBI:5589 Beilstein:3903504 CAS:71-52-3 Gmelin:49249 HMDB:HMDB0000595 KEGG:C00288 MetaCyc:HCO3 PDBeChem:BCT PMID:17215880 PMID:17505962 PMID:18439416 PMID:28732801 PMID:29150416 PMID:29460248 PMID:29466234 PMID:4208463 Wikipedia:Bicarbonate Hydrogencarbonate hydrogen(trioxidocarbonate)(1-) hydrogencarbonate hydrogencarbonate(1-) hydrogentrioxocarbonate(1-) hydrogentrioxocarbonate(IV) hydroxidodioxidocarbonate(1-) chebi_ontology Acid carbonate BICARBONATE ION Bicarbonate HCO3(-) HCO3- [CO2(OH)](-) hydrogen carbonate CHEBI:17544 hydrogencarbonate Beilstein:3903504 Beilstein CAS:71-52-3 ChemIDplus Gmelin:49249 Gmelin PMID:17215880 Europe PMC PMID:17505962 Europe PMC PMID:18439416 Europe PMC PMID:28732801 Europe PMC PMID:29150416 Europe PMC PMID:29460248 Europe PMC PMID:29466234 Europe PMC PMID:4208463 Europe PMC Hydrogencarbonate KEGG_COMPOUND hydrogen(trioxidocarbonate)(1-) IUPAC hydrogencarbonate IUPAC hydrogencarbonate UniProt hydrogencarbonate(1-) IUPAC hydrogentrioxocarbonate(1-) IUPAC hydrogentrioxocarbonate(IV) IUPAC hydroxidodioxidocarbonate(1-) IUPAC Acid carbonate KEGG_COMPOUND BICARBONATE ION PDBeChem Bicarbonate KEGG_COMPOUND HCO3(-) IUPAC HCO3- KEGG_COMPOUND [CO2(OH)](-) IUPAC hydrogen carbonate PDBeChem A minor stable isotope of calcium with relative atomic mass 42.95877 and 0.135 atom percent natural abundance. 0 [43Ca] InChI=1S/Ca/i1+3 OYPRJOBELJOOCE-AKLPVKDBSA-N 42.959 42.95877 [43Ca] CAS:14333-06-3 PMID:11859764 PMID:19117733 PMID:20463996 PMID:20574585 PMID:23163540 PMID:23398971 PMID:24874995 PMID:25306191 PMID:29770988 PMID:6548252 ((43)Ca)calcium chebi_ontology (43)20Ca (43)Ca (43)calcium Ca-43 calcium, isotope of mass 43 calcium-43 calcium-43 isotope CHEBI:176566 calcium-43 atom CAS:14333-06-3 ChemIDplus PMID:11859764 Europe PMC PMID:19117733 Europe PMC PMID:20463996 Europe PMC PMID:20574585 Europe PMC PMID:23163540 Europe PMC PMID:23398971 Europe PMC PMID:24874995 Europe PMC PMID:25306191 Europe PMC PMID:29770988 Europe PMC PMID:6548252 Europe PMC ((43)Ca)calcium IUPAC (43)20Ca ChEBI (43)Ca ChemIDplus (43)calcium ChEBI Ca-43 ChEBI calcium, isotope of mass 43 ChemIDplus calcium-43 ChemIDplus calcium-43 isotope ChEBI A stable isotope of molybdenum with relative atomic mass 97.90541, 24.29 atom percent natural abundance and nuclear spin 0. 0 [98Mo] InChI=1S/Mo/i1+2 ZOKXTWBITQBERF-NJFSPNSNSA-N 97.905 97.90541 [98Mo] CAS:14392-20-2 PMID:19720541 PMID:22796396 PMID:22970917 PMID:24593536 PMID:25087173 PMID:25168118 PMID:25880611 PMID:26397967 PMID:26808401 ((98)Mo)molybdenum chebi_ontology (98)42Mo (98)Mo Mo-98 molybdenum, isotope of mass 98 molybdenum-98 CHEBI:176570 molybdenum-98 atom CAS:14392-20-2 ChemIDplus PMID:19720541 Europe PMC PMID:22796396 Europe PMC PMID:22970917 Europe PMC PMID:24593536 Europe PMC PMID:25087173 SUBMITTER PMID:25168118 Europe PMC PMID:25880611 Europe PMC PMID:26397967 Europe PMC PMID:26808401 Europe PMC ((98)Mo)molybdenum IUPAC (98)42Mo ChEBI (98)Mo ChemIDplus Mo-98 ChEBI molybdenum, isotope of mass 98 ChemIDplus molybdenum-98 ChemIDplus A major stable isotope of strontium with relative atomic mass 87.90561 and 82.58 atom percent natural abundance. 0 [88Sr] InChI=1S/Sr/i1+0 CIOAGBVUUVVLOB-IGMARMGPSA-N 87.906 87.90561 [88Sr] CAS:14119-10-9 PMID:11893161 PMID:27829691 PMID:32350478 PMID:33328666 PMID:33834832 PMID:6337617 ((88)Sr)strontium chebi_ontology (88)38Sr (88)Sr (88)strontium Sr-88 strontium, isotope of mass 88 strontium-88 strontium-88 isotope CHEBI:176571 strontium-88 atom CAS:14119-10-9 ChemIDplus PMID:11893161 Europe PMC PMID:27829691 Europe PMC PMID:32350478 Europe PMC PMID:33328666 Europe PMC PMID:33834832 Europe PMC PMID:6337617 SUBMITTER ((88)Sr)strontium IUPAC (88)38Sr ChEBI (88)Sr ChemIDplus (88)strontium ChEBI Sr-88 ChEBI strontium, isotope of mass 88 ChemIDplus strontium-88 ChemIDplus strontium-88 isotope ChEBI A stable isotope of rubidium with relative atomic mass 84.91179, 72.17 atom percent natural abundance and nuclear spin 5/2. 0 [85Rb] InChI=1S/Rb/i1+0 IGLNJRXAVVLDKE-IGMARMGPSA-N 84.912 84.91179 [85Rb] CAS:13982-12-2 PMID:18026483 PMID:18033464 PMID:18291893 PMID:18382518 PMID:19855587 PMID:25087142 PMID:32909800 PMID:33709729 PMID:34170158 ((85)Rb)rubidium chebi_ontology (85)37Rb (85)Rb Rb-85 rubidium, isotope of mass 85 rubidium-85 CHEBI:176572 rubidium-85 atom CAS:13982-12-2 ChemIDplus PMID:18026483 Europe PMC PMID:18033464 Europe PMC PMID:18291893 Europe PMC PMID:18382518 Europe PMC PMID:19855587 Europe PMC PMID:25087142 SUBMITTER PMID:32909800 Europe PMC PMID:33709729 Europe PMC PMID:34170158 Europe PMC ((85)Rb)rubidium IUPAC (85)37Rb ChEBI (85)Rb ChemIDplus Rb-85 ChEBI rubidium, isotope of mass 85 ChemIDplus rubidium-85 ChemIDplus A stable isotope of selenium with relative atomic mass 81.91670, 8.82 atom percent natural abundance and nuclear spin 0. 0 [82Se] InChI=1S/Se/i1+3 BUGBHKTXTAQXES-AKLPVKDBSA-N 81.917 81.91670 [82Se] CAS:14687-58-2 Chemspider:4892236 PMID:16028633 PMID:18781022 PMID:21139275 PMID:22258472 PMID:23575454 PMID:29932707 PMID:30881205 PMID:31386478 PMID:31951429 PMID:33576665 PMID:6337549 ((82)Se)selenium chebi_ontology (82)34Se (82)Se Se-82 selenium, isotope of mass 82 selenium-82 CHEBI:176573 selenium-82 atom CAS:14687-58-2 ChemIDplus PMID:16028633 Europe PMC PMID:18781022 Europe PMC PMID:21139275 Europe PMC PMID:22258472 Europe PMC PMID:23575454 Europe PMC PMID:29932707 Europe PMC PMID:30881205 Europe PMC PMID:31386478 Europe PMC PMID:31951429 Europe PMC PMID:33576665 Europe PMC PMID:6337549 SUBMITTER ((82)Se)selenium IUPAC (82)34Se ChEBI (82)Se ChemIDplus Se-82 ChEBI selenium, isotope of mass 82 ChemIDplus selenium-82 ChemIDplus A stable isotope of zinc with relative atomic mass 65.92603, 27.7 atom percent natural abundance and nuclear spin 0. 0 [66Zn] InChI=1S/Zn/i1+1 HCHKCACWOHOZIP-OUBTZVSYSA-N 65.926 65.92603 [66Zn] CAS:14378-33-7 PMID:12447866 PMID:19836537 PMID:20155761 PMID:21047059 PMID:24196216 PMID:26065372 PMID:26808401 PMID:27189145 PMID:27306032 ((66)Zn)zinc chebi_ontology (66)30Zn (66)Zn Zn-66 zinc, isotope of mass 66 zinc-66 CHEBI:176574 zinc-66 atom PMID:20155761 Europe PMC PMID:21047059 Europe PMC PMID:24196216 Europe PMC PMID:26065372 Europe PMC PMID:26808401 Europe PMC PMID:27189145 Europe PMC PMID:27306032 Europe PMC ((66)Zn)zinc IUPAC (66)30Zn ChEBI (66)Zn ChemIDplus Zn-66 ChemIDplus zinc, isotope of mass 66 ChemIDplus zinc-66 ChemIDplus CAS:14378-33-7 ChemIDplus PMID:12447866 SUBMITTER PMID:19836537 Europe PMC A stable isotope of nickel with relative atomic mass 59.93079, 26.223 atom percent natural abundance and nuclear spin 0. 0 [60Ni] InChI=1S/Ni/i1+1 PXHVJJICTQNCMI-OUBTZVSYSA-N 59.931 59.93079 [60Ni] CAS:13981-80-1 PMID:15308160 PMID:22583786 PMID:23149182 PMID:25126912 PMID:25700212 PMID:26709546 PMID:29376683 ((60)Ni)nickel chebi_ontology (60)Ni Ni-60 nickel, isotope of mass 60 nickel-60 CHEBI:176575 nickel-60 atom CAS:13981-80-1 ChemIDplus PMID:15308160 Europe PMC PMID:22583786 Europe PMC PMID:23149182 Europe PMC PMID:25126912 Europe PMC PMID:25700212 Europe PMC PMID:26709546 Europe PMC PMID:29376683 Europe PMC ((60)Ni)nickel IUPAC (60)Ni ChEBI Ni-60 ChEBI nickel, isotope of mass 60 ChemIDplus nickel-60 ChemIDplus A stable isotope of cobalt with relative atomic mass 58.93319, 100 atom percent natural abundance and nuclear spin 7/2. 0 [59Co] InChI=1S/Co/i1+0 GUTLYIVDDKVIGB-IGMARMGPSA-N 58.933 58.93319 [59Co] PMID:10617436 PMID:10940985 PMID:11421673 PMID:11528329 PMID:12943912 PMID:19150229 PMID:19421527 PMID:25069794 PMID:25169133 PMID:26066447 PMID:26641288 PMID:27355901 PMID:30137661 PMID:31367328 PMID:32478347 ((59)Co)cobalt chebi_ontology (59)27Co (59)Co Co-59 cobalt, isotope of mass 59 cobalt-(59)Co cobalt-59 CHEBI:176578 cobalt-59 atom PMID:10617436 Europe PMC PMID:10940985 Europe PMC PMID:11421673 Europe PMC PMID:11528329 SUBMITTER PMID:12943912 Europe PMC PMID:19150229 Europe PMC PMID:19421527 Europe PMC PMID:25069794 Europe PMC PMID:25169133 Europe PMC PMID:26066447 Europe PMC PMID:26641288 Europe PMC PMID:27355901 Europe PMC PMID:30137661 Europe PMC PMID:31367328 Europe PMC PMID:32478347 Europe PMC ((59)Co)cobalt IUPAC (59)27Co ChEBI (59)Co ChEBI Co-59 ChEBI cobalt, isotope of mass 59 ChEBI cobalt-(59)Co ChEBI cobalt-59 ChEBI A stable isotope of manganese with relative atomic mass 54.93804, 100 atom percent natural abundance and nuclear spin 5/2. 0 [55Mn] InChI=1S/Mn/i1+0 PWHULOQIROXLJO-IGMARMGPSA-N 54.938 54.93804 [55Mn] PMID:20645339 PMID:21058720 PMID:21341708 PMID:24993844 PMID:25179135 PMID:25891681 ((55)Mn)manganese chebi_ontology (55)25Mn (55)Mn Mn-55 manganese, isotope of mass 55 manganese-55 CHEBI:176583 manganese-55 atom PMID:20645339 Europe PMC PMID:21058720 Europe PMC PMID:21341708 Europe PMC PMID:24993844 Europe PMC PMID:25179135 Europe PMC PMID:25891681 Europe PMC ((55)Mn)manganese IUPAC (55)25Mn ChEBI (55)Mn ChEBI Mn-55 ChEBI manganese, isotope of mass 55 ChEBI manganese-55 ChEBI A stable isotope of arsenic with relative atomic mass 74.921596, 100 atom percent natural abundance and nuclear spin 3/2. 0 [75As] InChI=1S/As/i1+0 RQNWIZPPADIBDY-IGMARMGPSA-N 74.922 74.92159 [75As] ((75)As)arsenic chebi_ontology (75)33As (75)As As-75 arsenic, isotope of mass 75 arsenic-75 CHEBI:176584 arsenic-75 atom ((75)As)arsenic IUPAC (75)33As ChEBI (75)As ChEBI As-75 ChEBI arsenic, isotope of mass 75 ChEBI arsenic-75 ChEBI A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. CHEBI:14202 CHEBI:4697 KEGG:C01351 Donor chebi_ontology Donator donneur CHEBI:17891 donor Donor KEGG_COMPOUND Donator ChEBI donneur ChEBI dinitrogen 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. CHEBI:14517 CHEBI:25054 CHEBI:6486 KEGG:C01356 Lipid lipids chebi_ontology CHEBI:18059 lipid Lipid KEGG_COMPOUND lipids IUPAC Any polysaccharide containing a substantial proportion of aminomonosaccharide residues. CHEBI:14361 CHEBI:24398 CHEBI:5495 KEGG:C02545 Wikipedia:Glycosaminoglycan Glycosaminoglycan glycosaminoglycan chebi_ontology Glykosaminoglykan glicosaminoglicano glycosaminoglycane glycosaminoglycans CHEBI:18085 glycosaminoglycan Glycosaminoglycan KEGG_COMPOUND glycosaminoglycan IUPAC Glykosaminoglykan ChEBI glicosaminoglicano IUPAC glycosaminoglycane IUPAC glycosaminoglycans ChEBI Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose). CHEBI:14399 CHEBI:24590 CHEBI:5709 GlyGen:G70994MS GlyTouCan:G70994MS KEGG:C00738 Hexose chebi_ontology WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/ hexoses CHEBI:18133 hexose Hexose KEGG_COMPOUND WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/ GlyTouCan hexoses ChEBI A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. CHEBI:14864 CHEBI:26205 CHEBI:8322 KEGG:C00420 Polysaccharide polysaccharides chebi_ontology Glycan Glycane Glykan Glykane glycans polisacarido polisacaridos CHEBI:18154 polysaccharide Polysaccharide KEGG_COMPOUND polysaccharides IUPAC Glycan KEGG_COMPOUND Glycane ChEBI Glykan ChEBI Glykane ChEBI glycans IUPAC polisacarido ChEBI polisacaridos IUPAC An iron group element atom that has atomic number 26. 0 Fe InChI=1S/Fe XEEYBQQBJWHFJM-UHFFFAOYSA-N 55.84500 55.93494 [Fe] CHEBI:13322 CHEBI:24872 CHEBI:5974 CAS:7439-89-6 DrugBank:DB01592 HMDB:HMDB0015531 KEGG:C00023 Reaxys:4122945 WebElements:Fe iron chebi_ontology 26Fe Eisen Fe Iron fer ferrum hierro iron CHEBI:18248 iron atom CAS:7439-89-6 ChemIDplus CAS:7439-89-6 KEGG COMPOUND CAS:7439-89-6 NIST Chemistry WebBook Reaxys:4122945 Reaxys iron IUPAC 26Fe IUPAC Eisen ChEBI Fe IUPAC Fe UniProt Iron KEGG_COMPOUND fer ChEBI ferrum IUPAC hierro ChEBI iron ChEBI That part of DNA or RNA that may be involved in pairing. CHEBI:13873 CHEBI:25598 CHEBI:2995 KEGG:C00701 Wikipedia:Nucleobase chebi_ontology Base nucleobases CHEBI:18282 nucleobase Base KEGG_COMPOUND nucleobases ChEBI 0 Mn InChI=1S/Mn PWHULOQIROXLJO-UHFFFAOYSA-N 54.93805 54.93804 [Mn] CHEBI:13382 CHEBI:25153 CHEBI:6681 CAS:7439-96-5 KEGG:C00034 WebElements:Mn manganese chebi_ontology 25Mn Mangan Manganese Mn manganese manganeso manganum CHEBI:18291 manganese atom CAS:7439-96-5 ChemIDplus CAS:7439-96-5 KEGG COMPOUND manganese IUPAC 25Mn IUPAC Mangan NIST_Chemistry_WebBook Manganese KEGG_COMPOUND Mn IUPAC Mn UniProt manganese ChEBI manganeso ChEBI manganum ChEBI The R-enantiomer of noradrenaline. 0 C8H11NO3 InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/t8-/m0/s1 SFLSHLFXELFNJZ-QMMMGPOBSA-N 169.17780 169.07389 NC[C@H](O)c1ccc(O)c(O)c1 CHEBI:1 CHEBI:14668 CHEBI:25592 CHEBI:258884 CHEBI:43725 Beilstein:2804840 Beilstein:4231961 CAS:51-41-2 DrugBank:DB00368 Drug_Central:1960 HMDB:HMDB0000216 KEGG:C00547 KEGG:D00076 KNApSAcK:C00001424 PDBeChem:LNR Reaxys:2804840 Wikipedia:Norepinephrine 4-[(1R)-2-amino-1-hydroxyethyl]benzene-1,2-diol chebi_ontology (-)-arterenol (-)-noradrenaline (-)-norepinephrine (R)-(-)-norepinephrine (R)-4-(2-amino-1-hydroxyethyl)-1,2-benzenediol (R)-norepinephrine 4-[(1R)-2-Amino-1-hydroxyethyl]-1,2-benzenediol Arterenol L-NOREPINEPHRINE L-Noradrenaline Noradrenaline Norepinephrine norepinefrina norepinephrine norepinephrinum CHEBI:18357 (R)-noradrenaline Beilstein:2804840 Beilstein Beilstein:4231961 ChemIDplus CAS:51-41-2 ChemIDplus CAS:51-41-2 KEGG COMPOUND Drug_Central:1960 DrugCentral Reaxys:2804840 Reaxys 4-[(1R)-2-amino-1-hydroxyethyl]benzene-1,2-diol IUPAC (-)-arterenol ChemIDplus (-)-noradrenaline IUPHAR (-)-norepinephrine ChemIDplus (R)-(-)-norepinephrine ChemIDplus (R)-4-(2-amino-1-hydroxyethyl)-1,2-benzenediol ChemIDplus (R)-norepinephrine ChemIDplus 4-[(1R)-2-Amino-1-hydroxyethyl]-1,2-benzenediol KEGG_COMPOUND Arterenol KEGG_COMPOUND L-NOREPINEPHRINE PDBeChem L-Noradrenaline KEGG_COMPOUND Noradrenaline KEGG_COMPOUND Norepinephrine KEGG_COMPOUND norepinefrina ChEBI norepinephrine ChemIDplus norepinephrine WHO_MedNet norepinephrinum ChEBI A phosphate ion that is the conjugate base of hydrogenphosphate. -3 O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 NBIIXXVUZAFLBC-UHFFFAOYSA-K 94.97136 94.95507 [O-]P([O-])([O-])=O CHEBI:14791 CHEBI:45024 CHEBI:7793 Beilstein:3903772 CAS:14265-44-2 Gmelin:1997 KEGG:C00009 PDBeChem:PO4 Reaxys:3903772 phosphate tetraoxidophosphate(3-) tetraoxophosphate(3-) tetraoxophosphate(V) chebi_ontology Orthophosphate PHOSPHATE ION PO4(3-) Phosphate [PO4](3-) CHEBI:18367 phosphate(3-) Beilstein:3903772 Beilstein CAS:14265-44-2 ChemIDplus CAS:14265-44-2 KEGG COMPOUND Gmelin:1997 Gmelin PDBeChem:PO4 ChEBI Reaxys:3903772 Reaxys phosphate IUPAC tetraoxidophosphate(3-) IUPAC tetraoxophosphate(3-) IUPAC tetraoxophosphate(V) IUPAC Orthophosphate KEGG_COMPOUND PHOSPHATE ION PDBeChem PO4(3-) IUPAC Phosphate KEGG_COMPOUND [PO4](3-) IUPAC A carbon group element atom with a symbol Fl and atomic number 114. 0 Fl InChI=1S/Fl WIHJCBVMYKIGOT-UHFFFAOYSA-N 289.000 289.00000 [Fl] PMID:16833611 PMID:17919027 PMID:19905506 PMID:20379506 PMID:20867370 PMID:23787759 PMID:24456007 PMID:29711350 PMID:36092655 Wikipedia:Flerovium chebi_ontology 114Fl 114Uuq E114 Fl Uuq eka-lead element 114 ununquadium CHEBI:194531 flerovium atom PMID:16833611 Europe PMC PMID:17919027 Europe PMC PMID:19905506 Europe PMC PMID:20379506 Europe PMC PMID:20867370 Europe PMC PMID:23787759 Europe PMC PMID:24456007 Europe PMC PMID:29711350 Europe PMC PMID:36092655 Europe PMC 114Fl ChEBI 114Uuq ChEBI E114 ChEBI Fl ChEBI Uuq ChEBI eka-lead ChEBI element 114 ChEBI ununquadium ChEBI A boron group element atom with a symbol Nh and atomic number 113. 0 Nh InChI=1S/Nh KUGNSLWRKGRKGS-UHFFFAOYSA-N 286.000 286.00000 [Nh] PMID:19049424 PMID:34142795 PMID:34917588 PMID:36149319 PMID:9913354 Wikipedia:Nihonium chebi_ontology 113Nh E113 Nh Uut eka-thallium element 113 ununtrium CHEBI:194533 nihonium atom PMID:19049424 Europe PMC PMID:34142795 Europe PMC PMID:34917588 Europe PMC PMID:36149319 Europe PMC PMID:9913354 Europe PMC 113Nh ChEBI E113 ChEBI Nh ChEBI Uut ChEBI eka-thallium ChEBI element 113 ChEBI ununtrium ChEBI A pnictogen atom with a symbol Mc and atomic number 115. 0 Mc InChI=1S/Mc QDXZEHQJHSHEQF-UHFFFAOYSA-N 289.000 289.00000 [Mc] PMID:24074079 PMID:34142795 Wikipedia:Moscovium chebi_ontology 115Mc E115 Mc Uup eka-bismuth element 115 ununpentium CHEBI:194535 moscovium atom PMID:24074079 Europe PMC PMID:34142795 Europe PMC 115Mc ChEBI E115 ChEBI Mc ChEBI Uup ChEBI eka-bismuth ChEBI element 115 ChEBI ununpentium ChEBI A chalcogen atom with a symbol Lv and atomic number 116. 0 Lv InChI=1S/Lv ONFASNXETZOODS-UHFFFAOYSA-N 293.000 293.00000 [Lv] PMID:17381195 PMID:27554416 Wikipedia:Livermorium chebi_ontology 116Lv E116 Lv Uuh eka-polonium element 116 ununhexium CHEBI:194537 livermorium atom PMID:17381195 Europe PMC PMID:27554416 Europe PMC 116Lv ChEBI E116 ChEBI Lv ChEBI Uuh ChEBI eka-polonium ChEBI element 116 ChEBI ununhexium ChEBI A halogen atom with a symbol Ts and atomic number 117. 0 Ts InChI=1S/Ts INMSAURDCVBGHH-UHFFFAOYSA-N 293.000 293.00000 [Ts] PMID:16483205 PMID:19367904 PMID:20395479 PMID:23090670 Wikipedia:Tennessine chebi_ontology 117Ts E117 Ts Uus eka-astatine element 117 ununseptium CHEBI:194539 tennessine atom PMID:16483205 Europe PMC PMID:19367904 Europe PMC PMID:20395479 Europe PMC PMID:23090670 Europe PMC 117Ts ChEBI E117 ChEBI Ts ChEBI Uus ChEBI eka-astatine ChEBI element 117 ChEBI ununseptium ChEBI A p-block element atom with a symbol Og and atomic number 118. 0 InChI=1S/Og GOANEQIZDYDFCO-UHFFFAOYSA-N 294.000 294.00000 [Og] PMID:10062781 PMID:11486061 PMID:19045133 PMID:23913741 PMID:36859080 Wikipedia:Oganesson chebi_ontology 118Og E118 Og Uuo eka-emanation eka-radon element 118 ununoctium CHEBI:194541 oganesson atom PMID:10062781 Europe PMC PMID:11486061 Europe PMC PMID:19045133 Europe PMC PMID:23913741 Europe PMC PMID:36859080 Europe PMC 118Og ChEBI E118 ChEBI Og ChEBI Uuo ChEBI eka-emanation ChEBI eka-radon ChEBI element 118 ChEBI ununoctium ChEBI 0 C24H42 InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18+,19+,20-,21+,22+,23+,24-/m1/s1 QSHQKIURKJITMZ-OBUPQJQESA-N 330.59028 330.32865 [H][C@@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCC Beilstein:2048472 5beta-cholane chebi_ontology CHEBI:20664 5beta-cholane Beilstein:2048472 Beilstein 5beta-cholane IUPAC An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids. acyl group alkanoyl chebi_ontology acyl groups alkanoyl group groupe acyle CHEBI:22221 acyl group acyl group IUPAC alkanoyl IUPAC acyl groups ChEBI alkanoyl group ChEBI groupe acyle IUPAC alkaline earth metals chebi_ontology Erdalkalimetall Erdalkalimetalle alkaline earth metal alkaline-earth metal alkaline-earth metals metal alcalino-terreux metal alcalinoterreo metales alcalinoterreos metaux alcalino-terreux CHEBI:22313 alkaline earth metal atom alkaline earth metals IUPAC Erdalkalimetall ChEBI Erdalkalimetalle ChEBI alkaline earth metal ChEBI alkaline-earth metal ChEBI alkaline-earth metals ChEBI metal alcalino-terreux ChEBI metal alcalinoterreo ChEBI metales alcalinoterreos ChEBI metaux alcalino-terreux ChEBI alkali metals chebi_ontology Alkalimetall Alkalimetalle alkali metal metal alcalin metal alcalino metales alcalinos metaux alcalins CHEBI:22314 alkali metal atom alkali metals IUPAC Alkalimetall ChEBI Alkalimetalle ChEBI alkali metal ChEBI metal alcalin ChEBI metal alcalino ChEBI metales alcalinos ChEBI metaux alcalins ChEBI Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids. Wikipedia:Alkaloid Alkaloid alkaloids chebi_ontology Alkaloide alcaloide alcaloides CHEBI:22315 alkaloid Alkaloid ChEBI alkaloids IUPAC Alkaloide ChEBI alcaloide ChEBI alcaloides ChEBI chebi_ontology aminoglycans CHEBI:22506 aminoglycan aminoglycans ChEBI A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion chebi_ontology Anionen aniones anions CHEBI:22563 anion Anion ChEBI anion ChEBI anion IUPAC Anionen ChEBI aniones ChEBI anions IUPAC A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. chebi_ontology antioxidants antioxydant antoxidant CHEBI:22586 antioxidant antioxidants ChEBI antioxydant ChEBI antoxidant ChEBI A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base). KEGG:C00701 Base base chebi_ontology Base1 Base2 Basen Nucleobase bases CHEBI:22695 base Base ChEBI base ChEBI base IUPAC Base1 KEGG_COMPOUND Base2 KEGG_COMPOUND Basen ChEBI Nucleobase KEGG_COMPOUND bases ChEBI chebi_ontology benzopyrroles CHEBI:22728 benzopyrrole benzopyrroles ChEBI Any compound that produces a peak used to reference an NMR spectrum during data pre-processing. chebi_ontology NMR chemical shift reference compounds NMR chemical shift standard NMR chemical shift standards NMR internal standard NMR internal standards NMR reference standard NMR reference standards CHEBI:228364 NMR chemical shift reference compound NMR chemical shift reference compounds ChEBI NMR chemical shift standard ChEBI NMR chemical shift standards ChEBI NMR internal standard ChEBI NMR internal standards ChEBI NMR reference standard ChEBI NMR reference standards ChEBI A sodium salt of the conjugate of any bile acid with either glycine or taurine. KEGG:C01558 chebi_ontology Bile acid bile salts CHEBI:22868 bile salt Bile acid KEGG_COMPOUND bile salts ChEBI 0 Br InChI=1S/Br WKBOTKDWSSQWDR-UHFFFAOYSA-N 79.90400 78.91834 [Br] WebElements:Br bromine chebi_ontology 35Br Br Brom brome bromine bromo bromum CHEBI:22927 bromine atom bromine IUPAC 35Br IUPAC Br ChEBI Brom ChEBI brome ChEBI bromine ChEBI bromo ChEBI bromum ChEBI 0 Cd InChI=1S/Cd BDOSMKKIYDKNTQ-UHFFFAOYSA-N 112.41100 113.90336 [Cd] CAS:7440-43-9 KEGG:C01413 WebElements:Cd cadmium chebi_ontology 48Cd Cd Kadmium cadmio cadmium CHEBI:22977 cadmium atom CAS:7440-43-9 ChemIDplus CAS:7440-43-9 KEGG COMPOUND CAS:7440-43-9 NIST Chemistry WebBook cadmium IUPAC 48Cd IUPAC Cd IUPAC Kadmium NIST_Chemistry_WebBook cadmio ChEBI cadmium ChEBI 0 Ca InChI=1S/Ca OYPRJOBELJOOCE-UHFFFAOYSA-N 40.07800 39.96259 [Ca] CAS:7440-70-2 DrugBank:DB01373 KEGG:C00076 WebElements:Ca calcium chebi_ontology 20Ca Ca Calcium Kalzium calcio calcium CHEBI:22984 calcium atom CAS:7440-70-2 ChemIDplus calcium IUPAC 20Ca IUPAC Ca IUPAC Ca UniProt Calcium KEGG_COMPOUND Kalzium ChEBI calcio ChEBI calcium ChEBI The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. 0 CH2NO 44.03272 44.01364 *C(N)=O PMID:24168430 carbamoyl chebi_ontology -C(O)NH2 -CONH2 aminocarbonyl carbamyl carbamyl group carboxamide CHEBI:23004 carbamoyl group PMID:24168430 Europe PMC carbamoyl IUPAC -C(O)NH2 ChEBI -CONH2 IUPAC aminocarbonyl IUPAC carbamyl ChEBI carbamyl group ChEBI carboxamide IUPAC carbon oxide 0 CO 28.01010 27.99491 O=C(*)* carbonyl carbonyl group chebi_ontology >C=O CHEBI:23019 carbonyl group carbonyl IUPAC carbonyl group ChEBI carbonyl group UniProt >C=O IUPAC chloride salt 0 Cl InChI=1S/Cl ZAMOUSCENKQFHK-UHFFFAOYSA-N 35.45270 34.96885 [Cl] WebElements:Cl chlorine chebi_ontology 17Cl Chlor Cl chlore chlorine chlorum cloro CHEBI:23116 chlorine atom chlorine IUPAC 17Cl IUPAC Chlor ChEBI Cl IUPAC chlore ChEBI chlorine ChEBI chlorum ChEBI cloro ChEBI chlorine molecular entity An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). Wikipedia:Cofactor_(biochemistry) cofactor cofactors chebi_ontology CHEBI:23357 cofactor cofactor IUPAC cofactors IUPAC Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI chebi_ontology Cyclopeptid Zyklopeptid cyclic peptides peptide cyclique peptido ciclico CHEBI:23449 cyclic peptide Cyclopeptid ChEBI Zyklopeptid ChEBI cyclic peptides ChEBI peptide cyclique IUPAC peptido ciclico IUPAC Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. chebi_ontology drugs medicine CHEBI:23888 drug drugs ChEBI medicine ChEBI chebi_ontology monoatomic cations CHEBI:23906 monoatomic cation monoatomic cations ChEBI A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. enzyme inhibitor chebi_ontology enzyme inhibitors inhibidor enzimatico inhibidores enzimaticos inhibiteur enzymatique inhibiteurs enzymatiques CHEBI:23924 enzyme inhibitor enzyme inhibitor IUPAC enzyme inhibitors ChEBI inhibidor enzimatico ChEBI inhibidores enzimaticos ChEBI inhibiteur enzymatique ChEBI inhibiteurs enzymatiques ChEBI 0 F InChI=1S/F YCKRFDGAMUMZLT-UHFFFAOYSA-N 18.99840 18.99840 [F] CAS:7782-41-4 WebElements:F fluorine chebi_ontology 9F F Fluor fluor fluorine fluorum CHEBI:24061 fluorine atom CAS:7782-41-4 ChemIDplus fluorine IUPAC 9F IUPAC F IUPAC Fluor ChemIDplus fluor ChEBI fluorine ChEBI fluorum ChEBI chebi_ontology CHEBI:24384 glycogens A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role biological function ChEBI A defined linked collection of atoms or a single atom within a molecular entity. group chebi_ontology Gruppe Rest groupe grupo grupos CHEBI:24433 group group IUPAC Gruppe ChEBI Rest ChEBI groupe IUPAC grupo IUPAC grupos IUPAC halogen molecular entity halogen halogens chebi_ontology Halogene group 17 elements group VII elements halogene halogenes halogeno halogenos CHEBI:24473 halogen halogen IUPAC halogens IUPAC Halogene ChEBI group 17 elements ChEBI group VII elements ChEBI halogene ChEBI halogenes ChEBI halogeno ChEBI halogenos ChEBI A cyclic compound having as ring members atoms of carbon and at least of one other element. chebi_ontology organic heterocycle organic heterocyclic compounds CHEBI:24532 organic heterocyclic compound organic heterocycle ChEBI organic heterocyclic compounds ChEBI A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond. heterodetic cyclic peptide chebi_ontology heterodetic cyclic peptides peptide cyclique heterodetique peptido ciclico heterodetico CHEBI:24533 heterodetic cyclic peptide heterodetic cyclic peptide IUPAC heterodetic cyclic peptides ChEBI peptide cyclique heterodetique IUPAC peptido ciclico heterodetico IUPAC Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. chebi_ontology endocrine hormones CHEBI:24621 hormone endocrine ChEBI hormones ChEBI Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. +1 [1H] InChI=1S/p+1/i/hH GPRLSGONYQIRFK-FTGQXOHASA-N 1.007 1.00728 [1H+] CAS:12408-02-5 KEGG:C00080 protium(1+) proton chebi_ontology (1)1H(+) (1)H(+) p p(+) CHEBI:24636 proton CAS:12408-02-5 ChemIDplus CAS:12408-02-5 NIST Chemistry WebBook protium(1+) IUPAC proton ChEBI proton IUPAC (1)1H(+) IUPAC (1)H(+) IUPAC p IUPAC p(+) IUPAC Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology CHEBI:24651 hydroxides Any member of the class of 5beta-cholanic acids carrying at least one hydroxy group at unspecified position. chebi_ontology hydroxy-5beta-cholanic acids CHEBI:24663 hydroxy-5beta-cholanic acid hydroxy-5beta-cholanic acids ChEBI Any compound containing an indole skeleton. chebi_ontology CHEBI:24828 indoles A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid oxoacids chebi_ontology oxacids oxiacids oxo acid oxy-acids oxyacids CHEBI:24833 oxoacid oxoacid IUPAC oxoacids IUPAC oxacids ChEBI oxiacids ChEBI oxo acid ChEBI oxy-acids ChEBI oxyacids ChEBI chebi_ontology inorganic anions CHEBI:24834 inorganic anion inorganic anions ChEBI A molecular entity that contains no carbon. chebi_ontology anorganische Verbindungen inorganic compounds inorganic entity inorganic molecular entities inorganics CHEBI:24835 inorganic molecular entity anorganische Verbindungen ChEBI inorganic compounds ChEBI inorganic entity ChEBI inorganic molecular entities ChEBI inorganics ChEBI chebi_ontology inorganic oxides CHEBI:24836 inorganic oxide inorganic oxides ChEBI inorganic salt Chemical element with atomic number 53. 0 I InChI=1S/I ZCYVEMRRCGMTRW-UHFFFAOYSA-N 126.90447 126.90447 [I] WebElements:I iodine chebi_ontology 53I I Iod J Jod iode iodine iodium yodo CHEBI:24859 iodine atom iodine IUPAC 53I IUPAC I ChEBI Iod ChEBI J ChEBI Jod ChEBI iode ChEBI iodine ChEBI iodium ChEBI yodo ChEBI A salt is an assembly of cations and anions. salt chebi_ontology Salz Salze ionic compound ionic compounds sal sales salts sel sels CHEBI:24866 salt salt IUPAC Salz ChEBI Salze ChEBI ionic compound ChEBI ionic compounds ChEBI sal ChEBI sales ChEBI salts ChEBI sel ChEBI sels ChEBI chebi_ontology monoatomic ions CHEBI:24867 monoatomic ion monoatomic ions ChEBI chebi_ontology organic salts organisches Salz CHEBI:24868 organic salt organic salts ChEBI organisches Salz ChEBI A molecular entity having a net electric charge. Ion ion chebi_ontology Ionen iones ions CHEBI:24870 ion Ion ChEBI ion ChEBI ion IUPAC Ionen ChEBI iones ChEBI ions ChEBI iron molecular entity iron compounds iron molecular entities iron molecular entity 0 Pb InChI=1S/Pb WABPQHHGFIMREM-UHFFFAOYSA-N 207.20000 207.97665 [Pb] KEGG:C06696 WebElements:Pb lead chebi_ontology 82Pb Blei Pb lead plomb plomo plumbum CHEBI:25016 lead atom lead IUPAC 82Pb IUPAC Blei ChEBI Pb IUPAC lead ChEBI plomb ChEBI plomo ChEBI plumbum IUPAC chebi_ontology CHEBI:25046 linear tetrapyrrole 0 Mg InChI=1S/Mg FYYHWMGAXLPEAU-UHFFFAOYSA-N 24.30500 23.98504 [Mg] CAS:7439-95-4 DrugBank:DB01378 Gmelin:16207 KEGG:C00305 WebElements:Mg magnesium chebi_ontology 12Mg Magnesium Mg magnesio magnesium CHEBI:25107 magnesium atom CAS:7439-95-4 ChemIDplus Gmelin:16207 Gmelin magnesium IUPAC 12Mg IUPAC Magnesium ChEBI Mg IUPAC Mg UniProt magnesio ChEBI magnesium ChEBI 0 Hg InChI=1S/Hg QSHDDOUJBYECFT-UHFFFAOYSA-N 200.59000 201.97064 [Hg] CAS:7439-97-6 WebElements:Hg mercury chebi_ontology 80Hg Hg Quecksilber azogue hydrargyrum liquid silver mercure mercurio mercury quicksilver CHEBI:25195 mercury atom CAS:7439-97-6 ChemIDplus mercury IUPAC 80Hg IUPAC Hg IUPAC Quecksilber ChemIDplus azogue ChEBI hydrargyrum IUPAC liquid silver ChemIDplus mercure ChemIDplus mercurio ChEBI mercury ChEBI quicksilver ChemIDplus Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites CHEBI:25212 metabolite metabolite IUPAC metabolites ChEBI primary metabolites ChEBI secondary metabolites ChEBI chebi_ontology a metal cation metal cations CHEBI:25213 metal cation a metal cation UniProt metal cations ChEBI A molecule all atoms of which have the same atomic number. chebi_ontology homoatomic molecule homoatomic molecules CHEBI:25362 elemental molecule homoatomic molecule ChEBI homoatomic molecules ChEBI Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule chebi_ontology Molekuel molecula molecules neutral molecular compounds CHEBI:25367 molecule molecule IUPAC Molekuel ChEBI molecula IUPAC molecules IUPAC neutral molecular compounds IUPAC A group of neurotransmitters and neuromodulators that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan. chebi_ontology monamines monoamines CHEBI:25375 monoamine molecular messenger monamines ChEBI monoamines ChEBI An oxoacid containing a single carboxy group. chebi_ontology monocarboxylic acids CHEBI:25384 monocarboxylic acid monocarboxylic acids ChEBI +1 0.00000 [*+] chebi_ontology monoatomic monocations monovalent inorganic cations CHEBI:25414 monoatomic monocation monoatomic monocations ChEBI monovalent inorganic cations ChEBI An endogenous compound that is used to transmit information across the synapse between a neuron and another cell. Wikipedia:Neurotransmitter chebi_ontology neurotransmitters CHEBI:25512 neurotransmitter neurotransmitters ChEBI 0 N 14.007 14.00307 WebElements:N nitrogen chebi_ontology 7N N Stickstoff azote nitrogen nitrogeno CHEBI:25555 nitrogen atom nitrogen IUPAC 7N IUPAC N IUPAC Stickstoff ChEBI azote IUPAC nitrogen ChEBI nitrogeno ChEBI nonmetal chebi_ontology Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals CHEBI:25585 nonmetal atom nonmetal IUPAC Nichtmetall ChEBI Nichtmetalle ChEBI no metal ChEBI no metales ChEBI non-metal ChEBI non-metaux ChEBI nonmetal ChEBI nonmetals ChEBI Any organic ion with a net negative charge. chebi_ontology organic anions CHEBI:25696 organic anion organic anions ChEBI Any organic ion with a net positive charge. chebi_ontology organic cations CHEBI:25697 organic cation organic cations ChEBI chebi_ontology organic ions CHEBI:25699 organic ion organic ions ChEBI organic oxide Compounds of the general formula SO3HOR where R is an organyl group chebi_ontology organic sulfates CHEBI:25704 organic sulfate organic sulfates ChEBI An oxide is a chemical compound of oxygen with other chemical elements. oxide chebi_ontology oxides CHEBI:25741 oxide oxide ChEBI oxides ChEBI 0 O InChI=1S/O QVGXLLKOCUKJST-UHFFFAOYSA-N 15.99940 15.99491 [O] KEGG:C00007 WebElements:O oxygen chebi_ontology 8O O Sauerstoff oxigeno oxygen oxygene CHEBI:25805 oxygen atom oxygen IUPAC 8O IUPAC O IUPAC Sauerstoff ChEBI oxigeno ChEBI oxygen ChEBI oxygene ChEBI oxygen molecular entity chebi_ontology oxygen molecular entities CHEBI:25806 oxygen molecular entity oxygen molecular entity ChEBI oxygen molecular entities ChEBI Any peptide with hormonal activity in animals, whether endocrine, neuroendocrine, or paracrine. chebi_ontology peptide hormones polypeptide hormone CHEBI:25905 peptide hormone peptide hormones ChEBI polypeptide hormone ChEBI Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. phosphates chebi_ontology phosphates CHEBI:26020 phosphate phosphates IUPAC phosphates ChEBI A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom. 0 H3O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N 97.99520 97.97690 [H]OP(=O)(O[H])O[H] Beilstein:1921286 CAS:7664-38-2 Drug_Central:4478 Gmelin:2000 HMDB:HMDB0002142 KEGG:C00009 KEGG:D05467 KNApSAcK:C00007408 PMID:11455380 PMID:15630224 PMID:17439666 PMID:17518491 PMID:22282755 PMID:22333268 PMID:22381614 PMID:22401268 Reaxys:1921286 Wikipedia:Phosphoric_Acid Phosphoric acid phosphoric acid tetraoxophosphoric acid trihydrogen tetraoxophosphate(3-) trihydroxidooxidophosphorus chebi_ontology H3PO4 Orthophosphoric acid Phosphate Phosphorsaeure Phosphorsaeureloesungen [PO(OH)3] acide phosphorique acidum phosphoricum orthophosphoric acid CHEBI:26078 phosphoric acid Beilstein:1921286 Beilstein CAS:7664-38-2 ChemIDplus CAS:7664-38-2 KEGG COMPOUND CAS:7664-38-2 NIST Chemistry WebBook Drug_Central:4478 DrugCentral Gmelin:2000 Gmelin PMID:11455380 Europe PMC PMID:15630224 Europe PMC PMID:17439666 Europe PMC PMID:17518491 Europe PMC PMID:22282755 Europe PMC PMID:22333268 Europe PMC PMID:22381614 Europe PMC PMID:22401268 Europe PMC Reaxys:1921286 Reaxys Phosphoric acid KEGG_COMPOUND phosphoric acid IUPAC tetraoxophosphoric acid IUPAC trihydrogen tetraoxophosphate(3-) IUPAC trihydroxidooxidophosphorus IUPAC H3PO4 IUPAC Orthophosphoric acid KEGG_COMPOUND Phosphate KEGG_COMPOUND Phosphorsaeure ChEBI Phosphorsaeureloesungen ChEBI [PO(OH)3] IUPAC acide phosphorique ChEBI acidum phosphoricum ChEBI orthophosphoric acid NIST_Chemistry_WebBook chebi_ontology CHEBI:26079 phosphoric acid derivative chebi_ontology phosphorus molecular entities CHEBI:26082 phosphorus molecular entity phosphorus molecular entities ChEBI 0 K InChI=1S/K ZLMJMSJWJFRBEC-UHFFFAOYSA-N 39.09830 38.96371 [K] CAS:7440-09-7 DrugBank:DB01345 KEGG:C00238 WebElements:K potassium chebi_ontology 19K K Kalium kalium potasio potassium CHEBI:26216 potassium atom CAS:7440-09-7 ChemIDplus potassium IUPAC 19K IUPAC K IUPAC Kalium ChemIDplus kalium IUPAC potasio ChEBI potassium ChEBI 0 Na InChI=1S/Na KEAYESYHFKHZAL-UHFFFAOYSA-N 22.98977 22.98977 [Na] CAS:7440-23-5 Gmelin:16221 KEGG:C01330 WebElements:Na sodium chebi_ontology 11Na Na Natrium natrium sodio sodium CHEBI:26708 sodium atom CAS:7440-23-5 ChemIDplus Gmelin:16221 Gmelin sodium IUPAC 11Na IUPAC Na IUPAC Natrium ChemIDplus natrium IUPAC sodio ChemIDplus sodium ChEBI sodium chloride chebi_ontology sodium compounds sodium molecular entities CHEBI:26712 sodium molecular entity sodium compounds ChEBI sodium molecular entities ChEBI Any alkali metal salt having sodium(1+) as the cation. chebi_ontology Natriumsalz Natriumsalze sodium salts CHEBI:26714 sodium salt Natriumsalz ChEBI Natriumsalze ChEBI sodium salts ChEBI Any steroid that acts as hormone. chebi_ontology Steroidhormon Steroidhormone hormona esteroide hormonas esteroideas hormone steroide hormones steroides steroid hormones CHEBI:26764 steroid hormone Steroidhormon ChEBI Steroidhormone ChEBI hormona esteroide ChEBI hormonas esteroideas ChEBI hormone steroide ChEBI hormones steroides ChEBI steroid hormones ChEBI An ester of an alcohol and sulfuric acid. 0 O4SR2 96.06300 95.95173 [*]OS(=O)(=O)O[*] chebi_ontology sulfate ester sulfuric acid ester sulfuric acid esters CHEBI:26819 sulfuric ester sulfate ester ChEBI sulfuric acid ester ChEBI sulfuric acid esters ChEBI Salts and esters of sulfuric acid sulfates chebi_ontology sulfuric acid derivative sulphates CHEBI:26820 sulfates sulfates ChEBI sulfuric acid derivative ChEBI sulphates ChEBI 0 S InChI=1S/S NINIDFKCEFEMDL-UHFFFAOYSA-N 32.06600 31.97207 [S] CAS:7704-34-9 KEGG:C00087 KEGG:D06527 PPDB:605 WebElements:S sulfur chebi_ontology 16S Elemental sulfur S Schwefel azufre soufre sulfur sulphur theion CHEBI:26833 sulfur atom CAS:7704-34-9 ChemIDplus CAS:7704-34-9 NIST Chemistry WebBook sulfur IUPAC 16S IUPAC Elemental sulfur KEGG_COMPOUND S IUPAC S KEGG_COMPOUND Schwefel ChEBI azufre ChEBI soufre ChEBI sulfur ChEBI sulfur UniProt sulphur ChEBI theion IUPAC sulfur molecular entity chebi_ontology sulfur molecular entities CHEBI:26835 sulfur molecular entity sulfur molecular entity ChEBI sulfur molecular entities ChEBI A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom. 0 H2O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4) QAOWNCQODCNURD-UHFFFAOYSA-N 98.07948 97.96738 [H]OS(=O)(=O)O[H] CAS:7664-93-9 Gmelin:2122 KEGG:C00059 KEGG:D05963 KNApSAcK:C00007530 MolBase:4 PMID:13568755 PMID:16122922 PMID:19397353 PMID:22047659 PMID:22136045 PMID:22204399 PMID:22267186 PMID:22296037 PMID:22364556 PMID:22435616 PPDB:606 Reaxys:2037554 Wikipedia:Sulfuric_acid Sulfuric acid dihydrogen tetraoxosulfate dihydroxidodioxidosulfur hydrogen tetraoxosulfate(2-) hydrogen tetraoxosulfate(VI) sulfuric acid tetraoxosulfuric acid chebi_ontology Acide sulfurique Acido sulfurico Acidum sulfuricum H2SO4 Schwefelsaeureloesungen [S(OH)2O2] [SO2(OH)2] sulphuric acid CHEBI:26836 sulfuric acid CAS:7664-93-9 ChemIDplus CAS:7664-93-9 KEGG COMPOUND CAS:7664-93-9 NIST Chemistry WebBook Gmelin:2122 Gmelin PMID:13568755 Europe PMC PMID:16122922 Europe PMC PMID:19397353 Europe PMC PMID:22047659 Europe PMC PMID:22136045 Europe PMC PMID:22204399 Europe PMC PMID:22267186 Europe PMC PMID:22296037 Europe PMC PMID:22364556 Europe PMC PMID:22435616 Europe PMC Reaxys:2037554 Reaxys Sulfuric acid KEGG_COMPOUND dihydrogen tetraoxosulfate IUPAC dihydroxidodioxidosulfur IUPAC hydrogen tetraoxosulfate(2-) IUPAC hydrogen tetraoxosulfate(VI) IUPAC sulfuric acid ChEBI sulfuric acid IUPAC tetraoxosulfuric acid IUPAC Acide sulfurique ChemIDplus Acido sulfurico ChemIDplus Acidum sulfuricum ChemIDplus H2SO4 IUPAC Schwefelsaeureloesungen ChemIDplus [S(OH)2O2] MolBase [SO2(OH)2] IUPAC sulphuric acid MolBase A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole tetrapyrroles chebi_ontology a tetrapyrrole CHEBI:26932 tetrapyrrole tetrapyrrole IUPAC tetrapyrroles IUPAC a tetrapyrrole UniProt 0 Sn InChI=1S/Sn ATJFFYVFTNAWJD-UHFFFAOYSA-N 118.71000 119.90220 [Sn] CAS:7440-31-5 UM-BBD_compID:c0585 WebElements:Sn tin chebi_ontology 50Sn Sn Zinn estano etain stannum tin CHEBI:27007 tin atom CAS:7440-31-5 ChemIDplus UM-BBD_compID:c0585 UM-BBD tin IUPAC 50Sn IUPAC Sn IUPAC Zinn ChemIDplus estano ChEBI etain ChEBI stannum IUPAC tin ChEBI Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Wikipedia:Micronutrient chebi_ontology micronutrients trace elements CHEBI:27027 micronutrient micronutrients ChEBI trace elements ChEBI An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell. transition element chebi_ontology Uebergangselement Uebergangsmetalle metal de transicion metal de transition metales de transicion metaux de transition transition element transition elements transition metal transition metals CHEBI:27081 transition element atom transition element IUPAC Uebergangselement ChEBI Uebergangsmetalle ChEBI metal de transicion ChEBI metal de transition ChEBI metales de transicion ChEBI metaux de transition ChEBI transition element ChEBI transition elements ChEBI transition metal ChEBI transition metals ChEBI Tryptamine and its substitution derivatives. chebi_ontology CHEBI:27162 tryptamines chebi_ontology heterobicyclic compounds organic heterobicyclic compounds CHEBI:27171 organic heterobicyclic compound heterobicyclic compounds ChEBI organic heterobicyclic compounds ChEBI A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid. chebi_ontology univalent acyl group univalent carboacyl groups univalent carboxylic acyl groups CHEBI:27207 univalent carboacyl group univalent acyl group ChEBI univalent carboacyl groups ChEBI univalent carboxylic acyl groups ChEBI 0 U InChI=1S/U JFALSRSLKYAFGM-UHFFFAOYSA-N 238.02890 238.05079 [U] CAS:7440-61-1 WebElements:U uranium chebi_ontology 92U U Uran uranio uranium CHEBI:27214 uranium atom CAS:7440-61-1 ChemIDplus uranium IUPAC 92U IUPAC U IUPAC Uran ChEBI uranio ChEBI uranium ChEBI 0 Zn InChI=1S/Zn HCHKCACWOHOZIP-UHFFFAOYSA-N 65.39000 63.92914 [Zn] CAS:7440-66-6 Gmelin:16321 KEGG:C00038 PDBeChem:ZN WebElements:Zn zinc chebi_ontology 30Zn Zink Zn Zn(II) Zn2+ cinc zinc zincum CHEBI:27363 zinc atom CAS:7440-66-6 ChemIDplus CAS:7440-66-6 KEGG COMPOUND Gmelin:16321 Gmelin zinc IUPAC 30Zn IUPAC Zink ChEBI Zn IUPAC Zn(II) KEGG_COMPOUND Zn2+ KEGG_COMPOUND cinc ChEBI zinc ChEBI zincum ChEBI A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer). zwitterion zwitterions chebi_ontology compose zwitterionique compuestos zwitterionicos zwitteriones zwitterionic compounds CHEBI:27369 zwitterion zwitterion IUPAC zwitterions IUPAC compose zwitterionique IUPAC compuestos zwitterionicos IUPAC zwitteriones IUPAC zwitterionic compounds IUPAC 0 B InChI=1S/B ZOXJGFHDIHLPTG-UHFFFAOYSA-N 10.81100 11.00930 [B] CHEBI:22915 CHEBI:3152 CAS:7440-42-8 KEGG:C06266 WebElements:B boron chebi_ontology 5B B Bor Boron boracium bore boro boron CHEBI:27560 boron atom CAS:7440-42-8 ChemIDplus CAS:7440-42-8 KEGG COMPOUND boron IUPAC 5B IUPAC B KEGG_COMPOUND Bor ChEBI Boron KEGG_COMPOUND boracium ChEBI bore ChEBI boro ChEBI boron ChEBI 0 As InChI=1S/As RQNWIZPPADIBDY-UHFFFAOYSA-N 74.92160 74.92159 [As] CHEBI:22630 CHEBI:2845 CAS:7440-38-2 KEGG:C06269 WebElements:As arsenic chebi_ontology 33As Arsen Arsenic As arsenic arsenico arsenicum CHEBI:27563 arsenic atom CAS:7440-38-2 ChemIDplus CAS:7440-38-2 KEGG COMPOUND arsenic IUPAC 33As IUPAC Arsen ChemIDplus Arsenic KEGG_COMPOUND As KEGG_COMPOUND arsenic ChEBI arsenico ChEBI arsenicum ChEBI 0 Se InChI=1S/Se BUGBHKTXTAQXES-UHFFFAOYSA-N 78.96000 79.91652 [Se] CHEBI:26627 CHEBI:9091 CAS:7782-49-2 DrugBank:DB11135 FooDB:FDB013400 HMDB:HMDB0001349 KEGG:C01529 WebElements:Se Wikipedia:Selenium selenium chebi_ontology 34Se Se Selen Selenium selenio selenium CHEBI:27568 selenium atom CAS:7782-49-2 ChemIDplus CAS:7782-49-2 NIST Chemistry WebBook selenium IUPAC 34Se IUPAC Se IUPAC Selen ChemIDplus Selenium KEGG_COMPOUND selenio ChEBI selenium ChEBI 0 Si InChI=1S/Si XUIMIQQOPSSXEZ-UHFFFAOYSA-N 28.08550 27.97693 [Si] CHEBI:26676 CHEBI:9140 CAS:7440-21-3 KEGG:C06263 WebElements:Si silicon chebi_ontology 14Si Si Silicon Silizium silicio silicium silicon CHEBI:27573 silicon atom CAS:7440-21-3 ChemIDplus silicon IUPAC 14Si IUPAC Si IUPAC Si KEGG_COMPOUND Silicon KEGG_COMPOUND Silizium ChEBI silicio ChEBI silicium ChEBI silicon ChEBI 0 C InChI=1S/C OKTJSMMVPCPJKN-UHFFFAOYSA-N 12.01070 12.00000 [C] CHEBI:23009 CHEBI:3399 CAS:7440-44-0 KEGG:C06265 WebElements:C carbon chebi_ontology 6C C Carbon Kohlenstoff carbon carbone carbonium carbono CHEBI:27594 carbon atom CAS:7440-44-0 ChemIDplus CAS:7440-44-0 KEGG COMPOUND carbon IUPAC 6C IUPAC C IUPAC C KEGG_COMPOUND Carbon KEGG_COMPOUND Kohlenstoff ChEBI carbon ChEBI carbone ChEBI carbonium ChEBI carbono ChEBI A cobalt group element atom that has atomic number 27. 0 Co InChI=1S/Co GUTLYIVDDKVIGB-UHFFFAOYSA-N 58.93320 58.93319 [Co] CHEBI:23335 CHEBI:3788 CAS:7440-48-4 KEGG:C00175 KEGG:C19171 PDBeChem:3CO WebElements:Co cobalt chebi_ontology 27Co Co Cobalt Kobalt cobalt cobalto cobaltum CHEBI:27638 cobalt atom CAS:7440-48-4 ChemIDplus CAS:7440-48-4 KEGG COMPOUND CAS:7440-48-4 NIST Chemistry WebBook cobalt IUPAC 27Co IUPAC Co IUPAC Co UniProt Cobalt KEGG_COMPOUND Kobalt NIST_Chemistry_WebBook cobalt ChEBI cobalto ChEBI cobaltum ChEBI 0 V InChI=1S/V LEONUFNNVUYDNQ-UHFFFAOYSA-N 50.94150 50.94396 [V] CHEBI:27274 CHEBI:9930 CAS:7440-62-2 KEGG:C06267 WebElements:V vanadium chebi_ontology 23V V Vanadium vanadio vanadium CHEBI:27698 vanadium atom CAS:7440-62-2 ChemIDplus CAS:7440-62-2 KEGG COMPOUND CAS:7440-62-2 NIST Chemistry WebBook vanadium IUPAC 23V IUPAC V IUPAC V KEGG_COMPOUND Vanadium KEGG_COMPOUND vanadio ChEBI vanadium ChEBI 0 W InChI=1S/W WFKWXMTUELFFGS-UHFFFAOYSA-N 183.84000 183.95093 [W] CHEBI:27170 CHEBI:9779 CAS:7440-33-7 Gmelin:16317 KEGG:C00753 PDBeChem:W WebElements:W Tungsten tungsten wolfram chebi_ontology 74W W Wolfram tungsten atom tungstene tungsteno volframio wolframio wolframium CHEBI:27998 tungsten CAS:7440-33-7 ChemIDplus CAS:7440-33-7 KEGG COMPOUND CAS:7440-33-7 NIST Chemistry WebBook Gmelin:16317 Gmelin Tungsten KEGG_COMPOUND tungsten IUPAC wolfram IUPAC 74W IUPAC W IUPAC W UniProt Wolfram NIST_Chemistry_WebBook tungsten atom ChEBI tungstene ChEBI tungsteno ChEBI volframio ChEBI wolframio ChEBI wolframium ChEBI A chromium group element atom that has atomic number 24. 0 Cr InChI=1S/Cr VYZAMTAEIAYCRO-UHFFFAOYSA-N 51.99610 51.94051 [Cr] CHEBI:23235 CHEBI:3678 CAS:7440-47-3 KEGG:C06268 WebElements:Cr chromium chebi_ontology 24Cr Chrom Chromium Cr chrome chromium cromo CHEBI:28073 chromium atom CAS:7440-47-3 ChemIDplus CAS:7440-47-3 KEGG COMPOUND chromium IUPAC 24Cr IUPAC Chrom ChemIDplus Chromium KEGG_COMPOUND Cr IUPAC Cr KEGG_COMPOUND chrome ChEBI chromium ChEBI cromo ChEBI A polydisperse, highly branched glucan composed of chains of D-glucopyranose residues in alpha(1->4) glycosidic linkage, joined together by alpha(1->6) glycosidic linkages. A small number of alpha(1->3) glycosidic linkages and some cumulative alpha(1->6) links also may occur. The branches in glycogen typically contain 8 to 12 glucose residues. CHEBI:24379 CHEBI:5466 CAS:9005-79-2 GlyGen:G99991IU GlyTouCan:G99991IU HMDB:HMDB0000757 KEGG:C00182 MetaCyc:CPD0-971 Wikipedia:Glycogen Glycogen chebi_ontology WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_b6-d1 animal starch liver starch CHEBI:28087 glycogen CAS:9005-79-2 ChemIDplus CAS:9005-79-2 KEGG COMPOUND Glycogen KEGG_COMPOUND WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_b6-d1 GlyTouCan animal starch ChemIDplus liver starch ChemIDplus Chemical element (nickel group element atom) with atomic number 28. 0 Ni InChI=1S/Ni PXHVJJICTQNCMI-UHFFFAOYSA-N 58.69340 57.93534 [Ni] CHEBI:25515 CHEBI:7552 CAS:7440-02-0 Gmelin:16229 KEGG:C00291 PMID:12756270 PMID:14634084 PMID:14734778 PMID:15165199 PMID:19828094 PMID:20477134 PMID:22762130 PMID:23142754 PMID:23317102 PMID:23692032 PMID:23692035 PMID:23723488 PMID:23834453 PMID:23857010 PMID:23895079 PMID:23909687 PMID:9060994 PMID:9886425 Reaxys:4122946 WebElements:Ni Wikipedia:Nickel nickel chebi_ontology 28Ni Ni Nickel Raney alloy niccolum nickel niquel CHEBI:28112 nickel atom CAS:7440-02-0 ChemIDplus CAS:7440-02-0 KEGG COMPOUND CAS:7440-02-0 NIST Chemistry WebBook Gmelin:16229 Gmelin PMID:12756270 Europe PMC PMID:14634084 Europe PMC PMID:14734778 Europe PMC PMID:15165199 Europe PMC PMID:19828094 Europe PMC PMID:20477134 Europe PMC PMID:22762130 Europe PMC PMID:23142754 Europe PMC PMID:23317102 Europe PMC PMID:23692032 Europe PMC PMID:23692035 Europe PMC PMID:23723488 Europe PMC PMID:23834453 Europe PMC PMID:23857010 Europe PMC PMID:23895079 Europe PMC PMID:23909687 Europe PMC PMID:9060994 Europe PMC PMID:9886425 Europe PMC Reaxys:4122946 Reaxys nickel IUPAC 28Ni IUPAC Ni IUPAC Ni UniProt Nickel ChEBI Raney alloy ChemIDplus niccolum ChEBI nickel ChEBI niquel ChEBI A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised. 0 CH3NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4) KXDHJXZQYSOELW-UHFFFAOYSA-N 61.04006 61.01638 NC(O)=O CHEBI:22504 CHEBI:23002 CHEBI:3386 CHEBI:44573 Beilstein:1734754 CAS:463-77-4 DrugBank:DB04261 Gmelin:130345 KEGG:C01563 PDBeChem:OUT Wikipedia:Carbamic_acid CARBAMIC ACID Carbamic acid carbamic acid chebi_ontology Aminoameisensaeure Aminoformic acid Carbamate Carbamidsaeure CHEBI:28616 carbamic acid Beilstein:1734754 Beilstein CAS:463-77-4 ChemIDplus CAS:463-77-4 KEGG COMPOUND Gmelin:130345 Gmelin CARBAMIC ACID PDBeChem Carbamic acid KEGG_COMPOUND carbamic acid IUPAC Aminoameisensaeure ChEBI Aminoformic acid KEGG_COMPOUND Carbamate KEGG_COMPOUND Carbamidsaeure ChEBI 0 P InChI=1S/P OAICVXFJPJFONN-UHFFFAOYSA-N 30.97376 30.97376 [P] CHEBI:26080 CHEBI:8168 CAS:7723-14-0 Gmelin:16235 KEGG:C06262 WebElements:P phosphorus chebi_ontology 15P P Phosphor Phosphorus fosforo phosphore phosphorus CHEBI:28659 phosphorus atom CAS:7723-14-0 ChemIDplus CAS:7723-14-0 KEGG COMPOUND Gmelin:16235 Gmelin phosphorus IUPAC 15P IUPAC P IUPAC P KEGG_COMPOUND Phosphor ChEBI Phosphorus KEGG_COMPOUND fosforo ChEBI phosphore ChEBI phosphorus ChEBI 0 Mo InChI=1S/Mo ZOKXTWBITQBERF-UHFFFAOYSA-N 95.94000 97.90541 [Mo] CHEBI:25369 CHEBI:49750 CHEBI:6968 CAS:7439-98-7 Gmelin:16205 KEGG:C00150 WebElements:Mo molybdenum chebi_ontology 42Mo Mo Molybdaen Molybdenum molibdeno molybdene molybdenum CHEBI:28685 molybdenum atom CAS:7439-98-7 ChemIDplus CAS:7439-98-7 KEGG COMPOUND CAS:7439-98-7 NIST Chemistry WebBook Gmelin:16205 Gmelin molybdenum IUPAC 42Mo IUPAC Mo IUPAC Mo UniProt Molybdaen ChEBI Molybdenum KEGG_COMPOUND molibdeno ChEBI molybdene ChEBI molybdenum ChEBI 0 Cu InChI=1S/Cu RYGMFSIKBFXOCR-UHFFFAOYSA-N 63.54600 62.92960 [Cu] CHEBI:23376 CHEBI:3874 CAS:7440-50-8 Gmelin:16269 KEGG:C00070 WebElements:Cu copper chebi_ontology 29Cu Copper Cu Kupfer cobre copper cuivre cuprum CHEBI:28694 copper atom CAS:7440-50-8 ChemIDplus CAS:7440-50-8 KEGG COMPOUND Gmelin:16269 Gmelin copper IUPAC 29Cu IUPAC Copper KEGG_COMPOUND Cu ChEBI Cu IUPAC Kupfer ChEBI cobre ChEBI copper ChEBI cuivre ChEBI cuprum IUPAC A primary amino compound that is the 5-hydroxy derivative of tryptamine. 0 C10H12N2O InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2 QZAYGJVTTNCVMB-UHFFFAOYSA-N 176.215 176.09496 C1=CC(=CC=2C(=CNC12)CCN)O CHEBI:1420 CHEBI:26652 CHEBI:49894 Beilstein:143524 CAS:50-67-9 Gmelin:1861995 HMDB:HMDB0000259 KEGG:C00780 KNApSAcK:C00001429 LINCS:LSM-6589 MetaCyc:SEROTONIN PDBeChem:SRO PMID:18593914 PMID:22770225 PMID:24136337 Reaxys:143524 Wikipedia:Serotonin 3-(2-aminoethyl)-1H-indol-5-ol SEROTONIN Serotonin chebi_ontology 3-(2-Aminoethyl)-1H-indol-5-ol 5-HT 5-Hydroxytryptamine Enteramine serotonine thrombocytin thrombotonin CHEBI:28790 serotonin Beilstein:143524 Beilstein CAS:50-67-9 ChemIDplus CAS:50-67-9 KEGG COMPOUND Gmelin:1861995 Gmelin PMID:18593914 Europe PMC PMID:22770225 Europe PMC PMID:24136337 Europe PMC Reaxys:143524 Reaxys 3-(2-aminoethyl)-1H-indol-5-ol IUPAC SEROTONIN PDBeChem Serotonin KEGG_COMPOUND 3-(2-Aminoethyl)-1H-indol-5-ol KEGG_COMPOUND 5-HT IUPHAR 5-Hydroxytryptamine KEGG_COMPOUND Enteramine KEGG_COMPOUND serotonine ChEBI thrombocytin ChemIDplus thrombotonin ChemIDplus An onium cation obtained by protonation of ammonia. +1 H4N InChI=1S/H3N/h1H3/p+1 QGZKDVFQNNGYKY-UHFFFAOYSA-O 18.03850 18.03383 [H][N+]([H])([H])[H] CHEBI:22534 CHEBI:49783 CHEBI:7435 CAS:14798-03-9 Gmelin:84 KEGG:C01342 MetaCyc:AMMONIUM MolBase:929 PDBeChem:NH4 PMID:11319011 PMID:11341317 PMID:12096804 PMID:14512268 PMID:14879753 PMID:16345391 PMID:16903292 PMID:17392693 PMID:18515490 PMID:19199063 PMID:19596600 PMID:19682559 PMID:19716251 PMID:21993530 PMID:22265469 PMID:22524020 PMID:22562341 PMID:22631217 Reaxys:16093784 Wikipedia:Ammonium ammonium azanium chebi_ontology Ammonium(1+) NH4(+) NH4+ [NH4](+) ammonium cation ammonium ion CHEBI:28938 ammonium CAS:14798-03-9 ChemIDplus CAS:14798-03-9 NIST Chemistry WebBook Gmelin:84 Gmelin PMID:11319011 Europe PMC PMID:11341317 Europe PMC PMID:12096804 Europe PMC PMID:14512268 Europe PMC PMID:14879753 Europe PMC PMID:16345391 Europe PMC PMID:16903292 Europe PMC PMID:17392693 Europe PMC PMID:18515490 Europe PMC PMID:19199063 Europe PMC PMID:19596600 Europe PMC PMID:19682559 Europe PMC PMID:19716251 Europe PMC PMID:21993530 Europe PMC PMID:22265469 Europe PMC PMID:22524020 Europe PMC PMID:22562341 Europe PMC PMID:22631217 Europe PMC Reaxys:16093784 Reaxys ammonium ChEBI ammonium IUPAC azanium IUPAC Ammonium(1+) ChemIDplus NH4(+) IUPAC NH4(+) UniProt NH4+ KEGG_COMPOUND [NH4](+) MolBase ammonium cation ChemIDplus ammonium ion PDBeChem A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid. -2 C2O4R 88.019 87.97966 [O-]C(=O)[*]C([O-])=O CHEBI:13632 CHEBI:23688 CHEBI:23689 CHEBI:38711 dicarboxylic acid dianion chebi_ontology a dicarboxylate dicarboxylate dicarboxylates dicarboxylic acid dianions CHEBI:28965 dicarboxylic acid dianion dicarboxylic acid dianion ChEBI a dicarboxylate UniProt dicarboxylate ChEBI dicarboxylates ChEBI dicarboxylic acid dianions ChEBI 0 CH2O3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4) BVKZGUZCCUSVTD-UHFFFAOYSA-N 62.02478 62.00039 OC(O)=O CHEBI:13351 CHEBI:23017 CHEBI:23744 CHEBI:3401 CAS:463-79-6 Gmelin:25554 KEGG:C01353 PDBeChem:CO3 Carbonic acid carbonic acid dihydroxidooxidocarbon chebi_ontology Dihydrogen carbonate H2CO3 Koehlensaeure [CO(OH)2] CHEBI:28976 carbonic acid CAS:463-79-6 ChemIDplus CAS:463-79-6 KEGG COMPOUND Gmelin:25554 Gmelin Carbonic acid KEGG_COMPOUND carbonic acid IUPAC dihydroxidooxidocarbon IUPAC Dihydrogen carbonate KEGG_COMPOUND H2CO3 IUPAC H2CO3 KEGG_COMPOUND Koehlensaeure ChEBI [CO(OH)2] IUPAC 0 Al InChI=1S/Al XAGFODPZIPBFFR-UHFFFAOYSA-N 26.98154 26.98154 [Al] CHEBI:22471 CHEBI:2616 CAS:7429-90-5 DrugBank:DB01370 Gmelin:16248 KEGG:C06264 WebElements:Al aluminium chebi_ontology 13Al Al Aluminium aluminio aluminium aluminum CHEBI:28984 aluminium atom CAS:7429-90-5 ChemIDplus CAS:7429-90-5 KEGG COMPOUND Gmelin:16248 Gmelin aluminium IUPAC 13Al IUPAC Al IUPAC Al KEGG_COMPOUND Aluminium ChEBI Aluminium KEGG_COMPOUND aluminio ChEBI aluminium ChEBI aluminum NIST_Chemistry_WebBook The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13626 CHEBI:13945 CHEBI:23026 CHEBI:58657 chebi_ontology a carboxylate carboxylic acid anions carboxylic anions CHEBI:29067 carboxylic acid anion a carboxylate UniProt carboxylic acid anions ChEBI carboxylic anions ChEBI A monoatomic monocation obtained from sodium. +1 Na InChI=1S/Na/q+1 FKNQFGJONOIPTF-UHFFFAOYSA-N 22.98977 22.98922 [Na+] CHEBI:26717 CHEBI:49766 CHEBI:9175 CAS:17341-25-2 Gmelin:15196 KEGG:C01330 PDBeChem:NA sodium cation sodium(1+) sodium(1+) ion sodium(I) cation chebi_ontology Na(+) Na+ SODIUM ION CHEBI:29101 sodium(1+) CAS:17341-25-2 ChemIDplus CAS:17341-25-2 NIST Chemistry WebBook Gmelin:15196 Gmelin sodium cation IUPAC sodium(1+) IUPAC sodium(1+) ion IUPAC sodium(I) cation IUPAC Na(+) IUPAC Na(+) UniProt Na+ KEGG_COMPOUND SODIUM ION PDBeChem The stable isotope of hydrogen with relative atomic mass 1.007825 and a natural abundance of 99.9885 atom percent (from Greek pirhoomegatauomicronsigma, first). 0 [1H] InChI=1S/H/i1+0 YZCKVEUIGOORGS-IGMARMGPSA-N 1.008 1.00783 [1H] protium chebi_ontology (1)1H (1)H hydrogen-1 protio protium CHEBI:29236 protium atom protium IUPAC (1)1H IUPAC (1)H IUPAC hydrogen-1 ChEBI protio ChEBI protium ChEBI The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). 0 D InChI=1S/H2/h1H/i1+1 UFHFLCQGNIYNRP-OUBTZVSYSA-N 2.014 2.01410 [2H] deuterium chebi_ontology (2)1H (2)H D Deuterium deuterio deuterium heavy hydrogen hidrogeno pesado hydrogen-2 schwerer Wasserstoff CHEBI:29237 deuterium atom deuterium IUPAC (2)1H IUPAC (2)H IUPAC D IUPAC Deuterium ChEBI deuterio ChEBI deuterium ChEBI heavy hydrogen ChEBI hidrogeno pesado ChEBI hydrogen-2 ChEBI schwerer Wasserstoff ChEBI The radioactive isotope of hydrogen with relative atomic mass 3.016049 and half-life of 12.33 years (from Greek taurhoiotatauomicronsigma, third). 0 T InChI=1S/H2/h1H/i1+2 UFHFLCQGNIYNRP-NJFSPNSNSA-N 3.016 3.01605 [3H] tritium chebi_ontology (3)1H (3)H T hydrogen-3 tritio tritium ueberschwerer Wasserstoff CHEBI:29238 tritium atom tritium IUPAC (3)1H IUPAC (3)H IUPAC T IUPAC hydrogen-3 ChEBI tritio ChEBI tritium ChEBI ueberschwerer Wasserstoff ChEBI 0 Au InChI=1S/Au PCHJSUWPFVWCPO-UHFFFAOYSA-N 196.96655 196.96657 [Au] CAS:7440-57-5 WebElements:Au gold chebi_ontology 79Au Au Gold aurum gold or oro CHEBI:29287 gold atom CAS:7440-57-5 ChemIDplus gold IUPAC 79Au IUPAC Au IUPAC Gold ChEBI aurum IUPAC gold ChEBI or ChEBI oro ChEBI -1 H2N InChI=1S/H2N/h1H2/q-1 HYGWNUKOUCZBND-UHFFFAOYSA-N 16.02262 16.01927 [H][N-][H] amide azanide dihydridonitrate(1-) chebi_ontology NH2(-) CHEBI:29337 azanide amide IUPAC azanide IUPAC dihydridonitrate(1-) IUPAC NH2(-) IUPAC A divalent inorganic anion resulting from the removal of two protons from ammonia. -2 HN InChI=1S/HN/h1H/q-2 DZQYTNGKSBCIOE-UHFFFAOYSA-N 15.01468 15.01200 [N--][H] azanediide hydridonitrate(2-) chebi_ontology NH(2-) imide CHEBI:29340 hydridonitrate(2-) azanediide IUPAC hydridonitrate(2-) IUPAC NH(2-) IUPAC imide IUPAC +1 HO2 InChI=1S/O2/c1-2/p+1 MYMOFIZGZYHOMD-UHFFFAOYSA-O 33.00674 32.99711 [H][O+]=O Gmelin:508 dioxidenium hydridodioxygen(1+) chebi_ontology HO2(+) HOO(+) [HO2](+) CHEBI:29793 hydridodioxygen(1+) Gmelin:508 Gmelin dioxidenium IUPAC hydridodioxygen(1+) IUPAC HO2(+) IUPAC HOO(+) ChEBI [HO2](+) ChEBI A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of acetic acid. -1 C2H3O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1 QTBSBXVTEAMEQO-UHFFFAOYSA-M 59.04402 59.01385 CC([O-])=O CHEBI:13704 CHEBI:22165 CHEBI:40480 Beilstein:1901470 CAS:71-50-1 DrugBank:DB03166 Gmelin:1379 KEGG:C00033 MetaCyc:ACET PDBeChem:ACT PMID:17190852 PMID:22211106 PMID:22371380 Reaxys:1901470 UM-BBD_compID:c0050 Wikipedia:Acetate acetate chebi_ontology ACETATE ION Azetat CH3-COO(-) Ethanoat MeCO2 anion acetic acid, ion(1-) ethanoate CHEBI:30089 acetate Beilstein:1901470 Beilstein CAS:71-50-1 ChemIDplus CAS:71-50-1 NIST Chemistry WebBook Gmelin:1379 Gmelin PMID:17190852 Europe PMC PMID:22211106 Europe PMC PMID:22371380 Europe PMC Reaxys:1901470 Reaxys UM-BBD_compID:c0050 UM-BBD acetate IUPAC acetate UniProt ACETATE ION PDBeChem Azetat ChEBI CH3-COO(-) IUPAC Ethanoat ChEBI MeCO2 anion NIST_Chemistry_WebBook acetic acid, ion(1-) ChemIDplus ethanoate ChEBI 0 Li InChI=1S/Li WHXSMMKQMYFTQS-UHFFFAOYSA-N 6.94100 7.01600 [Li] CAS:7439-93-2 WebElements:Li lithium chebi_ontology 3Li Li Lithium lithium litio CHEBI:30145 lithium atom CAS:7439-93-2 NIST Chemistry WebBook lithium IUPAC 3Li IUPAC Li IUPAC Lithium ChEBI lithium ChEBI litio ChEBI Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force. 0 0.0 0.0 * CHEBI:10581 CHEBI:14383 KEGG:C00205 photon chebi_ontology Lichtquant Light foton gamma hnu light quantum CHEBI:30212 photon photon IUPAC Lichtquant ChEBI Light KEGG_COMPOUND foton ChEBI gamma IUPAC hnu IUPAC hnu UniProt light quantum ChEBI Nucleus of the (4)He atom. +2 [4He] InChI=1S/He/q+2/i1+0 LBDSXVIYZYSRII-IGMARMGPSA-N 4.002 4.00151 [4He++] Gmelin:53474 alpha-particle helium-4(2+) chebi_ontology (4)He(2+) alpha CHEBI:30216 alpha-particle Gmelin:53474 Gmelin alpha-particle IUPAC alpha-particle IUPAC helium-4(2+) IUPAC (4)He(2+) IUPAC alpha IUPAC 0 He InChI=1S/He SWQJXJOGLNCZEY-UHFFFAOYSA-N 4.00260 4.00260 [He] CAS:7440-59-7 Drug_Central:4262 Gmelin:16294 WebElements:He helium chebi_ontology 2He He Helium helio helium CHEBI:30217 helium atom CAS:7440-59-7 NIST Chemistry WebBook Drug_Central:4262 DrugCentral Gmelin:16294 Gmelin helium IUPAC 2He IUPAC He IUPAC Helium ChEBI helio ChEBI helium ChEBI The stable isotope of helium with relative atomic mass 3.016029. The least abundant (0.000137 atom percent) isotope of naturally occurring helium. 0 [3He] InChI=1S/He/i1-1 SWQJXJOGLNCZEY-BJUDXGSMSA-N 3.016 3.01603 [3He] CAS:14762-55-1 Gmelin:14208 helium-3 chebi_ontology (3)2He (3)He (3He)helium helium, isotope of mass 3 helium-3 CHEBI:30218 helium-3 atom CAS:14762-55-1 ChemIDplus Gmelin:14208 Gmelin helium-3 IUPAC (3)2He IUPAC (3)He IUPAC (3He)helium ChemIDplus helium, isotope of mass 3 ChemIDplus helium-3 ChEBI The stable isotope of helium with relative atomic mass 4.002603. The most abundant (99.99 atom percent) isotope of naturally occurring helium. 0 [4He] InChI=1S/He/i1+0 SWQJXJOGLNCZEY-IGMARMGPSA-N 4.003 4.00260 [4He] Gmelin:14207 helium-4 chebi_ontology (4)2He (4)He helium-4 CHEBI:30219 helium-4 atom Gmelin:14207 Gmelin helium-4 IUPAC (4)2He IUPAC (4)He IUPAC helium-4 ChEBI Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. 0 1.008664904 neutron chebi_ontology (1)0n n CHEBI:30222 neutron neutron ChEBI neutron IUPAC (1)0n ChEBI n IUPAC +2 0.00000 [*++] CHEBI:23856 CHEBI:4665 KEGG:C00572 chebi_ontology Divalent cation divalent inorganic cations monoatomic dications CHEBI:30412 monoatomic dication Divalent cation KEGG_COMPOUND divalent inorganic cations ChEBI monoatomic dications ChEBI 0 At InChI=1S/At RYXHOMYVWAEKHL-UHFFFAOYSA-N 210.00000 210.00000 [At] CAS:7440-68-8 Gmelin:40440 WebElements:At astatine chebi_ontology 85At Astat At astate astatine astato CHEBI:30415 astatine atom CAS:7440-68-8 ChemIDplus CAS:7440-68-8 NIST Chemistry WebBook Gmelin:40440 Gmelin astatine IUPAC 85At IUPAC Astat ChEBI At IUPAC astate ChEBI astatine ChEBI astato ChEBI A metallic element first identified and named from the brilliant indigo (Latin indicum) blue line in its flame spectrum. 0 In InChI=1S/In APFVFJFRJDLVQX-UHFFFAOYSA-N 114.81800 114.90388 [In] CAS:7440-74-6 Gmelin:16297 WebElements:In indium chebi_ontology 49In In Indium indio indium CHEBI:30430 indium atom CAS:7440-74-6 ChemIDplus CAS:7440-74-6 NIST Chemistry WebBook Gmelin:16297 Gmelin indium IUPAC 49In IUPAC In IUPAC Indium ChEBI indio ChEBI indium ChEBI A metallic element first identified and named from the brilliant green line in its flame spectrum (from Greek thetaalphalambdalambdaomicronsigma, a green shoot). 0 Tl InChI=1S/Tl BKVIYDNLLOSFOA-UHFFFAOYSA-N 204.38330 204.97443 [Tl] CAS:7440-28-0 Gmelin:16308 WebElements:Tl thallium chebi_ontology 81Tl Tl talio CHEBI:30440 thallium CAS:7440-28-0 ChemIDplus CAS:7440-28-0 NIST Chemistry WebBook Gmelin:16308 Gmelin thallium IUPAC 81Tl IUPAC Tl IUPAC talio ChEBI 0 Ge InChI=1S/Ge GNPVGFCGXDBREM-UHFFFAOYSA-N 72.61000 73.92118 [Ge] CAS:7440-56-4 WebElements:Ge germanium chebi_ontology 32Ge Ge germanio germanium CHEBI:30441 germanium atom CAS:7440-56-4 ChemIDplus CAS:7440-56-4 NIST Chemistry WebBook germanium IUPAC 32Ge IUPAC Ge IUPAC germanio ChEBI germanium ChEBI 0 Te InChI=1S/Te PORWMNRCUJJQNO-UHFFFAOYSA-N 127.60000 129.90622 [Te] CAS:13494-80-9 Gmelin:16309 WebElements:Te tellurium chebi_ontology 52Te Te Tellur tellure tellurium teluro CHEBI:30452 tellurium atom CAS:13494-80-9 ChemIDplus CAS:13494-80-9 NIST Chemistry WebBook Gmelin:16309 Gmelin tellurium IUPAC 52Te IUPAC Te IUPAC Tellur ChEBI tellure ChEBI tellurium ChEBI teluro ChEBI Alkaline earth metal atom with atomic number 4. 0 Be InChI=1S/Be ATBAMAFKBVZNFJ-UHFFFAOYSA-N 9.01218 9.01218 [Be] CAS:7440-41-7 Gmelin:16265 PMID:10858219 PMID:11897645 PMID:14643414 PMID:16951350 PMID:18250483 PMID:18768897 PMID:24912188 Reaxys:14617151 WebElements:Be beryllium chebi_ontology 4Be Be Beryllium berilio beryllium CHEBI:30501 beryllium atom CAS:7440-41-7 ChemIDplus CAS:7440-41-7 NIST Chemistry WebBook Gmelin:16265 Gmelin PMID:10858219 Europe PMC PMID:11897645 Europe PMC PMID:14643414 Europe PMC PMID:16951350 Europe PMC PMID:18250483 Europe PMC PMID:18768897 Europe PMC PMID:24912188 Europe PMC Reaxys:14617151 Reaxys beryllium IUPAC 4Be IUPAC Be IUPAC Beryllium ChEBI berilio ChEBI beryllium ChEBI 0 Ag InChI=1S/Ag BQCADISMDOOEFD-UHFFFAOYSA-N 107.86820 106.90509 [Ag] CAS:7440-22-4 WebElements:Ag silver chebi_ontology 47Ag Ag Silber argent argentum plata silver CHEBI:30512 silver atom CAS:7440-22-4 ChemIDplus silver IUPAC 47Ag IUPAC Ag IUPAC Silber ChemIDplus argent ChEBI argentum IUPAC plata ChEBI silver ChEBI 0 Sb InChI=1S/Sb WATWJIUSRGPENY-UHFFFAOYSA-N 121.76000 120.90381 [Sb] WebElements:Sb antimony chebi_ontology 51Sb Antimon Sb antimoine antimonio antimony stibium CHEBI:30513 antimony atom antimony IUPAC 51Sb IUPAC Antimon ChEBI Sb IUPAC antimoine ChEBI antimonio ChEBI antimony ChEBI stibium IUPAC 0 Cs InChI=1S/Cs TVFDJXOCXUVLDH-UHFFFAOYSA-N 132.90545 132.90545 [Cs] WebElements:Cs caesium chebi_ontology 55Cs Caesium Cs Zaesium caesium cesio cesium CHEBI:30514 caesium atom caesium IUPAC 55Cs IUPAC Caesium ChEBI Cs IUPAC Zaesium ChEBI caesium ChEBI cesio ChEBI cesium ChEBI cesium IUPAC 0 Ru InChI=1S/Ru KJTLSVCANCCWHF-UHFFFAOYSA-N 101.07000 101.90434 [Ru] CAS:7440-18-8 WebElements:Ru ruthenium chebi_ontology 44Ru Ru Ruthenium rutenio ruthenium CHEBI:30682 ruthenium atom CAS:7440-18-8 ChemIDplus CAS:7440-18-8 NIST Chemistry WebBook ruthenium IUPAC 44Ru IUPAC Ru IUPAC Ruthenium ChEBI rutenio ChEBI ruthenium ChEBI 0 Os InChI=1S/Os SYQBFIAQOQZEGI-UHFFFAOYSA-N 190.23000 191.96148 [Os] CAS:7440-04-2 Gmelin:16234 WebElements:Os osmium chebi_ontology 76Os Os osmio osmium CHEBI:30687 osmium atom CAS:7440-04-2 ChemIDplus CAS:7440-04-2 NIST Chemistry WebBook Gmelin:16234 Gmelin osmium IUPAC 76Os IUPAC Os IUPAC osmio ChEBI osmium ChEBI Any member of a group of hydroxy-5beta-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration. KEGG:C01558 Bile acid chebi_ontology 5beta-bile acid 5beta-bile acids Bile salt Gallensaeure Gallensaeuren bile acids CHEBI:3098 bile acid Bile acid KEGG_COMPOUND 5beta-bile acid ChEBI 5beta-bile acids ChEBI Bile salt KEGG_COMPOUND Gallensaeure ChEBI Gallensaeuren ChEBI bile acids ChEBI 0 Ba InChI=1S/Ba DSAJWYNOEDNPEQ-UHFFFAOYSA-N 137.32700 137.90525 [Ba] WebElements:Ba barium chebi_ontology 56Ba Ba Barium bario barium baryum CHEBI:32594 barium atom barium IUPAC 56Ba IUPAC Ba IUPAC Barium ChEBI bario ChEBI barium ChEBI baryum ChEBI A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups. CHEBI:13814 CHEBI:22474 CHEBI:2641 KEGG:C00706 Amine amines chebi_ontology Amin Substituted amine CHEBI:32952 amine Amine KEGG_COMPOUND amines IUPAC Amin ChEBI Substituted amine KEGG_COMPOUND An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 KEGG:C00241 Amide amides chebi_ontology CHEBI:32988 amide Amide KEGG_COMPOUND amides IUPAC 0 Eu InChI=1S/Eu OGPBJKLSAFTDLK-UHFFFAOYSA-N 151.96400 152.92124 [Eu] CAS:7440-53-1 Gmelin:16279 WebElements:Eu europium chebi_ontology 63Eu Eu europio europium CHEBI:32999 europium atom CAS:7440-53-1 ChemIDplus Gmelin:16279 Gmelin europium IUPAC 63Eu IUPAC Eu IUPAC europio ChEBI europium ChEBI Intended use of the molecular entity or part thereof by humans. chebi_ontology CHEBI:33232 application A particle not known to have substructure. elementary particle chebi_ontology elementary particles CHEBI:33233 fundamental particle elementary particle IUPAC elementary particles ChEBI A monoatomic entity is a molecular entity consisting of a single atom. chebi_ontology atomic entity monoatomic entities CHEBI:33238 monoatomic entity atomic entity ChEBI monoatomic entities ChEBI chebi_ontology oxoacid derivatives CHEBI:33241 oxoacid derivative oxoacid derivatives ChEBI chebi_ontology inorganic hydrides CHEBI:33242 inorganic hydride inorganic hydrides ChEBI An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system. chebi_ontology organic fundamental parents organic parent hydrides CHEBI:33245 organic fundamental parent organic fundamental parents ChEBI organic parent hydrides ChEBI Any substituent group which does not contain carbon. chebi_ontology inorganic groups CHEBI:33246 inorganic group inorganic groups ChEBI Any substituent group or skeleton containing carbon. chebi_ontology organic groups CHEBI:33247 organic group organic groups ChEBI Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. organyl group organyl groups chebi_ontology groupe organyle grupo organilo grupos organilo CHEBI:33249 organyl group organyl group IUPAC organyl groups IUPAC groupe organyle IUPAC grupo organilo IUPAC grupos organilo IUPAC atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 MeSH:D004602 NCIt:C1940 NCIt:C48792 SNOMEDCT:290004009 atom chebi_ontology atome atomo atoms atomus element elements CHEBI:33250 atom uncharged atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI 0 H InChI=1S/H YZCKVEUIGOORGS-UHFFFAOYSA-N 1.00794 1.00783 [H] chebi_ontology atomic hydrogen CHEBI:33251 monoatomic hydrogen atomic hydrogen ChEBI A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. nucleus chebi_ontology Atomkern Kern noyau noyau atomique nuclei nucleo nucleo atomico nucleus atomi CHEBI:33252 Some people may be uncomfortable calling every proton an atomic nucleus This is equivalent to CHEBI:33252 atomic nucleus atomic nucleus nucleus IUPAC Atomkern ChEBI Kern ChEBI noyau IUPAC noyau atomique ChEBI nuclei ChEBI nucleo IUPAC nucleo atomico ChEBI nucleus atomi ChEBI Heavy nuclear particle: proton or neutron. nucleon chebi_ontology Nukleon Nukleonen nucleons CHEBI:33253 nucleon nucleon IUPAC nucleon IUPAC Nukleon ChEBI Nukleonen ChEBI nucleons ChEBI A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide primary amides chebi_ontology CHEBI:33256 primary amide primary amide IUPAC primary amides IUPAC A molecular entity all atoms of which have the same atomic number. chebi_ontology homoatomic entity homoatomic molecular entities homoatomic molecular entity CHEBI:33259 elemental molecular entity homoatomic entity ChEBI homoatomic molecular entities ChEBI homoatomic molecular entity ChEBI chebi_ontology CHEBI:33260 elemental hydrogen chebi_ontology CHEBI:33262 elemental oxygen 0 O2 31.999 31.98983 chebi_ontology CHEBI:33263 diatomic oxygen diatomic nitrogen elemental nitrogen An anion consisting of more than one atom. chebi_ontology polyatomic anions CHEBI:33273 polyatomic anion polyatomic anions ChEBI chebi_ontology chemical messenger CHEBI:33280 molecular messenger chemical messenger ChEBI A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:22582 PMID:12964249 PMID:22117953 PMID:22439833 PMID:22849268 PMID:22849276 PMID:22958833 chebi_ontology Antibiotika Antibiotikum antibiotic antibiotics antibiotique antimicrobial antimicrobial agents antimicrobials microbicide microbicides CHEBI:33281 antimicrobial agent PMID:12964249 Europe PMC PMID:22117953 Europe PMC PMID:22439833 Europe PMC PMID:22849268 Europe PMC PMID:22849276 Europe PMC PMID:22958833 Europe PMC Antibiotika ChEBI Antibiotikum ChEBI antibiotic ChEBI antibiotics ChEBI antibiotique IUPAC antimicrobial ChEBI antimicrobial agents ChEBI antimicrobials ChEBI microbicide ChEBI microbicides ChEBI A nutrient is a food component that an organism uses to survive and grow. chebi_ontology nutrients CHEBI:33284 nutrient nutrients ChEBI A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. chebi_ontology heteroorganic entities organoelement compounds CHEBI:33285 heteroorganic entity heteroorganic entities ChEBI organoelement compounds ChEBI An agrochemical is a substance that is used in agriculture or horticulture. Wikipedia:Agrochemical chebi_ontology agrichemical agrichemicals agricultural chemicals agrochemicals CHEBI:33286 agrochemical agrichemical ChEBI agrichemicals ChEBI agricultural chemicals ChEBI agrochemicals ChEBI A fertilizer is any substance that is added to soil or water to assist the growth of plants. chebi_ontology fertiliser fertilizers CHEBI:33287 fertilizer fertiliser ChEBI fertilizers ChEBI fuel A molecular entity containing one or more atoms of an alkali metal. chebi_ontology alkali metal molecular entities CHEBI:33296 alkali metal molecular entity alkali metal molecular entities ChEBI Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogens chebi_ontology group 15 elements group V elements nitrogenoideos nitrogenoides pnictogene pnictogenes CHEBI:33300 pnictogen pnictogens IUPAC group 15 elements ChEBI group V elements ChEBI nitrogenoideos ChEBI nitrogenoides ChEBI pnictogene ChEBI pnictogenes ChEBI 0 Bi InChI=1S/Bi JCXGWMGPZLAOME-UHFFFAOYSA-N 208.98038 208.98040 [Bi] CAS:7440-69-9 WebElements:Bi bismuth chebi_ontology 83Bi Bi Bismut Wismut bismuth bismuto CHEBI:33301 bismuth atom CAS:7440-69-9 ChemIDplus bismuth IUPAC 83Bi IUPAC Bi IUPAC Bismut ChEBI Wismut ChEBI bismuth ChEBI bismuto ChEBI A p-block molecular entity containing any pnictogen. pnictogen molecular entity chebi_ontology pnictogen molecular entities CHEBI:33302 pnictogen molecular entity pnictogen molecular entity ChEBI pnictogen molecular entities ChEBI Any p-block element belonging to the group 16 family of the periodic table. PMID:17084588 chalcogen chalcogens chebi_ontology Chalkogen Chalkogene anfigeno anfigenos calcogeno calcogenos chalcogene chalcogenes group 16 elements group VI elements CHEBI:33303 chalcogen PMID:17084588 Europe PMC chalcogen IUPAC chalcogens IUPAC Chalkogen ChEBI Chalkogene ChEBI anfigeno ChEBI anfigenos ChEBI calcogeno ChEBI calcogenos ChEBI chalcogene ChEBI chalcogenes ChEBI group 16 elements ChEBI group VI elements ChEBI Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chebi_ontology chalcogen compounds chalcogen molecular entities CHEBI:33304 chalcogen molecular entity chalcogen molecular entity ChEBI chalcogen compounds ChEBI chalcogen molecular entities ChEBI group 14 elements chebi_ontology carbon group element carbon group elements carbonoides cristallogene cristallogenes group IV elements CHEBI:33306 carbon group element atom group 14 elements IUPAC carbon group element ChEBI carbon group elements ChEBI carbonoides ChEBI cristallogene ChEBI cristallogenes ChEBI group IV elements ChEBI An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. 0 CO2R2 44.010 43.98983 [*]C(=O)O[*] CHEBI:13204 CHEBI:23028 CHEBI:3408 KEGG:C02391 Wikipedia:Ester Carboxylic ester carboxylic esters chebi_ontology a carboxylic ester carboxylic acid esters CHEBI:33308 carboxylic ester Carboxylic ester KEGG_COMPOUND carboxylic esters IUPAC a carboxylic ester UniProt carboxylic acid esters ChEBI noble gas noble gases chebi_ontology Edelgas Edelgase gas noble gases nobles gaz noble gaz nobles group 18 elements group VIII elements inert gases noble gas rare gases CHEBI:33309 noble gas atom noble gas IUPAC noble gases IUPAC Edelgas ChEBI Edelgase ChEBI gas noble ChEBI gases nobles ChEBI gaz noble ChEBI gaz nobles ChEBI group 18 elements IUPAC group VIII elements ChEBI inert gases ChEBI noble gas ChEBI rare gases ChEBI 0 Ne InChI=1S/Ne GKAOGPIIYCISHV-UHFFFAOYSA-N 20.17970 19.99244 [Ne] CAS:7440-01-9 WebElements:Ne neon chebi_ontology 10Ne Ne Neon neon CHEBI:33310 neon atom CAS:7440-01-9 ChemIDplus neon IUPAC 10Ne IUPAC Ne ChEBI Neon ChEBI neon ChEBI A radioactive metallic element discovered in 1898 by Marie Sklodowska Curie and named after her home country, Poland (Latin Polonia). 0 Po InChI=1S/Po HZEBHPIOVYHPMT-UHFFFAOYSA-N 209.00000 209.00000 [Po] CAS:7440-08-6 Gmelin:40435 WebElements:Po polonium chebi_ontology 84Po Po polonio polonium CHEBI:33313 polonium atom CAS:7440-08-6 ChemIDplus CAS:7440-08-6 NIST Chemistry WebBook Gmelin:40435 Gmelin polonium IUPAC 84Po IUPAC Po IUPAC polonio ChEBI polonium ChEBI 0 Rn InChI=1S/Rn SYUHGPGVQRZVTB-UHFFFAOYSA-N 222.00000 222.00000 [Rn] CAS:10043-92-2 Gmelin:16242 WebElements:Rn radon chebi_ontology 86Rn Rn niton radium emanation radon CHEBI:33314 radon atom CAS:10043-92-2 ChemIDplus CAS:10043-92-2 NIST Chemistry WebBook Gmelin:16242 Gmelin radon IUPAC 86Rn IUPAC Rn IUPAC niton ChemIDplus radium emanation ChemIDplus radon ChEBI 0 He 4.003 4.00260 chebi_ontology elemental helium CHEBI:33315 monoatomic helium elemental helium ChEBI +2 He InChI=1S/He/q+2 LBDSXVIYZYSRII-UHFFFAOYSA-N 4.00260 4.00151 [He++] helium(2+) chebi_ontology He(2+) CHEBI:33316 helium(2+) helium(2+) IUPAC He(2+) IUPAC group 13 elements chebi_ontology Element der Borgruppe boron group element boron group elements group III elements CHEBI:33317 boron group element atom group 13 elements IUPAC Element der Borgruppe ChEBI boron group element ChEBI boron group elements ChEBI group III elements ChEBI An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group elements chebi_ontology Hauptgruppenelement Hauptgruppenelemente main group element CHEBI:33318 main group element atom main group elements IUPAC Hauptgruppenelement ChEBI Hauptgruppenelemente ChEBI main group element ChEBI lanthanoids chebi_ontology Lanthanoid Lanthanoide Lanthanoidengruppe Lanthanoidenreiche Ln lanthanide lanthanides lanthanoid CHEBI:33319 lanthanoid atom lanthanoids IUPAC Lanthanoid ChEBI Lanthanoide ChEBI Lanthanoidengruppe ChEBI Lanthanoidenreiche ChEBI Ln ChEBI lanthanide ChEBI lanthanides ChEBI lanthanoid ChEBI actinoids chebi_ontology Actinoid Actinoide Actinoidenelemente Actinoidengruppe Aktinoide Aktinoidenelemente An actinide actinides actinoid CHEBI:33320 actinoid atom actinoids IUPAC Actinoid ChEBI Actinoide ChEBI Actinoidenelemente ChEBI Actinoidengruppe ChEBI Aktinoide ChEBI Aktinoidenelemente ChEBI An ChEBI actinide ChEBI actinides ChEBI actinoid ChEBI rare earth metals chebi_ontology rare earth metal CHEBI:33321 rare earth metal atom rare earth metals IUPAC rare earth metal ChEBI 0 Rb InChI=1S/Rb IGLNJRXAVVLDKE-UHFFFAOYSA-N 85.46780 84.91179 [Rb] CAS:7440-17-7 DrugBank:DB06749 Gmelin:16244 WebElements:Rb rubidium chebi_ontology 37Rb Rb rubidio rubidium CHEBI:33322 rubidium atom CAS:7440-17-7 ChemIDplus CAS:7440-17-7 NIST Chemistry WebBook Gmelin:16244 Gmelin rubidium IUPAC 37Rb IUPAC Rb IUPAC rubidio ChEBI rubidium ChEBI 0 Fr InChI=1S/Fr KLMCZVJOEAUDNE-UHFFFAOYSA-N 223.00000 223.00000 [Fr] CAS:7440-73-5 Gmelin:40458 WebElements:Fr francium chebi_ontology 87Fr Fr Franzium francio francium CHEBI:33323 francium atom CAS:7440-73-5 ChemIDplus CAS:7440-73-5 NIST Chemistry WebBook Gmelin:40458 Gmelin francium IUPAC 87Fr IUPAC Fr IUPAC Franzium ChEBI francio ChEBI francium ChEBI 0 Sr InChI=1S/Sr CIOAGBVUUVVLOB-UHFFFAOYSA-N 87.62000 87.90561 [Sr] CAS:7440-24-6 WebElements:Sr strontium chebi_ontology 38Sr Sr estroncio strontium CHEBI:33324 strontium atom CAS:7440-24-6 ChemIDplus CAS:7440-24-6 NIST Chemistry WebBook strontium IUPAC 38Sr IUPAC Sr IUPAC estroncio ChEBI strontium ChEBI 0 Ra InChI=1S/Ra HCWPIIXVSYCSAN-UHFFFAOYSA-N 226.00000 226.00000 [Ra] CAS:7440-14-4 WebElements:Ra radium chebi_ontology 88Ra Ra radio radium CHEBI:33325 radium atom CAS:7440-14-4 ChemIDplus CAS:7440-14-4 NIST Chemistry WebBook radium IUPAC 88Ra IUPAC Ra IUPAC radio ChEBI radium ChEBI 0 Sc InChI=1S/Sc SIXSYDAISGFNSX-UHFFFAOYSA-N 44.95591 44.95591 [Sc] CAS:7440-20-2 WebElements:Sc scandium chebi_ontology 21Sc Sc Skandium escandio scandium CHEBI:33330 scandium atom CAS:7440-20-2 ChemIDplus CAS:7440-20-2 NIST Chemistry WebBook scandium IUPAC 21Sc IUPAC Sc IUPAC Skandium ChEBI escandio ChEBI scandium ChEBI 0 Y InChI=1S/Y VWQVUPCCIRVNHF-UHFFFAOYSA-N 88.90585 88.90584 [Y] CAS:7440-65-5 Gmelin:16319 WebElements:Y yttrium chebi_ontology 39Y Y ytrio yttrium CHEBI:33331 yttrium atom CAS:7440-65-5 ChemIDplus CAS:7440-65-5 NIST Chemistry WebBook Gmelin:16319 Gmelin yttrium IUPAC 39Y IUPAC Y ChEBI ytrio ChEBI yttrium ChEBI group 3 elements chebi_ontology scandium group element scandium group elements CHEBI:33335 scandium group element atom group 3 elements IUPAC scandium group element ChEBI scandium group elements ChEBI 0 La InChI=1S/La FZLIPJUXYLNCLC-UHFFFAOYSA-N 138.90550 138.90636 [La] CAS:7439-91-0 Gmelin:16203 WebElements:La lanthanum chebi_ontology 57La La Lanthan lantano lanthane lanthanum CHEBI:33336 lanthanum atom CAS:7439-91-0 ChemIDplus CAS:7439-91-0 NIST Chemistry WebBook Gmelin:16203 Gmelin lanthanum IUPAC 57La IUPAC La ChEBI Lanthan ChEBI lantano ChEBI lanthane ChEBI lanthanum ChEBI 0 Ac InChI=1S/Ac QQINRWTZWGJFDB-UHFFFAOYSA-N 227.00000 227.00000 [Ac] CAS:7440-34-8 WebElements:Ac actinium chebi_ontology 89Ac Ac Aktinium actinio actinium CHEBI:33337 actinium atom CAS:7440-34-8 ChemIDplus CAS:7440-34-8 NIST Chemistry WebBook actinium IUPAC 89Ac IUPAC Ac IUPAC Aktinium ChEBI actinio ChEBI actinium ChEBI group 12 elements chebi_ontology zinc group element zinc group elements CHEBI:33340 zinc group element atom group 12 elements IUPAC zinc group element ChEBI zinc group elements ChEBI 0 Ti InChI=1S/Ti RTAQQCXQSZGOHL-UHFFFAOYSA-N 47.86700 47.94794 [Ti] CAS:7440-32-6 WebElements:Ti titanium chebi_ontology 22Ti Ti Titan titane titanio titanium CHEBI:33341 titanium atom CAS:7440-32-6 ChemIDplus CAS:7440-32-6 NIST Chemistry WebBook titanium IUPAC 22Ti IUPAC Ti IUPAC Titan ChEBI titane ChEBI titanio ChEBI titanium ChEBI 0 Zr InChI=1S/Zr QCWXUUIWCKQGHC-UHFFFAOYSA-N 91.22400 89.90470 [Zr] CAS:7440-67-7 WebElements:Zr zirconium chebi_ontology 40Zr Zirkonium Zr circonio zirconio zirconium CHEBI:33342 zirconium atom CAS:7440-67-7 ChemIDplus CAS:7440-67-7 NIST Chemistry WebBook zirconium IUPAC 40Zr IUPAC Zirkonium ChEBI Zr IUPAC circonio ChEBI zirconio ChEBI zirconium ChEBI 0 Hf InChI=1S/Hf VBJZVLUMGGDVMO-UHFFFAOYSA-N 178.49000 179.94656 [Hf] CAS:7440-58-6 WebElements:Hf hafnium chebi_ontology 72Hf Hf hafnio hafnium CHEBI:33343 hafnium atom CAS:7440-58-6 ChemIDplus CAS:7440-58-6 NIST Chemistry WebBook hafnium IUPAC 72Hf IUPAC Hf IUPAC hafnio ChEBI hafnium ChEBI 0 Nb InChI=1S/Nb GUCVJGMIXFAOAE-UHFFFAOYSA-N 92.90638 92.90637 [Nb] CAS:7440-03-1 WebElements:Nb niobium chebi_ontology 41Nb Nb Niob columbio columbium niobio niobium CHEBI:33344 niobium atom CAS:7440-03-1 ChemIDplus CAS:7440-03-1 NIST Chemistry WebBook niobium IUPAC 41Nb IUPAC Nb IUPAC Niob ChEBI columbio ChEBI columbium NIST_Chemistry_WebBook niobio ChEBI niobium ChEBI group 4 elements chebi_ontology titanium group element titanium group elements CHEBI:33345 titanium group element atom group 4 elements IUPAC titanium group element ChEBI titanium group elements ChEBI 0 Rf InChI=1S/Rf YGPLJIIQQIDVFJ-UHFFFAOYSA-N 261.00000 267.00000 [Rf] WebElements:Rf rutherfordium chebi_ontology 104Rf Ku Rf Unq kurchatovium rutherfordio rutherfordium unnilquadium CHEBI:33346 rutherfordium atom rutherfordium IUPAC 104Rf IUPAC Ku ChEBI Rf IUPAC Unq IUPAC kurchatovium ChEBI rutherfordio ChEBI rutherfordium ChEBI unnilquadium IUPAC group 5 elements chebi_ontology vanadium group element vanadium group elements CHEBI:33347 vanadium group element atom group 5 elements IUPAC vanadium group element ChEBI vanadium group elements ChEBI 0 Ta InChI=1S/Ta GUVRBAGPIYLISA-UHFFFAOYSA-N 180.94790 180.94800 [Ta] CAS:7440-25-7 WebElements:Ta tantalum chebi_ontology 73Ta Ta Tantal tantale tantalo tantalum CHEBI:33348 tantalum atom CAS:7440-25-7 ChemIDplus CAS:7440-25-7 NIST Chemistry WebBook tantalum IUPAC 73Ta IUPAC Ta IUPAC Tantal ChEBI tantale ChEBI tantalo ChEBI tantalum ChEBI 0 Db 262.00000 270.00000 [Db] WebElements:Db dubnium chebi_ontology 105Db Db Ha Ns Unp dubnio dubnium hahnium nielsbohrium unnilpentium CHEBI:33349 dubnium atom dubnium IUPAC 105Db IUPAC Db IUPAC Ha ChEBI Ns ChEBI Unp IUPAC dubnio ChEBI dubnium ChEBI hahnium ChEBI nielsbohrium ChEBI unnilpentium IUPAC group 6 elements chebi_ontology chromium group element chromium group elements CHEBI:33350 chromium group element atom group 6 elements IUPAC chromium group element ChEBI chromium group elements ChEBI 0 Sg 263.00000 271.00000 [Sg] WebElements:Sg seaborgium chebi_ontology 106Sg Sg Unh seaborgio seaborgium unnilhexium CHEBI:33351 seaborgium atom seaborgium IUPAC 106Sg IUPAC Sg IUPAC Unh ChEBI seaborgio ChEBI seaborgium ChEBI unnilhexium IUPAC group 7 elements chebi_ontology manganese group element manganese group elements CHEBI:33352 manganese group element atom group 7 elements IUPAC manganese group element ChEBI manganese group elements ChEBI 0 Tc InChI=1S/Tc GKLVYJBZJHMRIY-UHFFFAOYSA-N 98.00000 97.00000 [Tc] CAS:7440-26-8 Gmelin:16310 WebElements:Tc technetium chebi_ontology 43Tc Tc Technetium technetium tecnecio CHEBI:33353 technetium atom CAS:7440-26-8 ChemIDplus CAS:7440-26-8 NIST Chemistry WebBook Gmelin:16310 Gmelin technetium IUPAC 43Tc IUPAC Tc IUPAC Technetium ChEBI technetium ChEBI tecnecio ChEBI 0 Bh 264.00000 270.00000 [Bh] WebElements:Bh bohrium chebi_ontology 107Bh Bh Ns Uns bohrio bohrium nielsbohrium unnilseptium CHEBI:33355 bohrium atom bohrium IUPAC 107Bh IUPAC Bh IUPAC Ns ChEBI Uns IUPAC bohrio ChEBI bohrium ChEBI nielsbohrium ChEBI unnilseptium IUPAC group 8 elements chebi_ontology iron group element iron group elements CHEBI:33356 iron group element atom group 8 elements IUPAC iron group element ChEBI iron group elements ChEBI 0 Hs 265.00000 277.00000 [Hs] WebElements:Hs hassium chebi_ontology 108Hs Ha Hs Uno hahnium hassio hassium unniloctium CHEBI:33357 hassium atom hassium IUPAC 108Hs IUPAC Ha ChEBI Hs IUPAC Uno IUPAC hahnium ChEBI hassio ChEBI hassium ChEBI unniloctium IUPAC group 9 elements chebi_ontology cobalt group element cobalt group elements CHEBI:33358 cobalt group element atom group 9 elements IUPAC cobalt group element ChEBI cobalt group elements ChEBI A cobalt group element atom of atomic number 45. 0 Rh InChI=1S/Rh MHOVAHRLVXNVSD-UHFFFAOYSA-N 102.90550 102.90550 [Rh] CAS:7440-16-6 PMID:2936374 WebElements:Rh Wikipedia:Rhodium rhodium chebi_ontology 45Rh Rh rhodium rodio CHEBI:33359 rhodium atom CAS:7440-16-6 ChemIDplus CAS:7440-16-6 NIST Chemistry WebBook PMID:2936374 Europe PMC rhodium IUPAC 45Rh IUPAC Rh ChEBI rhodium ChEBI rodio ChEBI 0 Mt 0.00000 0.00000 [Mt] WebElements:Mt meitnerium chebi_ontology 109Mt Mt Une meitnerio meitnerium unnilennium CHEBI:33361 meitnerium atom meitnerium IUPAC 109Mt IUPAC Mt IUPAC Une IUPAC meitnerio ChEBI meitnerium ChEBI unnilennium IUPAC group 10 elements chebi_ontology nickel group element nickel group elements CHEBI:33362 nickel group element atom group 10 elements IUPAC nickel group element ChEBI nickel group elements ChEBI Chemical element (nickel group element atom) with atomic number 46. 0 Pd InChI=1S/Pd KDLHZDBZIXYQEI-UHFFFAOYSA-N 106.42000 105.90348 [Pd] CAS:7440-05-3 PMID:25097477 Reaxys:4937491 WebElements:Pd Wikipedia:Palladium palladium chebi_ontology 46Pd Pd paladio CHEBI:33363 palladium CAS:7440-05-3 ChemIDplus CAS:7440-05-3 NIST Chemistry WebBook PMID:25097477 Europe PMC Reaxys:4937491 Reaxys palladium IUPAC 46Pd IUPAC Pd IUPAC paladio ChEBI 0 Pt InChI=1S/Pt BASFCYQUMIYNBI-UHFFFAOYSA-N 195.078 194.96479 [Pt] CAS:7440-06-4 WebElements:Pt platinum chebi_ontology 78Pt Platin Pt platine platino CHEBI:33364 platinum CAS:7440-06-4 ChemIDplus CAS:7440-06-4 NIST Chemistry WebBook platinum IUPAC 78Pt IUPAC Platin ChEBI Pt IUPAC platine ChEBI platino ChEBI chebi_ontology PGM Platinmetalle Platinoide platinoid platinum group metal platinum group metals platinum metals CHEBI:33365 platinum group metal atom PGM ChEBI Platinmetalle ChEBI Platinoide ChEBI platinoid ChEBI platinum group metal ChEBI platinum group metals ChEBI platinum metals ChEBI group 11 elements chebi_ontology coinage metals copper group element copper group elements CHEBI:33366 copper group element atom group 11 elements IUPAC coinage metals ChEBI copper group element ChEBI copper group elements ChEBI 0 Ds InChI=1S/Ds NCBMSFCPDGXTHD-UHFFFAOYSA-N 0.00000 0.00000 [Ds] WebElements:Ds darmstadtium chebi_ontology 110Ds Ds Uun darmstadtio ununnilium CHEBI:33367 darmstadtium darmstadtium IUPAC 110Ds IUPAC Ds IUPAC Uun IUPAC darmstadtio ChEBI ununnilium IUPAC A copper group element atom with atomic number 111. The the ninth member of the 6d series of transition metals, it is an extremely radioactive, synthetic element. Average mass is around 281. 0 Rg InChI=1S/Rg LJROPTGWFUZRDB-UHFFFAOYSA-N 0.000 0.00000 [Rg] WebElements:Rg Wikipedia:Roentgenium roentgenium chebi_ontology 111Rg Rg Roentgenium Uuu roentgenio roentgenium unununium CHEBI:33368 roentgenium atom roentgenium IUPAC 111Rg IUPAC Rg IUPAC Roentgenium ChEBI Uuu ChEBI roentgenio ChEBI roentgenium ChEBI unununium ChEBI 0 Ce InChI=1S/Ce GWXLDORMOJMVQZ-UHFFFAOYSA-N 140.11600 139.90544 [Ce] CAS:7440-45-1 Gmelin:16275 WebElements:Ce cerium chebi_ontology 58Ce Ce Cer Zer cerio CHEBI:33369 cerium CAS:7440-45-1 ChemIDplus CAS:7440-45-1 NIST Chemistry WebBook Gmelin:16275 Gmelin cerium ChEBI cerium IUPAC 58Ce IUPAC Ce IUPAC Cer ChEBI Zer ChEBI cerio ChEBI 0 [99Tc] InChI=1S/Tc/i1+1 GKLVYJBZJHMRIY-OUBTZVSYSA-N 98.906 98.90625 [99Tc] CAS:14133-76-7 Gmelin:41657 technetium-99 chebi_ontology (99)43Tc (99)Tc technetium, isotope of mass 99 CHEBI:33371 technetium-99 CAS:14133-76-7 ChemIDplus Gmelin:41657 Gmelin technetium-99 IUPAC (99)43Tc IUPAC (99)Tc IUPAC technetium, isotope of mass 99 ChemIDplus 0 Nd InChI=1S/Nd QEFYFXOXNSNQGX-UHFFFAOYSA-N 144.24000 141.90773 [Nd] CAS:7440-00-8 Gmelin:16212 WebElements:Nd neodymium chebi_ontology 60Nd Nd Neodym neodimio neodyme neodymium CHEBI:33372 neodymium atom CAS:7440-00-8 ChemIDplus CAS:7440-00-8 NIST Chemistry WebBook Gmelin:16212 Gmelin neodymium IUPAC 60Nd IUPAC Nd IUPAC Neodym ChEBI neodimio ChEBI neodyme ChEBI neodymium ChEBI 0 Pm InChI=1S/Pm VQMWBBYLQSCNPO-UHFFFAOYSA-N 145.00000 145.00000 [Pm] CAS:7440-12-2 Gmelin:16237 WebElements:Pm promethium chebi_ontology 61Pm Pm Promethium promethium prometio CHEBI:33373 promethium atom CAS:7440-12-2 ChemIDplus CAS:7440-12-2 NIST Chemistry WebBook Gmelin:16237 Gmelin promethium IUPAC 61Pm IUPAC Pm IUPAC Promethium ChEBI promethium ChEBI prometio ChEBI 0 Sm InChI=1S/Sm KZUNJOHGWZRPMI-UHFFFAOYSA-N 150.36000 151.91974 [Sm] CAS:7440-19-9 Gmelin:16301 WebElements:Sm samarium chebi_ontology 62Sm Sm samario samarium CHEBI:33374 samarium atom CAS:7440-19-9 ChemIDplus CAS:7440-19-9 NIST Chemistry WebBook Gmelin:16301 Gmelin samarium IUPAC 62Sm IUPAC Sm IUPAC samario ChEBI samarium ChEBI 0 Gd InChI=1S/Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N 157.25000 157.92411 [Gd] CAS:7440-54-2 Gmelin:16286 WebElements:Gd gadolinium chebi_ontology 64Gd Gd gadolinio gadolinium CHEBI:33375 gadolinium atom CAS:7440-54-2 ChemIDplus CAS:7440-54-2 NIST Chemistry WebBook Gmelin:16286 Gmelin gadolinium IUPAC 64Gd IUPAC Gd IUPAC gadolinio ChEBI gadolinium ChEBI 0 Tb InChI=1S/Tb GZCRRIHWUXGPOV-UHFFFAOYSA-N 158.92534 158.92535 [Tb] CAS:7440-27-9 Gmelin:16311 WebElements:Tb terbium chebi_ontology 65Tb Tb terbio terbium CHEBI:33376 terbium atom CAS:7440-27-9 ChemIDplus CAS:7440-27-9 NIST Chemistry WebBook Gmelin:16311 Gmelin terbium IUPAC 65Tb IUPAC Tb IUPAC terbio ChEBI terbium ChEBI 0 Dy InChI=1S/Dy KBQHZAAAGSGFKK-UHFFFAOYSA-N 162.50000 163.92918 [Dy] CAS:7429-91-6 Gmelin:16278 WebElements:Dy dysprosium chebi_ontology 66Dy Dy disprosio dysprosium CHEBI:33377 dysprosium atom CAS:7429-91-6 ChemIDplus CAS:7429-91-6 NIST Chemistry WebBook Gmelin:16278 Gmelin dysprosium IUPAC 66Dy IUPAC Dy IUPAC disprosio ChEBI dysprosium ChEBI 0 Er InChI=1S/Er UYAHIZSMUZPPFV-UHFFFAOYSA-N 167.26000 165.93030 [Er] CAS:7440-52-0 Gmelin:16280 WebElements:Er erbium chebi_ontology 68Er Er erbio CHEBI:33379 erbium CAS:7440-52-0 ChemIDplus CAS:7440-52-0 NIST Chemistry WebBook Gmelin:16280 Gmelin erbium IUPAC 68Er IUPAC Er IUPAC erbio ChEBI 0 Tm InChI=1S/Tm FRNOGLGSGLTDKL-UHFFFAOYSA-N 168.93421 168.93422 [Tm] CAS:7440-30-4 Gmelin:16307 WebElements:Tm thulium chebi_ontology 69Tm Tm thulium tulio CHEBI:33380 thulium atom CAS:7440-30-4 ChemIDplus CAS:7440-30-4 NIST Chemistry WebBook Gmelin:16307 Gmelin thulium IUPAC 69Tm IUPAC Tm ChEBI thulium ChEBI tulio ChEBI 0 Yb InChI=1S/Yb NAWDYIZEMPQZHO-UHFFFAOYSA-N 173.04000 173.93887 [Yb] CAS:7440-64-4 Gmelin:16320 WebElements:Yb ytterbium chebi_ontology 70Yb Yb yterbio CHEBI:33381 ytterbium CAS:7440-64-4 ChemIDplus CAS:7440-64-4 NIST Chemistry WebBook Gmelin:16320 Gmelin ytterbium IUPAC 70Yb IUPAC Yb IUPAC yterbio ChEBI 0 Lu InChI=1S/Lu OHSVLFRHMCKCQY-UHFFFAOYSA-N 174.96700 174.94078 [Lu] CAS:7439-94-3 Gmelin:16202 WebElements:Lu lutetium chebi_ontology 71Lu Cassiopeium Lu Lutetium cassiopium lutecio lutecium lutetium CHEBI:33382 lutetium atom CAS:7439-94-3 ChemIDplus CAS:7439-94-3 NIST Chemistry WebBook Gmelin:16202 Gmelin lutetium IUPAC 71Lu IUPAC Cassiopeium ChEBI Lu IUPAC Lutetium ChEBI cassiopium ChEBI lutecio ChEBI lutecium ChEBI lutetium ChEBI 0 Th InChI=1S/Th ZSLUVFAKFWKJRC-UHFFFAOYSA-N 232.03810 232.03806 [Th] CAS:7440-29-1 KEGG:C19157 WebElements:Th thorium chebi_ontology 90Th Th torio CHEBI:33385 thorium CAS:7440-29-1 ChemIDplus CAS:7440-29-1 KEGG COMPOUND CAS:7440-29-1 NIST Chemistry WebBook thorium IUPAC 90Th IUPAC Th IUPAC torio ChEBI 0 Pa InChI=1S/Pa XLROVYAPLOFLNU-UHFFFAOYSA-N 231.03588 231.03589 [Pa] CAS:7440-13-3 WebElements:Pa protactinium chebi_ontology 91Pa Pa brevium protactinio protactinium protoactinium CHEBI:33386 protactinium atom CAS:7440-13-3 ChemIDplus CAS:7440-13-3 NIST Chemistry WebBook protactinium IUPAC 91Pa IUPAC Pa IUPAC brevium ChEBI protactinio ChEBI protactinium ChEBI protoactinium NIST_Chemistry_WebBook 0 Np InChI=1S/Np LFNLGNPSGWYGGD-UHFFFAOYSA-N 237.00000 237.00000 [Np] CAS:7439-99-8 WebElements:Np neptunium chebi_ontology 93Np Np neptunio neptunium CHEBI:33387 neptunium atom CAS:7439-99-8 ChemIDplus CAS:7439-99-8 NIST Chemistry WebBook neptunium IUPAC 93Np IUPAC Np IUPAC neptunio ChEBI neptunium ChEBI 0 Pu InChI=1S/Pu OYEHPCDNVJXUIW-UHFFFAOYSA-N 244.00000 244.00000 [Pu] CAS:7440-07-5 KEGG:C19159 WebElements:Pu plutonium chebi_ontology 94Pu Pu plutonio plutonium CHEBI:33388 plutonium atom CAS:7440-07-5 ChemIDplus CAS:7440-07-5 KEGG COMPOUND CAS:7440-07-5 NIST Chemistry WebBook plutonium IUPAC 94Pu IUPAC Pu ChEBI plutonio ChEBI plutonium ChEBI 0 Am InChI=1S/Am LXQXZNRPTYVCNG-UHFFFAOYSA-N 243.00000 243.00000 [Am] CAS:7440-35-9 WebElements:Am americium chebi_ontology 95Am Am Americium Amerizium americio americium CHEBI:33389 americium atom CAS:7440-35-9 ChemIDplus CAS:7440-35-9 NIST Chemistry WebBook americium IUPAC 95Am IUPAC Am IUPAC Americium ChEBI Amerizium ChEBI americio ChEBI americium ChEBI 0 Cm InChI=1S/Cm NIWWFAAXEMMFMS-UHFFFAOYSA-N 247.00000 247.00000 [Cm] CAS:7440-51-9 WebElements:Cm curium chebi_ontology 96Cm Cm curio curium CHEBI:33390 curium atom CAS:7440-51-9 ChemIDplus CAS:7440-51-9 NIST Chemistry WebBook curium IUPAC 96Cm IUPAC Cm IUPAC curio ChEBI curium ChEBI 0 Bk InChI=1S/Bk PWVKJRSRVJTHTR-UHFFFAOYSA-N 247.00000 247.00000 [Bk] CAS:7440-40-6 WebElements:Bk berkelium chebi_ontology 97Bk Berkelium Bk berkelio berkelium CHEBI:33391 berkelium atom CAS:7440-40-6 ChemIDplus CAS:7440-40-6 NIST Chemistry WebBook berkelium IUPAC 97Bk IUPAC Berkelium ChEBI Bk ChEBI berkelio ChEBI berkelium ChEBI 0 Cf InChI=1S/Cf HGLDOAKPQXAFKI-UHFFFAOYSA-N 251.00000 251.00000 [Cf] CAS:7440-71-3 WebElements:Cf californium chebi_ontology 98Cf Cf Kalifornium californio californium CHEBI:33392 californium atom CAS:7440-71-3 ChemIDplus CAS:7440-71-3 NIST Chemistry WebBook californium IUPAC 98Cf ChEBI Cf IUPAC Kalifornium ChEBI californio ChEBI californium ChEBI 0 Es InChI=1S/Es CKBRQZNRCSJHFT-UHFFFAOYSA-N 252.00000 252.00000 [Es] CAS:7429-92-7 WebElements:Es einsteinium chebi_ontology 99Es Es einsteinio einsteinium CHEBI:33393 einsteinium atom CAS:7429-92-7 ChemIDplus CAS:7429-92-7 NIST Chemistry WebBook einsteinium IUPAC 99Es IUPAC Es IUPAC einsteinio ChEBI einsteinium ChEBI 0 Fm InChI=1S/Fm MIORUQGGZCBUGO-UHFFFAOYSA-N 257.00000 257.00000 [Fm] CAS:7440-72-4 WebElements:Fm fermium chebi_ontology 100Fm Fm fermio CHEBI:33394 fermium CAS:7440-72-4 ChemIDplus CAS:7440-72-4 NIST Chemistry WebBook fermium IUPAC 100Fm IUPAC Fm IUPAC fermio ChEBI 0 Md InChI=1S/Md MQVSLOYRCXQRPM-UHFFFAOYSA-N 258.00000 258.00000 [Md] CAS:7440-11-1 WebElements:Md mendelevium chebi_ontology 101Md Md Mendelevium Unu mendelevio mendelevium unnilunium CHEBI:33395 mendelevium atom CAS:7440-11-1 ChemIDplus CAS:7440-11-1 NIST Chemistry WebBook mendelevium IUPAC 101Md IUPAC Md IUPAC Mendelevium ChEBI Unu IUPAC mendelevio ChEBI mendelevium ChEBI unnilunium IUPAC 0 No InChI=1S/No ORQBXQOJMQIAOY-UHFFFAOYSA-N 259.00000 259.00000 [No] CAS:10028-14-5 WebElements:No Nobelium nobelium chebi_ontology 102No No Unb nobelio unnilbium CHEBI:33396 nobelium CAS:10028-14-5 ChemIDplus CAS:10028-14-5 NIST Chemistry WebBook Nobelium ChEBI nobelium ChEBI nobelium IUPAC 102No IUPAC No IUPAC Unb IUPAC nobelio ChEBI unnilbium IUPAC 0 Lr InChI=1S/Lr CNQCVBJFEGMYDW-UHFFFAOYSA-N 262.00000 262.00000 [Lr] CAS:22537-19-5 WebElements:Lr lawrencium chebi_ontology 103Lr Lr Unt laurencio lawrencio lawrencium unniltrium CHEBI:33397 lawrencium atom CAS:22537-19-5 ChemIDplus lawrencium IUPAC 103Lr IUPAC Lr IUPAC Unt IUPAC laurencio ChEBI lawrencio ChEBI lawrencium ChEBI unniltrium IUPAC chebi_ontology oxoacids of sulfur sulfur oxoacids CHEBI:33402 sulfur oxoacid oxoacids of sulfur ChEBI sulfur oxoacids ChEBI chebi_ontology pnictogen oxoacids CHEBI:33408 pnictogen oxoacid pnictogen oxoacids ChEBI sulfur oxoacid derivative chebi_ontology sulfur oxoacid derivatives CHEBI:33424 sulfur oxoacid derivative sulfur oxoacid derivative ChEBI sulfur oxoacid derivatives ChEBI A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons. phosphorus oxoacid chebi_ontology Oxosaeure des Phosphors oxoacids of phosphorus phosphorus oxoacids CHEBI:33457 phosphorus oxoacid phosphorus oxoacid ChEBI Oxosaeure des Phosphors ChEBI oxoacids of phosphorus ChEBI phosphorus oxoacids ChEBI pnictogen oxoanion chebi_ontology pnictogen oxoanions CHEBI:33459 pnictogen oxoanion pnictogen oxoanion ChEBI pnictogen oxoanions ChEBI phosphorus oxoanion chebi_ontology oxoanions of phosphorus phosphorus oxoanions CHEBI:33461 phosphorus oxoanion phosphorus oxoanion ChEBI oxoanions of phosphorus ChEBI phosphorus oxoanions ChEBI elemental pnictogen sulfur oxoanion chebi_ontology oxoanions of sulfur sulfur oxoanions CHEBI:33482 sulfur oxoanion sulfur oxoanion ChEBI oxoanions of sulfur ChEBI sulfur oxoanions ChEBI chalcogen oxoacid chebi_ontology chalcogen oxoacids CHEBI:33484 chalcogen oxoacid chalcogen oxoacid ChEBI chalcogen oxoacids ChEBI chalcogen oxoanion chebi_ontology chalcogen oxoanions CHEBI:33485 chalcogen oxoanion chalcogen oxoanion ChEBI chalcogen oxoanions ChEBI 0 [220Rn] InChI=1S/Rn/i1-2 SYUHGPGVQRZVTB-YPZZEJLDSA-N 220.011 220.01138 [220Rn] CAS:22481-48-7 Gmelin:297037 radon-220 chebi_ontology (220)86Rn (220)Rn Tn radon, isotope of mass 220 radon-220 thoron CHEBI:33491 radon-220 atom CAS:22481-48-7 ChemIDplus Gmelin:297037 Gmelin radon-220 IUPAC (220)86Rn IUPAC (220)Rn IUPAC Tn ChEBI radon, isotope of mass 220 ChemIDplus radon-220 ChEBI thoron ChemIDplus 0 [222Rn] InChI=1S/Rn/i1+0 SYUHGPGVQRZVTB-IGMARMGPSA-N 222.018 222.01757 [222Rn] CAS:14859-67-7 radon-222 chebi_ontology (222)86Rn (222)Rn radon, isotope of mass 222 radon-222 CHEBI:33492 radon-222 atom CAS:14859-67-7 ChemIDplus radon-222 IUPAC (222)86Rn IUPAC (222)Rn IUPAC radon, isotope of mass 222 ChemIDplus radon-222 ChEBI 0 [219Rn] InChI=1S/Rn/i1-3 SYUHGPGVQRZVTB-OIOBTWANSA-N 219.009 219.00947 [219Rn] CAS:14835-02-0 Gmelin:297039 radon-219 chebi_ontology (219)86Rn (219)Rn An actinon radon, isotope of mass 219 radon-219 CHEBI:33493 radon-219 atom CAS:14835-02-0 ChemIDplus Gmelin:297039 Gmelin radon-219 IUPAC (219)86Rn IUPAC (219)Rn IUPAC An ChEBI actinon ChEBI radon, isotope of mass 219 ChemIDplus radon-219 ChEBI A molecular entity containing one or more atoms of a transition element. transition element molecular entities transition metal molecular entity transition element molecular entity actinoid molecular entity uranium molecular entity chebi_ontology alkali metal cations CHEBI:33504 alkali metal cation alkali metal cations ChEBI A zinc group element atom with a symbol Cn and atomic number 112. All its isotopes are intensely radioactive. Prior to its discovery, it had the placeholder name ununbium (in accordance with IUPAC recommendations). Following its discovery (in Darmstadt, 1996) and subsequent confirmation, the name copernicium was adopted in 2010. 0 Cn InChI=1S/Cn NOTIIDSZELDPOP-UHFFFAOYSA-N NaN 0.00000 [Cn] Wikipedia:Copernicium copernicium chebi_ontology 112Cn 112Cp 112Uub Cn Uub ununbium CHEBI:33517 copernicium atom copernicium IUPAC 112Cn ChEBI 112Cp IUPAC 112Uub IUPAC Cn IUPAC Uub IUPAC ununbium ChEBI ununbium IUPAC An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. CHEBI:25217 CHEBI:6788 KEGG:C00050 PMID:21784043 Wikipedia:Metal chebi_ontology elemental metal elemental metals metal element metal elements metals CHEBI:33521 metal atom PMID:21784043 Europe PMC elemental metal ChEBI elemental metals ChEBI metal element ChEBI metal elements ChEBI metals ChEBI An amino-acid anion obtained by deprotonation of any alpha-amino acid. alpha-amino-acid anion chebi_ontology alpha-amino acid anions alpha-amino-acid anions CHEBI:33558 alpha-amino-acid anion alpha-amino-acid anion ChEBI alpha-amino acid anions ChEBI alpha-amino-acid anions ChEBI chebi_ontology s-block element s-block elements CHEBI:33559 s-block element atom s-block element ChEBI s-block elements ChEBI Any main group element atom belonging to the p-block of the periodic table. chebi_ontology p-block element p-block elements CHEBI:33560 p-block element atom p-block element ChEBI p-block elements ChEBI chebi_ontology d-block element d-block elements CHEBI:33561 d-block element atom d-block element ChEBI d-block elements ChEBI chebi_ontology f-block element f-block elements CHEBI:33562 f-block element atom f-block element ChEBI f-block elements ChEBI Any compound containing an o-diphenol component. 0 C6H2O2R4 106.079 106.00548 OC1=C(O)C(*)=C(*)C(*)=C1* CHEBI:134187 CHEBI:13628 CHEBI:18862 KEGG:C15571 chebi_ontology 1,2-benzenediols a catechol benzene-1,2-diols CHEBI:33566 catechols 1,2-benzenediols ChEBI a catechol UniProt benzene-1,2-diols ChEBI 4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution. 0 C8H9NO2R2 151.163 151.06333 CHEBI:23056 CHEBI:3468 KEGG:C02012 Catecholamine catecholamines chebi_ontology catecholamines CHEBI:33567 catecholamine Catecholamine KEGG_COMPOUND catecholamines IUPAC catecholamines ChEBI A catecholamine in which C-1 of the aminoethyl side-chain is hydroxy-substituted. 0 C8H11NO3 InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2 SFLSHLFXELFNJZ-UHFFFAOYSA-N 169.17788 169.07389 NCC(O)c1ccc(O)c(O)c1 Beilstein:2210994 CAS:138-65-8 Gmelin:863925 LINCS:LSM-5181 4-(2-amino-1-hydroxyethyl)benzene-1,2-diol chebi_ontology noradrenalina norepinephrine CHEBI:33569 noradrenaline Beilstein:2210994 Beilstein CAS:138-65-8 ChemIDplus CAS:138-65-8 NIST Chemistry WebBook Gmelin:863925 Gmelin 4-(2-amino-1-hydroxyethyl)benzene-1,2-diol IUPAC noradrenalina ChEBI norepinephrine ChEBI CHEBI:22705 CHEBI:22711 chebi_ontology CHEBI:33570 benzenediols The S-enantiomer of noradrenaline. 0 C8H11NO3 InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/t8-/m1/s1 SFLSHLFXELFNJZ-MRVPVSSYSA-N 169.17788 169.07389 NC[C@@H](O)c1ccc(O)c(O)c1 Beilstein:2937999 LINCS:LSM-37072 Reaxys:2937999 4-[(1S)-2-amino-1-hydroxyethyl]benzene-1,2-diol chebi_ontology CHEBI:33571 (S)-noradrenaline Beilstein:2937999 Beilstein Reaxys:2937999 Reaxys 4-[(1S)-2-amino-1-hydroxyethyl]benzene-1,2-diol IUPAC A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13428 CHEBI:13627 CHEBI:23027 PMID:17147560 PMID:18433345 Wikipedia:Carboxylic_acid carboxylic acid carboxylic acids chebi_ontology Carbonsaeure Carbonsaeuren Karbonsaeure RC(=O)OH acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos CHEBI:33575 carboxylic acid PMID:17147560 Europe PMC PMID:18433345 Europe PMC carboxylic acid IUPAC carboxylic acids IUPAC Carbonsaeure ChEBI Carbonsaeuren ChEBI Karbonsaeure ChEBI RC(=O)OH IUPAC acide carboxylique IUPAC acides carboxyliques IUPAC acido carboxilico IUPAC acidos carboxilicos IUPAC A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. chebi_ontology main group compounds main group molecular entities CHEBI:33579 main group molecular entity main group compounds ChEBI main group molecular entities ChEBI carbon group molecular entity chebi_ontology carbon group molecular entities CHEBI:33582 carbon group molecular entity carbon group molecular entity ChEBI carbon group molecular entities ChEBI A main group molecular entity containing one or more atoms of any noble gas. noble gas molecular entity chebi_ontology noble gas compounds noble gas molecular entities CHEBI:33583 noble gas molecular entity noble gas molecular entity ChEBI noble gas compounds ChEBI noble gas molecular entities ChEBI Any molecule that consists of a series of atoms joined together to form a ring. Wikipedia:Cyclic_compound chebi_ontology cyclic compounds CHEBI:33595 cyclic compound cyclic compounds ChEBI chebi_ontology hydrogen compounds hydrogen molecular entities CHEBI:33608 hydrogen molecular entity hydrogen compounds ChEBI hydrogen molecular entities ChEBI chebi_ontology polycyclic compounds CHEBI:33635 polycyclic compound polycyclic compounds ChEBI A molecule that features two fused rings. chebi_ontology bicyclic compounds CHEBI:33636 bicyclic compound bicyclic compounds ChEBI A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. aromatic compounds aromatic molecular entity chebi_ontology aromatics aromatische Verbindungen CHEBI:33655 aromatic compound aromatic compounds IUPAC aromatic molecular entity IUPAC aromatics ChEBI aromatische Verbindungen ChEBI chebi_ontology organic aromatic compounds CHEBI:33659 organic aromatic compound organic aromatic compounds ChEBI A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compounds chebi_ontology polyheterocyclic compounds CHEBI:33671 heteropolycyclic compound heteropolycyclic compounds IUPAC polyheterocyclic compounds ChEBI A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compounds chebi_ontology CHEBI:33672 heterobicyclic compound heterobicyclic compounds IUPAC An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity chebi_ontology s-block compounds s-block molecular entities CHEBI:33674 s-block molecular entity s-block molecular entity ChEBI s-block compounds ChEBI s-block molecular entities ChEBI A main group molecular entity that contains one or more atoms of a p-block element. chebi_ontology p-block compounds p-block molecular entities p-block molecular entitiy CHEBI:33675 p-block molecular entity p-block compounds ChEBI p-block molecular entities ChEBI p-block molecular entitiy ChEBI A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element. d-block molecular entity d-block compounds d-block molecular entities d-block molecular entity f-block molecular entity helium molecular entity chebi_ontology helium compounds helium molecular entities CHEBI:33679 helium molecular entity helium molecular entity ChEBI helium compounds ChEBI helium molecular entities ChEBI chebi_ontology CHEBI:33680 elemental helium Hydrides are chemical compounds of hydrogen with other chemical elements. chebi_ontology CHEBI:33692 hydrides oxygen hydride chebi_ontology hydrides of oxygen oxygen hydrides CHEBI:33693 oxygen hydride oxygen hydride ChEBI hydrides of oxygen ChEBI oxygen hydrides ChEBI A macromolecule formed by a living organism. biopolymer chebi_ontology Biopolymere biomacromolecules biopolymers CHEBI:33694 biomacromolecule biopolymer IUPAC Biopolymere ChEBI biomacromolecules ChEBI biopolymers ChEBI chebi_ontology genetically encoded biomacromolecules genetically encoded biopolymers information biomacromolecules information biopolymers information macromolecule information macromolecules CHEBI:33695 information biomacromolecule genetically encoded biomacromolecules ChEBI genetically encoded biopolymers ChEBI information biomacromolecules ChEBI information biopolymers ChEBI information macromolecule ChEBI information macromolecules ChEBI A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acids chebi_ontology NA Nukleinsaeure Nukleinsaeuren acide nucleique acides nucleiques acido nucleico acidos nucleicos CHEBI:33696 nucleic acid nucleic acids IUPAC NA ChEBI Nukleinsaeure ChEBI Nukleinsaeuren ChEBI acide nucleique ChEBI acides nucleiques ChEBI acido nucleico ChEBI acidos nucleicos ChEBI High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. CAS:63231-63-0 ribonucleic acid ribonucleic acids chebi_ontology RNA RNS Ribonukleinsaeure pentosenucleic acids ribonucleic acids ribose nucleic acid yeast nucleic acid CHEBI:33697 ribonucleic acid CAS:63231-63-0 ChemIDplus ribonucleic acid IUPAC ribonucleic acids IUPAC RNA IUPAC RNA UniProt RNS ChEBI Ribonukleinsaeure ChEBI pentosenucleic acids ChemIDplus ribonucleic acids ChEBI ribose nucleic acid ChEBI yeast nucleic acid ChEBI chebi_ontology canonical amino-acid residue canonical amino-acid residues common amino acid residues proteinogenic amino-acid residues standard amino acid residues standard amino-acid residues CHEBI:33700 proteinogenic amino-acid residue canonical amino-acid residue ChEBI canonical amino-acid residues ChEBI common amino acid residues ChEBI proteinogenic amino-acid residues ChEBI standard amino acid residues ChEBI standard amino-acid residues ChEBI A cation consisting of more than one atom. chebi_ontology polyatomic cations CHEBI:33702 polyatomic cation polyatomic cations ChEBI An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group. 0 C2H4NO2R 74.05870 74.02420 NC([*])C(O)=O CHEBI:10208 CHEBI:13779 CHEBI:22442 CHEBI:2642 KEGG:C00045 KEGG:C05167 alpha-amino acid chebi_ontology Amino acid Amino acids alpha-amino acids alpha-amino carboxylic acids CHEBI:33704 alpha-amino acid alpha-amino acid IUPAC Amino acid KEGG_COMPOUND Amino acids KEGG_COMPOUND alpha-amino acids ChEBI alpha-amino acids JCBN alpha-amino carboxylic acids IUPAC When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. amino-acid residue chebi_ontology amino acid residue amino-acid residues CHEBI:33708 amino-acid residue amino-acid residue IUPAC amino acid residue ChEBI amino-acid residues JCBN A carboxylic acid containing one or more amino groups. CHEBI:13815 CHEBI:22477 Wikipedia:Amino_acid chebi_ontology Aminocarbonsaeure Aminokarbonsaeure Aminosaeure amino acids CHEBI:33709 amino acid Aminocarbonsaeure ChEBI Aminokarbonsaeure ChEBI Aminosaeure ChEBI amino acids ChEBI An amino-acid residue derived from an alpha-amino acid. 0 C2H2NOR 56.043 56.01364 *-NC([*])C(-*)=O chebi_ontology alpha-amino-acid residues an alpha-amino acid residue CHEBI:33710 alpha-amino-acid residue alpha-amino-acid residues ChEBI an alpha-amino acid residue UniProt carbohydrate acid chebi_ontology carbohydrate acids CHEBI:33720 carbohydrate acid carbohydrate acid ChEBI carbohydrate acids ChEBI carbohydrate acid anion chebi_ontology carbohydrate acid anions CHEBI:33721 carbohydrate acid anion carbohydrate acid anion ChEBI carbohydrate acid anions ChEBI iron group molecular entity iron group molecular entities iron group molecular entity copper group molecular entity nickel group molecular entity platinum molecular entity chebi_ontology canonical nucleoside residues common nucleoside residues nucleoside residue standard nucleoside residues CHEBI:33791 canonical nucleoside residue canonical nucleoside residues ChEBI common nucleoside residues CBN nucleoside residue CBN standard nucleoside residues ChEBI chebi_ontology N Nuc canonical ribonucleoside residues common ribonucleoside residue common ribonucleoside residues standard ribonucleoside residues CHEBI:33792 canonical ribonucleoside residue N CBN Nuc CBN canonical ribonucleoside residues ChEBI common ribonucleoside residue CBN common ribonucleoside residues CBN standard ribonucleoside residues ChEBI chebi_ontology canonical deoxyribonucleoside residues common 2'-deoxyribonucleoside residue common 2'-deoxyribonucleoside residues dN dNuc standard deoxyribonucleoside residues CHEBI:33793 canonical deoxyribonucleoside residue canonical deoxyribonucleoside residues ChEBI common 2'-deoxyribonucleoside residue CBN common 2'-deoxyribonucleoside residues CBN dN CBN dNuc CBN standard deoxyribonucleoside residues ChEBI The stable isotope of oxygen with relative atomic mass 17.999160 and 0.205 atom percent natural abundance. 0 [18O] InChI=1S/O/i1+2 QVGXLLKOCUKJST-NJFSPNSNSA-N 17.999 17.99916 [18O] CAS:14797-71-8 Gmelin:17562 oxygen-18 chebi_ontology (18)8O (18)O heavy oxygen oxygen, isotope of mass 18 oxygen-18 schwerer Sauerstoff CHEBI:33815 oxygen-18 atom CAS:14797-71-8 ChemIDplus Gmelin:17562 Gmelin oxygen-18 IUPAC (18)8O IUPAC (18)O IUPAC heavy oxygen ChEBI oxygen, isotope of mass 18 ChemIDplus oxygen-18 ChEBI schwerer Sauerstoff ChEBI The stable isotope of oxygen with relative atomic mass 15.994914. The most abundant (99.76 atom percent) isotope of naturally occurring oxygen. 0 [16O] InChI=1S/O/i1+0 QVGXLLKOCUKJST-IGMARMGPSA-N 15.995 15.99491 [16O] Gmelin:17560 oxygen-16 chebi_ontology (16)8O (16)O oxygen-16 CHEBI:33818 oxygen-16 atom Gmelin:17560 Gmelin oxygen-16 IUPAC (16)8O IUPAC (16)O IUPAC oxygen-16 ChEBI The stable isotope of oxygen with relative atomic mass 16.999131. The least abundant (0.038 atom percent) isotope of naturally occurring oxygen. 0 [17O] InChI=1S/O/i1+1 QVGXLLKOCUKJST-OUBTZVSYSA-N 16.999 16.99913 [17O] CAS:13968-48-4 Gmelin:17561 oxygen-17 chebi_ontology (17)8O (17)O oxygen, isotope of mass 17 oxygen-17 CHEBI:33819 oxygen-17 atom CAS:13968-48-4 ChemIDplus Gmelin:17561 Gmelin oxygen-17 IUPAC (17)8O IUPAC (17)O IUPAC oxygen, isotope of mass 17 ChemIDplus oxygen-17 ChEBI An organic compound having at least one hydroxy group attached to a carbon atom. CHEBI:64710 hydroxy compounds chebi_ontology organic alcohol organic hydroxy compounds CHEBI:33822 organic hydroxy compound hydroxy compounds IUPAC organic alcohol ChEBI organic hydroxy compounds ChEBI Any organic molecule that consists of atoms connected in the form of a ring. chebi_ontology organic cyclic compounds CHEBI:33832 organic cyclic compound organic cyclic compounds ChEBI A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). heteroarenes chebi_ontology hetarenes CHEBI:33833 heteroarene heteroarenes IUPAC hetarenes IUPAC Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion. COMe:PRX000001 conjugated proteins chebi_ontology complex protein CHEBI:33837 conjugated protein conjugated proteins IUPAC complex protein COMe A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. Wikipedia:Macromolecule macromolecule chebi_ontology macromolecules polymer polymer molecule polymers CHEBI:33839 macromolecule macromolecule IUPAC macromolecules ChEBI polymer ChEBI polymer molecule IUPAC polymers ChEBI Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring. 0 C6HOR5 89.072 89.00274 C1(=C(C(=C(C(=C1*)*)*)*)*)O CHEBI:13664 CHEBI:13825 CHEBI:25969 CHEBI:2857 KEGG:C15584 MetaCyc:Phenols Wikipedia:Phenols phenols chebi_ontology Aryl alcohol a phenol arenols CHEBI:33853 phenols phenols IUPAC Aryl alcohol KEGG_COMPOUND a phenol UniProt arenols IUPAC A substance used in a chemical reaction to detect, measure, examine, or produce other substances. reagent chebi_ontology reactif reactivo reagents CHEBI:33893 reagent reagent IUPAC reactif IUPAC reactivo IUPAC reagents ChEBI A hexose with a (potential) aldehyde group at one end. CHEBI:2558 aldohexose chebi_ontology aldohexoses CHEBI:33917 aldohexose aldohexose ChEBI aldohexoses ChEBI Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals. chebi_ontology macronutrients CHEBI:33937 macronutrient macronutrients ChEBI halide salt gold molecular entity An ammonium ion that is the conjugate acid of serotonin; major species at pH 7.3. +1 C10H13N2O InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2/p+1 QZAYGJVTTNCVMB-UHFFFAOYSA-O 177.22250 177.10224 [NH3+]CCc1c[nH]c2ccc(O)cc12 2-(5-hydroxy-1H-indol-3-yl)ethanaminium chebi_ontology serotonin serotonin cation CHEBI:350546 serotonin(1+) 2-(5-hydroxy-1H-indol-3-yl)ethanaminium IUPAC serotonin UniProt serotonin cation ChEBI chebi_ontology nitrogen hydrides CHEBI:35106 nitrogen hydride nitrogen hydrides ChEBI Saturated acyclic nitrogen hydrides having the general formula NnHn+2. chebi_ontology azanes CHEBI:35107 azane azanes ChEBI A substance that diminishes the rate of a chemical reaction. inhibitor chebi_ontology inhibidor inhibiteur inhibitors CHEBI:35222 inhibitor inhibitor IUPAC inhibidor ChEBI inhibiteur ChEBI inhibitors ChEBI A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction. catalyst chebi_ontology Katalysator catalizador catalyseur CHEBI:35223 catalyst catalyst IUPAC Katalysator ChEBI catalizador ChEBI catalyseur ChEBI fossil fuel The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group. amino acid zwitterion chebi_ontology CHEBI:35238 amino acid zwitterion amino acid zwitterion ChEBI A derivative of ammonium, NH4(+), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups. +1 NR4 14.00670 14.00307 [*][N+]([*])([*])[*] CHEBI:26470 CHEBI:8693 KEGG:C06703 quaternary ammonium ion chebi_ontology Quaternary amine a quaternary ammonium quaternary ammonium ions CHEBI:35267 quaternary ammonium ion quaternary ammonium ion IUPAC Quaternary amine KEGG_COMPOUND a quaternary ammonium UniProt quaternary ammonium ions ChEBI A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc). chebi_ontology ammonium ion derivatives azanium ion derivative azanium ion derivatives CHEBI:35274 ammonium ion derivative ammonium ion derivatives ChEBI azanium ion derivative ChEBI azanium ion derivatives ChEBI A choline ester formed from choline and a carboxylic acid. +1 C6H13NO2R 131.17290 131.09463 C[N+](C)(C)CCOC([*])=O CHEBI:13245 CHEBI:22227 CHEBI:2463 KEGG:C01777 chebi_ontology acylcholines an acylcholine CHEBI:35287 acylcholine acylcholines ChEBI an acylcholine UniProt Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene. 0 C19H31R 259.450 259.24258 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCCC4)C CHEBI:13687 CHEBI:26768 CHEBI:9263 KEGG:C00377 MetaCyc:Steroids Steroid steroids chebi_ontology a steroid CHEBI:35341 steroid Steroid KEGG_COMPOUND steroids IUPAC a steroid UniProt CHEBI:24748 CHEBI:5814 KEGG:C02159 chebi_ontology Hydroxysteroid hydroxy steroids hydroxysteroids CHEBI:35350 hydroxy steroid Hydroxysteroid KEGG_COMPOUND hydroxy steroids ChEBI hydroxysteroids ChEBI Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compounds chebi_ontology organonitrogens CHEBI:35352 organonitrogen compound organonitrogen compounds IUPAC organonitrogens ChEBI Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group. CHEBI:25407 CHEBI:6984 KEGG:C06698 Monosaccharide monosaccharides chebi_ontology Monosaccharid Monosacharid monosacarido monosacaridos CHEBI:35381 monosaccharide Monosaccharide KEGG_COMPOUND monosaccharides IUPAC Monosaccharid ChEBI Monosacharid ChEBI monosacarido ChEBI monosacaridos IUPAC An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. CHEBI:33274 CHEBI:33436 oxoanion chebi_ontology oxoacid anions oxoanions CHEBI:35406 oxoanion oxoanion ChEBI oxoacid anions ChEBI oxoanions ChEBI A substance that reduces or suppresses inflammation. chebi_ontology anti-inflammatory drugs antiinflammatory agent antiinflammatory drug antiinflammatory drugs CHEBI:35472 anti-inflammatory drug anti-inflammatory drugs ChEBI antiinflammatory agent ChEBI antiinflammatory drug ChEBI antiinflammatory drugs ChEBI chebi_ontology alkali metal salts CHEBI:35479 alkali metal salt alkali metal salts ChEBI natural product fundamental parents chebi_ontology CHEBI:35507 natural product fundamental parent natural product fundamental parents IUPAC chebi_ontology steroid fundamental parents CHEBI:35508 steroid fundamental parent steroid fundamental parents ChEBI 0 C24H42 InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18?,19+,20-,21+,22+,23+,24-/m1/s1 QSHQKIURKJITMZ-BRPMRXRMSA-N 330.59028 330.32865 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC cholane chebi_ontology CHEBI:35519 cholane cholane IUPAC A drug that mimics the effects of stimulating postganglionic adrenergic sympathetic nerves. Included in this class are drugs that directly stimulate adrenergic receptors and drugs that act indirectly by provoking the release of adrenergic transmitters. chebi_ontology sympathomimetic sympathomimetics CHEBI:35524 sympathomimetic agent sympathomimetic ChEBI sympathomimetics ChEBI A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. chebi_ontology cardiovascular agent cardiovascular drugs CHEBI:35554 cardiovascular drug cardiovascular agent ChEBI cardiovascular drugs ChEBI An agent that selectively binds to and activates alpha-adrenergic receptors. chebi_ontology alpha-adrenergic agonists alpha-adrenergic receptor agonist alpha-adrenoceptor agonists CHEBI:35569 alpha-adrenergic agonist alpha-adrenergic agonists ChEBI alpha-adrenergic receptor agonist ChEBI alpha-adrenoceptor agonists IUPHAR A negative ion consisting solely of carbon and oxygen atoms, and therefore having the general formula CxOy(n-) for some integers x, y and n. carbon oxoanion chebi_ontology carbon oxoanions oxocarbon anion oxocarbon anions CHEBI:35604 carbon oxoanion carbon oxoanion ChEBI carbon oxoanions ChEBI oxocarbon anion ChEBI oxocarbon anions ChEBI chebi_ontology carbon oxoacids oxoacids of carbon CHEBI:35605 carbon oxoacid carbon oxoacids ChEBI oxoacids of carbon ChEBI A drug used to cause dilation of the blood vessels. chebi_ontology vasodilator vasodilator agents CHEBI:35620 vasodilator agent vasodilator ChEBI vasodilator agents ChEBI Any carboxylic acid containing two carboxy groups. CHEBI:23692 CHEBI:36172 CHEBI:4501 KEGG:C02028 Dicarboxylic acid chebi_ontology dicarboxylic acids CHEBI:35692 dicarboxylic acid Dicarboxylic acid KEGG_COMPOUND dicarboxylic acids ChEBI dicarboxylic acid anion chebi_ontology dicarboxylic acid anions CHEBI:35693 dicarboxylic acid anion dicarboxylic acid anion ChEBI dicarboxylic acid anions ChEBI A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. CHEBI:23960 CHEBI:4859 KEGG:C00287 Wikipedia:Ester Ester chebi_ontology esters CHEBI:35701 ester Ester KEGG_COMPOUND esters ChEBI chebi_ontology glycosaminoglycan sulfate glycosaminoglycan sulfates sulfated glycosaminoglycans CHEBI:35722 sulfated glycosaminoglycan glycosaminoglycan sulfate ChEBI glycosaminoglycan sulfates ChEBI sulfated glycosaminoglycans ChEBI chebi_ontology carbohydrate sulfates carbohydrate sulphates CHEBI:35724 carbohydrate sulfate carbohydrate sulfates ChEBI carbohydrate sulphates ChEBI A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated. -1 CO2R 44.01000 43.98983 [O-]C([*])=O CHEBI:13657 CHEBI:25382 CHEBI:3407 KEGG:C00060 chebi_ontology Carboxylate Monocarboxylate a monocarboxylate monocarboxylates monocarboxylic acid anions CHEBI:35757 monocarboxylic acid anion Carboxylate KEGG_COMPOUND Monocarboxylate KEGG_COMPOUND a monocarboxylate UniProt monocarboxylates ChEBI monocarboxylic acid anions ChEBI A phosphorus oxoanion that is the conjugate base of phosphoric acid. chebi_ontology Pi phosphate phosphate ions CHEBI:35780 phosphate ion Pi ChEBI phosphate ChEBI phosphate ions ChEBI pnictogen hydride chebi_ontology pnictogen hydrides CHEBI:35881 pnictogen hydride pnictogen hydride ChEBI pnictogen hydrides ChEBI A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function. chebi_ontology neurotransmitter agents CHEBI:35942 neurotransmitter agent neurotransmitter agents ChEBI CHEBI:22867 CHEBI:50419 LIPID_MAPS_class:LMST04 chebi_ontology bile acids and derivatives cholanoids CHEBI:36078 cholanoid LIPID_MAPS_class:LMST04 LIPID MAPS bile acids and derivatives LIPID_MAPS cholanoids ChEBI A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. CHEBI:13677 CHEBI:14911 MO:683 MeSH:D011506 NCIt:C17021 PRO:000000001 SNOMEDCT:88878007 proteins chebi_ontology CHEBI:36080 protein proteins IUPAC inorganic chloride chebi_ontology bile acid anions CHEBI:36235 bile acid anion bile acid anions ChEBI A steroid acid that consists of cholane having a carboxy group in place of the methyl group at position 24. 0 C24H40O2 InChI=1S/C24H40O2/c1-16(7-12-22(25)26)19-10-11-20-18-9-8-17-6-4-5-14-23(17,2)21(18)13-15-24(19,20)3/h16-21H,4-15H2,1-3H3,(H,25,26)/t16-,17?,18+,19-,20+,21+,23+,24-/m1/s1 RPKLZQLYODPWTM-KBMWBBLPSA-N 360.57320 360.30283 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC(O)=O CAS:25312-65-6 Patent:JP2008069152 Reaxys:13246008 cholan-24-oic acid chebi_ontology CHEBI:36237 cholanic acid CAS:25312-65-6 ChemIDplus Reaxys:13246008 Reaxys cholan-24-oic acid IUPAC 0 C24H40O2 InChI=1S/C24H40O2/c1-16(7-12-22(25)26)19-10-11-20-18-9-8-17-6-4-5-14-23(17,2)21(18)13-15-24(19,20)3/h16-21H,4-15H2,1-3H3,(H,25,26)/t16-,17+,18+,19-,20+,21+,23+,24-/m1/s1 RPKLZQLYODPWTM-LVVAJZGHSA-N 360.57320 360.30283 [H][C@@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCC(O)=O Beilstein:3214794 CAS:546-18-9 LIPID_MAPS_instance:LMST04010441 5beta-cholan-24-oic acid 5beta-cholanic acid chebi_ontology (5beta)-cholan-24-oic acid (5beta,17beta)-gamma-methylandrostane-17-butanoic acid 5beta-cholanoic acid ursocholanic acid CHEBI:36238 5beta-cholanic acid Beilstein:3214794 Beilstein CAS:546-18-9 ChemIDplus LIPID_MAPS_instance:LMST04010441 LIPID MAPS 5beta-cholan-24-oic acid IUPAC 5beta-cholanic acid ChemIDplus (5beta)-cholan-24-oic acid ChemIDplus (5beta,17beta)-gamma-methylandrostane-17-butanoic acid ChemIDplus 5beta-cholanoic acid ChemIDplus ursocholanic acid ChemIDplus Members of the class of cholanic acids based on a 5beta-cholane skeleton. chebi_ontology CHEBI:36248 5beta-cholanic acids A salt of a bile acid. chebi_ontology bile acid salts CHEBI:36277 bile acid salt bile acid salts ChEBI CHEBI:23166 CHEBI:23211 chebi_ontology CHEBI:36278 cholanic acids Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). chebi_ontology leptons CHEBI:36338 lepton leptons ChEBI Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). chebi_ontology baryons CHEBI:36339 baryon baryons ChEBI Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion chebi_ontology fermions CHEBI:36340 fermion fermion IUPAC fermions ChEBI Particle of integer spin quantum number following Bose-Einstein statistics. Bosons are named after Satyendra Nath Bose. boson chebi_ontology bosons CHEBI:36341 boson boson IUPAC bosons ChEBI A particle smaller than an atom. Wikipedia:Subatomic_particle chebi_ontology subatomic particles CHEBI:36342 subatomic particle subatomic particle subatomic particles ChEBI A subatomic particle known to have substructure (i.e. consisting of smaller particles). chebi_ontology composite particles CHEBI:36343 composite particle composite particles ChEBI Hadron is a subatomic particle which experiences the strong force. chebi_ontology hadrons CHEBI:36344 hadron hadrons ChEBI A hadron with zero or integer spin; a strongly interacting boson. The term is derived from the Greek muepsilonsigmaomicronsigma (medium, middle). chebi_ontology mesons CHEBI:36345 meson mesons ChEBI A nucleus or any of its constituents in any of their energy states. nuclear particle chebi_ontology CHEBI:36347 nuclear particle nuclear particle IUPAC The collective name for zero-spin mesons pi(+), pi(-) and pi(0). pi meson pion chebi_ontology pi-meson CHEBI:36348 pi meson pi meson ChEBI pion IUPAC pi-meson ChEBI Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.113428913(17) u, or 105.658389(34) MeV. -1 0.113428913 muon chebi_ontology Mueon My-Teilchen Myon mu(-) negative muon CHEBI:36356 muon muon IUPAC Mueon ChEBI My-Teilchen ChEBI Myon ChEBI mu(-) IUPAC negative muon ChEBI Any molecular entity consisting of more than one atom. chebi_ontology polyatomic entities CHEBI:36357 polyatomic entity polyatomic entities ChEBI An ion consisting of more than one atom. chebi_ontology polyatomic ions CHEBI:36358 polyatomic ion polyatomic ions ChEBI phosphorus oxoacid derivative chebi_ontology CHEBI:36359 phosphorus oxoacid derivative phosphorus oxoacid derivative ChEBI chebi_ontology CHEBI:36360 phosphorus oxoacids and derivatives Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compounds chebi_ontology CHEBI:36586 carbonyl compound carbonyl compounds IUPAC Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. oxo compounds chebi_ontology organic oxo compounds CHEBI:36587 organic oxo compound oxo compounds IUPAC organic oxo compounds ChEBI Compounds based on a biladiene skeleton. chebi_ontology CHEBI:36735 biladienes chalcogen hydride chebi_ontology chalcogen hydrides CHEBI:36902 chalcogen hydride chalcogen hydride ChEBI chalcogen hydrides ChEBI argon molecular entity chebi_ontology inorganic ions CHEBI:36914 inorganic ion inorganic ions ChEBI chebi_ontology inorganic cations CHEBI:36915 inorganic cation inorganic cations ChEBI A monoatomic or polyatomic species having one or more elementary charges of the proton. CHEBI:23058 CHEBI:3473 KEGG:C01373 Cation cation chebi_ontology Kation Kationen cationes cations CHEBI:36916 cation Cation KEGG_COMPOUND cation ChEBI cation IUPAC Kation ChEBI Kationen ChEBI cationes ChEBI cations ChEBI 0 [14C] InChI=1S/C/i1+2 OKTJSMMVPCPJKN-NJFSPNSNSA-N 14.003 14.00324 [14C] CAS:14762-75-5 Wikipedia:Carbon-14 carbon-14 chebi_ontology (14)6C (14)C carbon, isotope of mass 14 carbon-14 CHEBI:36927 carbon-14 atom CAS:14762-75-5 ChemIDplus carbon-14 IUPAC (14)6C IUPAC (14)C IUPAC carbon, isotope of mass 14 ChemIDplus carbon-14 ChEBI 0 [13C] InChI=1S/C/i1+1 OKTJSMMVPCPJKN-OUBTZVSYSA-N 13.003 13.00335 [13C] CAS:14762-74-4 carbon-13 carbon-13 atom chebi_ontology (13)6C (13)C carbon, isotope of mass 13 carbon-13 CHEBI:36928 carbon-13 atom CAS:14762-74-4 ChemIDplus carbon-13 IUPAC carbon-13 atom ChemIDplus (13)6C IUPAC (13)C IUPAC carbon, isotope of mass 13 ChemIDplus carbon-13 ChEBI 0 [11C] InChI=1S/C/i1-1 OKTJSMMVPCPJKN-BJUDXGSMSA-N 11.011 11.01143 [11C] CAS:14333-33-6 carbon-11 chebi_ontology (11)6C (11)C carbon, isotope of mass 11 carbon-11 CHEBI:36929 carbon-11 atom CAS:14333-33-6 ChemIDplus carbon-11 IUPAC (11)6C IUPAC (11)C IUPAC carbon, isotope of mass 11 ChemIDplus carbon-11 ChEBI 0 [10C] InChI=1S/C/i1-2 OKTJSMMVPCPJKN-YPZZEJLDSA-N 10.017 10.01685 [10C] CAS:15578-68-4 carbon-10 chebi_ontology (10)6C (10)C carbon, isotope of mass 10 carbon-10 CHEBI:36930 carbon-10 atom CAS:15578-68-4 ChemIDplus carbon-10 IUPAC (10)6C IUPAC (10)C IUPAC carbon, isotope of mass 10 ChemIDplus carbon-10 ChEBI 0 [12C] InChI=1S/C/i1+0 OKTJSMMVPCPJKN-IGMARMGPSA-N 12.000 12.00000 [12C] carbon-12 chebi_ontology (12)6C (12)C carbon-12 CHEBI:36931 carbon-12 atom carbon-12 IUPAC (12)6C IUPAC (12)C IUPAC carbon-12 ChEBI The radioactive isotope of oxygen with relative atomic mass 15.003065. The longest-lived oxygen radionuclide with half-life of 122.2 s. 0 [15O] InChI=1S/O/i1-1 QVGXLLKOCUKJST-BJUDXGSMSA-N 15.003 15.00307 [15O] CAS:13982-43-9 Gmelin:316575 oxygen-15 chebi_ontology (15)8O (15)O oxygen, isotope of mass 15 oxygen-15 CHEBI:36932 oxygen-15 atom CAS:13982-43-9 ChemIDplus Gmelin:316575 Gmelin oxygen-15 IUPAC (15)8O IUPAC (15)O IUPAC oxygen, isotope of mass 15 ChemIDplus oxygen-15 ChEBI 0 [19O] InChI=1S/O/i1+3 QVGXLLKOCUKJST-AKLPVKDBSA-N 19.004 19.00358 [19O] CAS:13982-18-8 oxygen-19 chebi_ontology (19)8O (19)O oxygen-19 CHEBI:36933 oxygen-19 atom CAS:13982-18-8 ChemIDplus oxygen-19 IUPAC (19)8O IUPAC (19)O IUPAC oxygen-19 ChEBI The stable isotope of nitrogen with relative atomic mass 15.000109. The least abundant (0.368 atom percent) isotope of naturally occurring nitrogen. 0 N 14.007 14.00307 CAS:14390-96-6 nitrogen-15 chebi_ontology (15)7N (15)N nitrogen, isotope of mass 15 nitrogen-15 CHEBI:36934 nitrogen-15 atom CAS:14390-96-6 ChemIDplus nitrogen-15 IUPAC (15)7N IUPAC (15)N IUPAC nitrogen, isotope of mass 15 ChemIDplus nitrogen-15 ChEBI The radioactive isotope of nitrogen with relative atomic mass 13.0057386. The longest-lived nitrogen radionuclide with half-life of 9.965 min. 0 N 14.007 14.00307 CAS:13981-22-1 nitrogen-13 chebi_ontology (13)7N (13)N nitrogen, isotope of mass 13 nitrogen-13 CHEBI:36935 nitrogen-13 atom CAS:13981-22-1 ChemIDplus nitrogen-13 IUPAC (13)7N IUPAC (13)N IUPAC nitrogen, isotope of mass 13 ChemIDplus nitrogen-13 ChEBI 0 N 14.007 14.00307 CAS:13981-62-9 nitrogen-16 chebi_ontology (16)7N (16)N nitrogen, isotope of mass 16 nitrogen-16 CHEBI:36936 nitrogen-16 atom CAS:13981-62-9 ChemIDplus nitrogen-16 IUPAC (16)7N IUPAC (16)N IUPAC nitrogen, isotope of mass 16 ChemIDplus nitrogen-16 ChEBI 0 N 14.007 14.00307 CAS:14914-35-3 nitrogen-17 chebi_ontology (17)7N (17)N nitrogen-17 CHEBI:36937 nitrogen-17 atom CAS:14914-35-3 ChemIDplus nitrogen-17 IUPAC (17)7N IUPAC (17)N ChEBI nitrogen-17 ChEBI The stable isotope of nitrogen with relative atomic mass 14.003074. The most abundant (99.63 atom percent) isotope of naturally occurring nitrogen. 0 N 14.007 14.00307 nitrogen-14 chebi_ontology (14)7N (14)N nitrogen-14 CHEBI:36938 nitrogen-14 atom nitrogen-14 IUPAC (14)7N IUPAC (14)N IUPAC nitrogen-14 ChEBI The radioactive isotope of fluorine with relative atomic mass 18.000938. The longest-lived fluorine radionuclide with half-life of 109.77 min. 0 [18F] InChI=1S/F/i1-1 YCKRFDGAMUMZLT-BJUDXGSMSA-N 18.001 18.00094 [18F] CAS:13981-56-1 DrugBank:DB13134 Wikipedia:Fluorine-18 fluorine-18 chebi_ontology (18)9F (18)F fluorine, isotope of mass 18 fluorine-18 CHEBI:36939 fluorine-18 atom CAS:13981-56-1 ChemIDplus fluorine-18 IUPAC (18)9F IUPAC (18)F IUPAC fluorine, isotope of mass 18 ChemIDplus fluorine-18 ChEBI The stable isotope of fluorine with relative atomic mass 18.998403 and nuclear spin (1)/2. 0 [19F] InChI=1S/F/i1+0 YCKRFDGAMUMZLT-IGMARMGPSA-N 18.998 18.99840 [19F] fluorine-19 chebi_ontology (19)9F (19)F fluorine-19 CHEBI:36940 fluorine-19 atom fluorine-19 IUPAC (19)9F IUPAC (19)F ChEBI fluorine-19 ChEBI chalcocarbonic acid chalcocarbonic acids chebi_ontology chalcocarbonic acids CHEBI:36961 chalcocarbonic acid chalcocarbonic acid ChEBI chalcocarbonic acids IUPAC chalcocarbonic acids ChEBI An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound chebi_ontology organochalcogen compounds CHEBI:36962 organochalcogen compound organochalcogen compound ChEBI organochalcogen compounds ChEBI An organochalcogen compound containing at least one carbon-oxygen bond. PMID:17586126 organooxygen compound chebi_ontology organooxygen compounds CHEBI:36963 organooxygen compound PMID:17586126 Europe PMC organooxygen compound ChEBI organooxygen compounds ChEBI The radioactive isotope of helium with relative atomic mass 6.01889 and half-life of 806.7 ms. 0 [6He] InChI=1S/He/i1+2 SWQJXJOGLNCZEY-NJFSPNSNSA-N 6.019 6.01889 [6He] helium-6 chebi_ontology (6)2He (6)He helium-6 CHEBI:37003 helium-6 atom helium-6 IUPAC (6)2He IUPAC (6)He IUPAC helium-6 ChEBI The radioactive isotope of helium with relative atomic mass 8.03392 and half-life of 119.0 ms. 0 [8He] InChI=1S/He/i1+4 SWQJXJOGLNCZEY-RNFDNDRNSA-N 8.034 8.03392 [8He] helium-8 chebi_ontology (8)2He (8)He helium-8 CHEBI:37004 helium-8 atom helium-8 IUPAC (8)2He IUPAC (8)He IUPAC helium-8 ChEBI amino-acid anion chebi_ontology amino acid anions amino-acid anions CHEBI:37022 amino-acid anion amino-acid anion ChEBI amino acid anions ChEBI amino-acid anions ChEBI A polysaccharide composed of glucose residues. C12H22O11(C6H10O5)n CHEBI:24255 CHEBI:5392 CAS:9037-91-6 KEGG:C01379 Glucan glucan chebi_ontology glucans CHEBI:37163 glucan CAS:9037-91-6 ChemIDplus Glucan KEGG_COMPOUND glucan IUPAC glucans ChEBI Glycans composed of a single type of monosaccharide residue. They are named by replacing the ending '-ose' of the sugar by '-an'. homopolysaccharide chebi_ontology homoglycan homopolysaccharides CHEBI:37164 homopolysaccharide homopolysaccharide IUPAC homoglycan IUPAC homopolysaccharides ChEBI chebi_ontology organic hydrides CHEBI:37175 organic hydride organic hydrides ChEBI mononuclear parent hydrides chebi_ontology mononuclear hydride mononuclear hydrides CHEBI:37176 mononuclear parent hydride mononuclear parent hydrides IUPAC mononuclear hydride ChEBI mononuclear hydrides IUPAC chebi_ontology CHEBI:37246 elemental sodium The radioactive isotope of polonium with relative atomic mass 209.98286 and half-life of 138.376 days; the only naturally occurring isotope of polonium. 0 [210Po] InChI=1S/Po/i1+1 HZEBHPIOVYHPMT-OUBTZVSYSA-N 209.983 209.98286 [210Po] CAS:13981-52-7 Gmelin:76756 polonium-210 chebi_ontology (210)84Po (210)Po polonium, isotope of mass 210 polonium-210 CHEBI:37340 polonium-210 atom CAS:13981-52-7 ChemIDplus Gmelin:76756 Gmelin polonium-210 IUPAC (210)84Po IUPAC (210)Po IUPAC polonium, isotope of mass 210 ChemIDplus polonium-210 ChEBI The radioactive isotope of polonium with relative atomic mass 210.986637 and half-life of 0.516 s. 0 [211Po] InChI=1S/Po/i1+2 HZEBHPIOVYHPMT-NJFSPNSNSA-N 210.987 210.98664 [211Po] CAS:15735-83-8 Gmelin:41683 polonium-211 chebi_ontology (211)84Po (211)Po polonium, isotope of mass 211 polonium-211 CHEBI:37341 polonium-211 atom CAS:15735-83-8 ChemIDplus Gmelin:41683 Gmelin polonium-211 IUPAC (211)84Po IUPAC (211)Po IUPAC polonium, isotope of mass 211 ChemIDplus polonium-211 ChEBI The radioactive isotope of polonium with relative atomic mass 211.988852 and half-life of 0.299 mus. 0 [212Po] InChI=1S/Po/i1+3 HZEBHPIOVYHPMT-AKLPVKDBSA-N 211.989 211.98885 [212Po] CAS:15389-34-1 Gmelin:41677 polonium-212 chebi_ontology (212)84Po (212)Po polonium, isotope of mass 212 polonium-212 CHEBI:37342 polonium-212 atom CAS:15389-34-1 ChemIDplus Gmelin:41677 Gmelin polonium-212 IUPAC (212)84Po IUPAC (212)Po IUPAC polonium, isotope of mass 212 ChemIDplus polonium-212 ChEBI The radioactive isotope of polonium with relative atomic mass 212.9928425 and half-life of 4.2 mus. 0 [213Po] InChI=1S/Po/i1+4 HZEBHPIOVYHPMT-RNFDNDRNSA-N 212.993 212.99284 [213Po] CAS:15756-57-7 polonium-213 chebi_ontology (213)84Po (213)Po polonium, isotope of mass 213 polonium-213 CHEBI:37343 polonium-213 atom CAS:15756-57-7 ChemIDplus polonium-213 IUPAC (213)84Po IUPAC (213)Po IUPAC polonium, isotope of mass 213 ChemIDplus polonium-213 ChEBI The radioactive isotope of polonium with relative atomic mass 213.995186 and half-life of 164.3 mus. 0 [214Po] InChI=1S/Po/i1+5 HZEBHPIOVYHPMT-BKFZFHPZSA-N 213.995 213.99519 [214Po] CAS:15735-67-8 Gmelin:41679 polonium-214 chebi_ontology (214)84Po (214)Po polonium, isotope of mass 214 polonium-214 CHEBI:37344 polonium-214 atom CAS:15735-67-8 ChemIDplus Gmelin:41679 Gmelin polonium-214 IUPAC (214)84Po IUPAC (214)Po IUPAC polonium, isotope of mass 214 ChemIDplus polonium-214 ChEBI The radioactive isotope of polonium with relative atomic mass 214.999415 and half-life of 1.781 ms. 0 [215Po] InChI=1S/Po/i1+6 HZEBHPIOVYHPMT-LZFNBGRKSA-N 214.999 214.99941 [215Po] CAS:15706-52-2 Gmelin:41680 polonium-215 chebi_ontology (215)84Po (215)Po polonium, isotope of mass 215 polonium-215 CHEBI:37345 polonium-215 atom CAS:15706-52-2 ChemIDplus Gmelin:41680 Gmelin polonium-215 IUPAC (215)84Po IUPAC (215)Po IUPAC polonium, isotope of mass 215 ChemIDplus polonium-215 ChEBI The radioactive isotope of polonium with relative atomic mass 216.001905 and half-life of 0.145 s. 0 [216Po] InChI=1S/Po/i1+7 HZEBHPIOVYHPMT-RKEGKUSMSA-N 216.002 216.00191 [216Po] CAS:15756-58-8 Gmelin:41684 polonium-216 chebi_ontology (216)84Po (216)Po polonium, isotope of mass 216 polonium-216 CHEBI:37346 polonium-216 atom CAS:15756-58-8 ChemIDplus Gmelin:41684 Gmelin polonium-216 IUPAC (216)84Po IUPAC (216)Po IUPAC polonium, isotope of mass 216 ChemIDplus polonium-216 ChEBI The radioactive isotope of polonium with relative atomic mass 217.006253 and half-life of < 10 s. 0 [217Po] InChI=1S/Po/i1+8 HZEBHPIOVYHPMT-CONNIKPHSA-N 217.006 217.00625 [217Po] polonium-217 chebi_ontology (217)84Po (217)Po polonium-217 CHEBI:37347 polonium-217 atom polonium-217 IUPAC (217)84Po IUPAC (217)Po IUPAC polonium-217 ChEBI The radioactive isotope of polonium with relative atomic mass 218.008966 and half-life of 3.10 min. 0 [218Po] InChI=1S/Po/i1+9 HZEBHPIOVYHPMT-KUYOKYOWSA-N 218.009 218.00897 [218Po] CAS:15422-74-9 Gmelin:41685 polonium-218 chebi_ontology (218)84Po (218)Po polonium, isotope of mass 218 polonium-218 CHEBI:37348 polonium-218 atom CAS:15422-74-9 ChemIDplus Gmelin:41685 Gmelin polonium-218 IUPAC (218)84Po IUPAC (218)Po IUPAC polonium, isotope of mass 218 ChemIDplus polonium-218 ChEBI 0 [190Po] InChI=1S/Po/i1-19 HZEBHPIOVYHPMT-BTCYYSDASA-N 189.994 189.99429 [190Po] polonium-190 chebi_ontology (190)84Po (190)Po polonium-190 CHEBI:37350 polonium-190 atom polonium-190 IUPAC (190)84Po IUPAC (190)Po IUPAC polonium-190 ChEBI 0 [191Po] InChI=1S/Po/i1-18 HZEBHPIOVYHPMT-ZWLOOBQPSA-N 190.995 190.99465 [191Po] polonium-191 chebi_ontology (191)84Po (191)Po polonium-191 CHEBI:37351 polonium-191 atom polonium-191 IUPAC (191)84Po IUPAC (191)Po IUPAC polonium-191 ChEBI 0 [192Po] InChI=1S/Po/i1-17 HZEBHPIOVYHPMT-MEAORNGASA-N 191.990 191.99033 [192Po] polonium-192 chebi_ontology (192)84Po (192)Po polonium-192 CHEBI:37352 polonium-192 atom polonium-192 IUPAC (192)84Po IUPAC (192)Po IUPAC polonium-192 ChEBI 0 [193Po] InChI=1S/Po/i1-16 HZEBHPIOVYHPMT-KLOSUXQXSA-N 192.991 192.99110 [193Po] polonium-193 chebi_ontology (193)84Po (193)Po polonium-193 CHEBI:37353 polonium-193 atom polonium-193 IUPAC (193)84Po IUPAC (193)Po IUPAC polonium-193 ChEBI 0 [194Po] InChI=1S/Po/i1-15 HZEBHPIOVYHPMT-LPJXZZDMSA-N 193.988 193.98828 [194Po] polonium-194 chebi_ontology (194)84Po (194)Po polonium-194 CHEBI:37354 polonium-194 atom polonium-194 IUPAC (194)84Po IUPAC (194)Po IUPAC polonium-194 ChEBI 0 [195Po] InChI=1S/Po/i1-14 HZEBHPIOVYHPMT-DWTUDRKQSA-N 194.988 194.98804 [195Po] polonium-195 chebi_ontology (195)84Po (195)Po polonium-195 CHEBI:37355 polonium-195 atom polonium-195 IUPAC (195)84Po IUPAC (195)Po IUPAC polonium-195 ChEBI 0 [196Po] InChI=1S/Po/i1-13 HZEBHPIOVYHPMT-QAPNMCNYSA-N 195.985 195.98547 [196Po] polonium-196 chebi_ontology (196)84Po (196)Po polonium-196 CHEBI:37356 polonium-196 atom polonium-196 IUPAC (196)84Po IUPAC (196)Po IUPAC polonium-196 ChEBI 0 [197Po] InChI=1S/Po/i1-12 HZEBHPIOVYHPMT-DFNMHJECSA-N 196.986 196.98557 [197Po] polonium-197 chebi_ontology (197)84Po (197)Po polonium-197 CHEBI:37357 polonium-197 atom polonium-197 IUPAC (197)84Po ChEBI (197)Po ChEBI polonium-197 ChEBI 0 [198Po] InChI=1S/Po/i1-11 HZEBHPIOVYHPMT-DSSHQIQSSA-N 197.984 197.98402 [198Po] polonium-198 chebi_ontology (198)84Po (198)Po polonium-198 CHEBI:37358 polonium-198 atom polonium-198 IUPAC (198)84Po IUPAC (198)Po IUPAC polonium-198 ChEBI 0 [199Po] InChI=1S/Po/i1-10 HZEBHPIOVYHPMT-CBESVEIWSA-N 198.985 198.98504 [199Po] polonium-199 chebi_ontology (199)84Po (199)Po polonium-199 CHEBI:37359 polonium-199 atom polonium-199 IUPAC (199)84Po IUPAC (199)Po IUPAC polonium-199 ChEBI 0 [200Po] InChI=1S/Po/i1-9 HZEBHPIOVYHPMT-DBXDQKISSA-N 199.982 199.98173 [200Po] polonium-200 chebi_ontology (200)84Po (200)Po polonium-200 CHEBI:37360 polonium-200 atom polonium-200 IUPAC (200)84Po IUPAC (200)Po IUPAC polonium-200 ChEBI 0 [201Po] InChI=1S/Po/i1-8 HZEBHPIOVYHPMT-QQVBLGSISA-N 200.982 200.98221 [201Po] polonium-201 chebi_ontology (201)84Po (201)Po polonium-201 CHEBI:37361 polonium-201 atom polonium-201 IUPAC (201)84Po IUPAC (201)Po IUPAC polonium-201 ChEBI 0 [202Po] InChI=1S/Po/i1-7 HZEBHPIOVYHPMT-NOHWODKXSA-N 201.981 201.98070 [202Po] polonium-202 chebi_ontology (202)84Po (202)Po polonium-202 CHEBI:37362 polonium-202 atom polonium-202 IUPAC (202)84Po IUPAC (202)Po IUPAC polonium-202 ChEBI The radioactive isotope of polonium with relative atomic mass 202.981413 and half-life of 36.7 min. 0 [203Po] InChI=1S/Po/i1-6 HZEBHPIOVYHPMT-VENIDDJXSA-N 202.981 202.98141 [203Po] CAS:16729-74-1 polonium-203 chebi_ontology (203)84Po (203)Po polonium, isotope of mass 203 polonium-203 CHEBI:37363 polonium-203 atom CAS:16729-74-1 ChemIDplus polonium-203 IUPAC (203)84Po IUPAC (203)Po IUPAC polonium, isotope of mass 203 ChemIDplus polonium-203 ChEBI 0 [204Po] InChI=1S/Po/i1-5 HZEBHPIOVYHPMT-FTXFMUIASA-N 203.980 203.98031 [204Po] polonium-204 chebi_ontology (204)84Po (204)Po polonium-204 CHEBI:37364 polonium-204 atom polonium-204 IUPAC (204)84Po IUPAC (204)Po IUPAC polonium-204 ChEBI The radioactive isotope of polonium with relative atomic mass 204.981165 and half-life of 1.66 h. 0 [205Po] InChI=1S/Po/i1-4 HZEBHPIOVYHPMT-AHCXROLUSA-N 204.981 204.98117 [205Po] CAS:16729-76-3 polonium-205 chebi_ontology (205)84Po (205)Po polonium, isotope of mass 205 polonium-205 CHEBI:37365 polonium-205 atom CAS:16729-76-3 ChemIDplus polonium-205 IUPAC (205)84Po IUPAC (205)Po IUPAC polonium, isotope of mass 205 ChemIDplus polonium-205 ChEBI The radioactive isotope of polonium with relative atomic mass 205.98047 and half-life of 8.8 days. 0 [206Po] InChI=1S/Po/i1-3 HZEBHPIOVYHPMT-OIOBTWANSA-N 205.980 205.98047 [206Po] polonium-206 chebi_ontology (206)84Po (206)Po polonium-206 CHEBI:37366 polonium-206 atom polonium-206 IUPAC (206)84Po IUPAC (206)Po IUPAC polonium-206 ChEBI The radioactive isotope of polonium with relative atomic mass 206.981578 and half-life of 5.80 h. 0 [207Po] InChI=1S/Po/i1-2 HZEBHPIOVYHPMT-YPZZEJLDSA-N 206.982 206.98158 [207Po] CAS:15720-45-3 polonium-207 chebi_ontology (207)84Po (207)Po polonium, isotope of mass 207 polonium-207 CHEBI:37367 polonium-207 atom CAS:15720-45-3 ChemIDplus polonium-207 IUPAC (207)84Po IUPAC (207)Po IUPAC polonium, isotope of mass 207 ChemIDplus polonium-207 ChEBI The radioactive isotope of polonium with relative atomic mass 207.98123 and half-life of 2.898 years. 0 [208Po] InChI=1S/Po/i1-1 HZEBHPIOVYHPMT-BJUDXGSMSA-N 207.981 207.98123 [208Po] polonium-208 chebi_ontology (208)84Po (208)Po polonium-208 CHEBI:37368 polonium-208 atom polonium-208 IUPAC (208)84Po IUPAC (208)Po IUPAC polonium-208 ChEBI The radioactive isotope of polonium with relative atomic mass 208.982404 and half-life of 102 years. 0 [209Po] InChI=1S/Po/i1+0 HZEBHPIOVYHPMT-IGMARMGPSA-N 208.982 208.98242 [209Po] polonium-209 chebi_ontology (209)84Po (209)Po polonium-209 CHEBI:37369 polonium-209 atom polonium-209 IUPAC (209)84Po IUPAC (209)Po IUPAC polonium-209 ChEBI Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid. CHEBI:25425 CHEBI:7011 KEGG:C05114 Mucopolysaccharide mucopolysaccharides chebi_ontology Mucopolysaccharid Mukopolysaccharid mucopolisacarido mucopolisacaridos CHEBI:37395 mucopolysaccharide Mucopolysaccharide KEGG_COMPOUND mucopolysaccharides IUPAC Mucopolysaccharid ChEBI Mukopolysaccharid ChEBI mucopolisacarido ChEBI mucopolisacaridos IUPAC An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid). CHEBI:13800 CHEBI:13801 CHEBI:22209 CHEBI:2426 KEGG:C00174 Acid acid chebi_ontology Saeure Saeuren acide acido acids CHEBI:37527 acid Acid KEGG_COMPOUND acid IUPAC Saeure ChEBI Saeuren ChEBI acide IUPAC acido ChEBI acids ChEBI A molecular entity consisting of two or more chemical elements. chebi_ontology chemical compound heteroatomic molecular entities CHEBI:37577 heteroatomic molecular entity chemical compound ChEBI heteroatomic molecular entities ChEBI halide An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. 0 CNOR3 42.01680 41.99799 [*]C(=O)N([*])[*] CHEBI:35354 CHEBI:35355 carboxamides chebi_ontology carboxamides primary carboxamide CHEBI:37622 carboxamide carboxamides IUPAC carboxamides ChEBI primary carboxamide ChEBI The stable isotope of thallium with relative atomic mass 202.9723. The least abundant (29.524 atom percent) isotope of naturally occurring thallium. 0 [203Tl] InChI=1S/Tl/i1-1 BKVIYDNLLOSFOA-BJUDXGSMSA-N 202.972 202.97234 [203Tl] CAS:14280-48-9 thallium-203 chebi_ontology (203)81Tl (203)Tl thallium, isotope of mass 203 CHEBI:37802 thallium-203 CAS:14280-48-9 ChemIDplus thallium-203 IUPAC (203)81Tl IUPAC (203)Tl IUPAC thallium, isotope of mass 203 ChemIDplus The stable isotope of thallium with relative atomic mass 204.9744. The most abundant (70.476 atom percent) isotope of naturally occurring thallium. 0 [205Tl] InChI=1S/Tl/i1+1 BKVIYDNLLOSFOA-OUBTZVSYSA-N 204.974 204.97443 [205Tl] CAS:14280-49-0 Gmelin:557319 thallium-205 chebi_ontology (205)81Tl (205)Tl thallium, isotope of mass 205 CHEBI:37803 thallium-205 CAS:14280-49-0 ChemIDplus Gmelin:557319 Gmelin thallium-205 IUPAC (205)81Tl IUPAC (205)Tl IUPAC thallium, isotope of mass 205 ChemIDplus The radioactive isotope of thallium with relative atomic mass 200.9708 and half-life of 72.912 hours. 0 [201Tl] InChI=1S/Tl/i1-3 BKVIYDNLLOSFOA-OIOBTWANSA-N 200.971 200.97080 [201Tl] CAS:15064-65-0 thallium-201 chebi_ontology (201)81Tl (201)Tl thallium, isotope of mass 201 CHEBI:37804 thallium-201 CAS:15064-65-0 ChemIDplus thallium-201 IUPAC (201)81Tl IUPAC (201)Tl IUPAC thallium, isotope of mass 201 ChemIDplus The radioactive isotope of thallium with relative atomic mass 198.9698 and half-life of 7.42 hours. 0 [199Tl] InChI=1S/Tl/i1-5 BKVIYDNLLOSFOA-FTXFMUIASA-N 198.970 198.96981 [199Tl] CAS:15064-66-1 Gmelin:1491863 thallium-199 chebi_ontology (199)81Tl (199)Tl thallium, isotope of mass 199 CHEBI:37805 thallium-199 CAS:15064-66-1 ChemIDplus Gmelin:1491863 Gmelin thallium-199 IUPAC (199)81Tl IUPAC (199)Tl IUPAC thallium, isotope of mass 199 ChemIDplus sulfuric acid derivative chebi_ontology sulfuric acid derivatives CHEBI:37826 sulfuric acid derivative sulfuric acid derivative ChEBI sulfuric acid derivatives ChEBI A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid. carboacyl groups carboxylic acyl group chebi_ontology carboxylic acyl groups CHEBI:37838 carboacyl group carboacyl groups IUPAC carboxylic acyl group IUPAC carboxylic acyl groups IUPAC An agent that selectively binds to and activates adrenergic receptors. chebi_ontology adrenergic agonists adrenergic receptor agonist adrenoceptor agonists adrenomimetic adrenomimetics CHEBI:37886 adrenergic agonist adrenergic agonists ChEBI adrenergic receptor agonist ChEBI adrenoceptor agonists IUPHAR adrenomimetic ChEBI adrenomimetics ChEBI Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter. chebi_ontology adrenergic agents adrenergic drug adrenergic drugs adrenergic neuron agents adrenergics CHEBI:37962 adrenergic agent adrenergic agents ChEBI adrenergic drug ChEBI adrenergic drugs ChEBI adrenergic neuron agents ChEBI adrenergics ChEBI The stable isotope of aluminium with relative atomic mass 26.98153 and nuclear spin (5)/2. 0 [27Al] InChI=1S/Al/i1+0 XAGFODPZIPBFFR-IGMARMGPSA-N 26.982 26.98154 [27Al] aluminium-27 chebi_ontology (27)13Al (27)Al aluminium-27 aluminum, isotope of mass 27 aluminum-27 CHEBI:37968 aluminium-27 atom aluminium-27 IUPAC (27)13Al IUPAC (27)Al IUPAC aluminium-27 ChEBI aluminum, isotope of mass 27 ChEBI aluminum-27 ChEBI The radioactive isotope of aluminium with relative atomic mass 25.986892 and half-life of 717,000 years. 0 [26Al] InChI=1S/Al/i1-1 XAGFODPZIPBFFR-BJUDXGSMSA-N 25.987 25.98689 [26Al] CAS:14682-66-7 aluminium-26 chebi_ontology (26)13Al (26)Al aluminium-26 aluminum, isotope of mass 26 aluminum-26 CHEBI:37969 aluminium-26 atom CAS:14682-66-7 ChemIDplus aluminium-26 IUPAC (26)13Al IUPAC (26)Al IUPAC aluminium-26 ChEBI aluminum, isotope of mass 26 ChemIDplus aluminum-26 ChemIDplus The radioactive isotope of aluminium with relative atomic mass 27.981910 and half-life of 2.25 min. 0 [28Al] InChI=1S/Al/i1+1 XAGFODPZIPBFFR-OUBTZVSYSA-N 27.982 27.98191 [28Al] CAS:14999-04-3 aluminium-28 chebi_ontology (28)13Al (28)Al aluminium-28 aluminum, isotope of mass 28 aluminum-28 CHEBI:37970 aluminium-28 atom CAS:14999-04-3 ChemIDplus aluminium-28 IUPAC (28)13Al IUPAC (28)Al IUPAC aluminium-28 ChEBI aluminum, isotope of mass 28 ChemIDplus aluminum-28 ChemIDplus The stable isotope of phosphorus with relative atomic mass 30.973762 and nuclear spin (1)/2. 0 [31P] InChI=1S/P/i1+0 OAICVXFJPJFONN-IGMARMGPSA-N 30.974 30.97376 [31P] phosphorus-31 chebi_ontology (31)15P (31)P phosphorus-31 CHEBI:37971 phosphorus-31 atom phosphorus-31 IUPAC (31)15P IUPAC (31)P IUPAC phosphorus-31 ChEBI The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. 0 [32P] InChI=1S/P/i1+1 OAICVXFJPJFONN-OUBTZVSYSA-N 31.974 31.97391 [32P] CAS:14596-37-3 KEGG:C19162 phosphorus-32 chebi_ontology (32)15P (32)P Phosphorus, isotope of mass 32 phosphorus, isotope of mass 32 phosphorus-32 CHEBI:37972 phosphorus-32 atom CAS:14596-37-3 ChemIDplus CAS:14596-37-3 KEGG COMPOUND phosphorus-32 IUPAC (32)15P IUPAC (32)P IUPAC Phosphorus, isotope of mass 32 KEGG_COMPOUND phosphorus, isotope of mass 32 ChemIDplus phosphorus-32 ChEBI The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. 0 [33P] InChI=1S/P/i1+2 OAICVXFJPJFONN-NJFSPNSNSA-N 32.972 32.97173 [33P] CAS:15749-66-3 phosphorus-33 chebi_ontology (33)15P (33)P phosphorus, isotope of mass 33 phosphorus-33 CHEBI:37973 phosphorus-33 atom CAS:15749-66-3 ChemIDplus phosphorus-33 IUPAC (33)15P IUPAC (33)P IUPAC phosphorus, isotope of mass 33 ChemIDplus phosphorus-33 ChEBI The stable isotope of silicon with relative atomic mass 28.9764947, 4.683 atom percent natural abundancy, and nuclear spin (1)/2. 0 [29Si] InChI=1S/Si/i1+1 XUIMIQQOPSSXEZ-OUBTZVSYSA-N 28.976 28.97649 [29Si] silicon-29 chebi_ontology (29)14Si (29)Si silicon-29 CHEBI:37974 silicon-29 atom silicon-29 IUPAC (29)14Si IUPAC (29)Si IUPAC silicon-29 ChEBI The stable isotope of silicon with relative atomic mass 27.9769265. The most abundant (92.23 atom percent) isotope of naturally occurring silicon. 0 [28Si] InChI=1S/Si/i1+0 XUIMIQQOPSSXEZ-IGMARMGPSA-N 27.977 27.97693 [28Si] silicon-28 chebi_ontology (28)14Si (28)Si silicon-28 CHEBI:37975 silicon-28 atom silicon-28 IUPAC (28)14Si IUPAC (28)Si IUPAC silicon-28 ChEBI The stable isotope of silicon with relative atomic mass 29.9737702. The least abundant (3.09 atom percent) isotope of naturally occurring silicon. 0 [30Si] InChI=1S/Si/i1+2 XUIMIQQOPSSXEZ-NJFSPNSNSA-N 29.974 29.97377 [30Si] silicon-30 chebi_ontology (30)14Si (30)Si silicon-30 CHEBI:37976 silicon-30 atom silicon-30 IUPAC (30)14Si IUPAC (30)Si IUPAC silicon-30 ChEBI The radioactive isotope of silicon with relative atomic mass 30.975363, half-life of 2.62 hours and nuclear spin (3)/2. 0 [31Si] InChI=1S/Si/i1+3 XUIMIQQOPSSXEZ-AKLPVKDBSA-N 30.975 30.97536 [31Si] CAS:14276-49-4 silicon-31 chebi_ontology (31)14Si (31)Si silicon, isotope of mass 31 silicon-31 CHEBI:37977 silicon-31 atom CAS:14276-49-4 ChemIDplus silicon-31 IUPAC (31)14Si IUPAC (31)Si IUPAC silicon, isotope of mass 31 ChemIDplus silicon-31 ChEBI The radioactive isotope of silicon with relative atomic mass 31.974148. The longest-lived silicon radionuclide with half-life of 172 years. 0 [32Si] InChI=1S/Si/i1+4 XUIMIQQOPSSXEZ-RNFDNDRNSA-N 31.974 31.97415 [32Si] CAS:15092-72-5 silicon-32 chebi_ontology (32)14Si (32)Si silicon, isotope of mass 32 silicon-32 CHEBI:37978 silicon-32 atom CAS:15092-72-5 ChemIDplus silicon-32 IUPAC (32)14Si IUPAC (32)Si IUPAC silicon, isotope of mass 32 ChemIDplus silicon-32 ChEBI The stable isotope of sulfur with relative atomic mass 31.972071. The most abundant (95.02 atom percent) isotope of naturally occurring sulfur. 0 [32S] InChI=1S/S/i1+0 NINIDFKCEFEMDL-IGMARMGPSA-N 31.972 31.97207 [32S] CAS:13981-57-2 sulfur-32 chebi_ontology (32)16S (32)S sulfur, isotope of mass 32 sulfur-32 sulphur-32 CHEBI:37979 sulfur-32 atom CAS:13981-57-2 ChemIDplus sulfur-32 IUPAC (32)16S IUPAC (32)S IUPAC sulfur, isotope of mass 32 ChemIDplus sulfur-32 ChEBI sulphur-32 ChEBI The stable isotope of sulfur with relative atomic mass 32.9714585, 0.75 atom percent natural abundance, and nuclear spin (3)/2. 0 [33S] InChI=1S/S/i1+1 NINIDFKCEFEMDL-OUBTZVSYSA-N 32.971 32.97146 [33S] CAS:14257-58-0 sulfur-33 chebi_ontology (33)16S (33)S sulfur, isotope of mass 33 sulfur-33 sulphur-33 CHEBI:37980 sulfur-33 atom CAS:14257-58-0 ChemIDplus sulfur-33 IUPAC (33)16S IUPAC (33)S IUPAC sulfur, isotope of mass 33 ChemIDplus sulfur-33 ChEBI sulphur-33 ChEBI The stable isotope of sulfur with relative atomic mass 33.9678668 and 4.21 atom percent natural abundance. 0 [34S] InChI=1S/S/i1+2 NINIDFKCEFEMDL-NJFSPNSNSA-N 33.968 33.96787 [34S] CAS:13965-97-4 sulfur-34 chebi_ontology (34)16S (34)S sulfur, isotope of mass 34 sulfur-34 sulphur-34 CHEBI:37981 sulfur-34 atom CAS:13965-97-4 ChemIDplus sulfur-34 IUPAC (34)16S IUPAC (34)S IUPAC sulfur, isotope of mass 34 ChemIDplus sulfur-34 ChEBI sulphur-34 ChEBI The stable isotope of sulfur with relative atomic mass 35.9670809. The least abundant (0.02 atom percent) isotope of naturally occurring sulfur. 0 [36S] InChI=1S/S/i1+4 NINIDFKCEFEMDL-RNFDNDRNSA-N 35.967 35.96708 [36S] CAS:14682-80-5 sulfur-36 chebi_ontology (36)16S (36)S sulfur, isotope of mass 36 sulfur-36 sulphur-36 CHEBI:37982 sulfur-36 atom CAS:14682-80-5 ChemIDplus sulfur-36 IUPAC (36)16S IUPAC (36)S IUPAC sulfur, isotope of mass 36 ChemIDplus sulfur-36 ChEBI sulphur-36 ChEBI The radioactive isotope of sulfur with relative atomic mass 34.9690322 and nuclear spin (3)/2. The longest-lived sulfur radionuclide with half-life of 87.5 days. 0 [35S] InChI=1S/S/i1+3 NINIDFKCEFEMDL-AKLPVKDBSA-N 34.969 34.96903 [35S] CAS:15117-53-0 sulfur-35 chebi_ontology (35)16S (35)S sulfur, isotope of mass 35 sulfur-35 sulphur-35 CHEBI:37983 sulfur-35 atom CAS:15117-53-0 ChemIDplus sulfur-35 IUPAC (35)16S IUPAC (35)S IUPAC sulfur, isotope of mass 35 ChemIDplus sulfur-35 ChEBI sulphur-35 ChEBI The radioactive isotope of sulfur with relative atomic mass 36.9711257 and half-life of 5.05 min. 0 [37S] InChI=1S/S/i1+5 NINIDFKCEFEMDL-BKFZFHPZSA-N 36.971 36.97113 [37S] CAS:15753-06-7 sulfur-37 chebi_ontology (37)16S (37)S sulfur, isotope of mass 37 sulfur-37 sulphur-37 CHEBI:37984 sulfur-37 atom CAS:15753-06-7 ChemIDplus sulfur-37 IUPAC (37)16S IUPAC (37)S IUPAC sulfur, isotope of mass 37 ChemIDplus sulfur-37 ChEBI sulphur-37 ChEBI The radioactive isotope of sulfur with relative atomic mass 37.97116 and half-life of 170.3 min. 0 [38S] InChI=1S/S/i1+6 NINIDFKCEFEMDL-LZFNBGRKSA-N 37.971 37.97116 [38S] CAS:15759-21-4 sulfur-38 chebi_ontology (38)16S (38)S sulfur, isotope of mass 38 sulfur-38 sulphur-38 CHEBI:37985 sulfur-38 atom CAS:15759-21-4 ChemIDplus sulfur-38 IUPAC (38)16S IUPAC (38)S IUPAC sulfur, isotope of mass 38 ChemIDplus sulfur-38 ChEBI sulphur-38 ChEBI A compound composed of two or more pyrrole units. Beilstein:8538310 chebi_ontology PPys poly(pyrrole)s polypyrroles CHEBI:38077 polypyrrole Beilstein:8538310 Beilstein PPys ChEBI poly(pyrrole)s ChEBI polypyrroles ChEBI Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. chebi_ontology heterocyclic organonitrogen compounds organonitrogen heterocyclic compounds CHEBI:38101 organonitrogen heterocyclic compound heterocyclic organonitrogen compounds ChEBI organonitrogen heterocyclic compounds ChEBI CHEBI:25429 CHEBI:38075 chebi_ontology organic heteropolycyclic compounds CHEBI:38166 organic heteropolycyclic compound organic heteropolycyclic compounds ChEBI chebi_ontology polycyclic heteroarenes CHEBI:38180 polycyclic heteroarene polycyclic heteroarenes ChEBI Any drug used for its actions on cholinergic systems. Included here are agonists and antagonists, drugs that affect the life cycle of acetylcholine, and drugs that affect the survival of cholinergic neurons. chebi_ontology cholinergic agent cholinergic drugs cholinomimetic CHEBI:38323 cholinergic drug cholinergic agent ChEBI cholinergic drugs ChEBI cholinomimetic ChEBI Any drug that binds to and activates cholinergic receptors. chebi_ontology acetylcholine agonist acetylcholine agonists acetylcholine receptor agonist cholinergic agonists cholinomimetic cholinomimetics CHEBI:38324 cholinergic agonist acetylcholine agonist ChEBI acetylcholine agonists ChEBI acetylcholine receptor agonist IUPHAR cholinergic agonists ChEBI cholinomimetic ChEBI cholinomimetics ChEBI Any drug that binds to and activates a muscarinic cholinergic receptor. chebi_ontology muscarinic acetylcholine receptor agonist muscarinic agonists muscarinic cholinergic agonist muscarinic cholinergic agonists CHEBI:38325 muscarinic agonist muscarinic acetylcholine receptor agonist ChEBI muscarinic agonists ChEBI muscarinic cholinergic agonist ChEBI muscarinic cholinergic agonists ChEBI CHEBI:22503 CHEBI:24792 chebi_ontology aminoalkylindoles CHEBI:38631 aminoalkylindole aminoalkylindoles ChEBI organic sodium salt chebi_ontology organic sodium salts CHEBI:38700 organic sodium salt organic sodium salt ChEBI organic sodium salts ChEBI inorganic sodium salt Any dianion containing at least one carboxy group. carboxylic acid dianion chebi_ontology carboxylic acid dianions CHEBI:38716 carboxylic acid dianion carboxylic acid dianion ChEBI carboxylic acid dianions ChEBI An alkaloid containing an indole skeleton. CHEBI:24795 CHEBI:5901 KEGG:C06073 Wikipedia:Indole_alkaloid Indole alkaloid chebi_ontology indole alkaloids CHEBI:38958 indole alkaloid Indole alkaloid KEGG_COMPOUND indole alkaloids ChEBI A molecular entity capable of donating a hydron to an acceptor (Bronsted base). Bronsted acid chebi_ontology Bronsted-Saeure acide de Bronsted donneur d'hydron hydron donor CHEBI:39141 Bronsted acid Bronsted acid IUPAC Bronsted-Saeure ChEBI acide de Bronsted IUPAC donneur d'hydron IUPAC hydron donor IUPAC A molecular entity capable of accepting a hydron from a donor (Bronsted acid). Bronsted base chebi_ontology Bronsted-Base accepteur d'hydron base de Bronsted hydron acceptor CHEBI:39142 Bronsted base Bronsted base IUPAC Bronsted-Base ChEBI accepteur d'hydron IUPAC base de Bronsted IUPAC hydron acceptor IUPAC A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct. Lewis base chebi_ontology Lewis-Base base de Lewis donneur d'une paire d'electrons electron donor CHEBI:39144 Lewis base Lewis base IUPAC Lewis-Base ChEBI base de Lewis IUPAC donneur d'une paire d'electrons ChEBI electron donor ChEBI A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated. -1 H2O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1 NBIIXXVUZAFLBC-UHFFFAOYSA-M 96.98724 96.96962 [H]OP([O-])(=O)O[H] CHEBI:29137 CHEBI:39739 DrugBank:DB02831 Gmelin:1999 PDBeChem:2HP dihydrogen(tetraoxidophosphate)(1-) dihydrogenphosphate dihydrogentetraoxophosphate(1-) dihydrogentetraoxophosphate(V) dihydroxidodioxidophosphate(1-) chebi_ontology DIHYDROGENPHOSPHATE ION H2PO4(-) [PO2(OH)2](-) CHEBI:39745 dihydrogenphosphate Gmelin:1999 Gmelin dihydrogen(tetraoxidophosphate)(1-) IUPAC dihydrogenphosphate IUPAC dihydrogentetraoxophosphate(1-) IUPAC dihydrogentetraoxophosphate(V) IUPAC dihydroxidodioxidophosphate(1-) IUPAC DIHYDROGENPHOSPHATE ION PDBeChem H2PO4(-) IUPAC [PO2(OH)2](-) IUPAC -2 CO3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-2 BVKZGUZCCUSVTD-UHFFFAOYSA-L 60.00890 59.98584 [O-]C([O-])=O CHEBI:29201 CHEBI:41605 Beilstein:3600898 CAS:3812-32-6 Gmelin:1559 PDBeChem:CO3 carbonate trioxidocarbonate(2-) chebi_ontology CARBONATE ION CO3(2-) Karbonat [CO3](2-) CHEBI:41609 carbonate Beilstein:3600898 Beilstein CAS:3812-32-6 ChemIDplus Gmelin:1559 Gmelin carbonate IUPAC trioxidocarbonate(2-) IUPAC CARBONATE ION PDBeChem CO3(2-) ChEBI Karbonat ChEBI [CO3](2-) IUPAC 0 HO 17.00734 17.00274 *O[H] CHEBI:24706 CHEBI:43171 PDBeChem:OH HYDROXY GROUP hydroxy hydroxy group chebi_ontology -OH hydroxyl hydroxyl group CHEBI:43176 hydroxy group HYDROXY GROUP PDBeChem hydroxy IUPAC hydroxy group UniProt -OH IUPAC hydroxyl ChEBI hydroxyl group ChEBI A phosphate ion that is the conjugate base of dihydrogenphosphate. -2 HO4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-2 NBIIXXVUZAFLBC-UHFFFAOYSA-L 95.97930 95.96234 OP([O-])([O-])=O CHEBI:29139 CHEBI:43470 Gmelin:1998 MolBase:1628 PDBeChem:PI PDBeChem:PO4 hydrogen(tetraoxidophosphate)(2-) hydrogenphosphate hydrogentetraoxophosphate(2-) hydrogentetraoxophosphate(V) hydroxidotrioxidophosphate(2-) chebi_ontology HPO4(2-) HYDROGENPHOSPHATE ION INORGANIC PHOSPHATE GROUP [P(OH)O3](2-) [PO3(OH)](2-) hydrogen phosphate phosphate CHEBI:43474 hydrogenphosphate Gmelin:1998 Gmelin hydrogen(tetraoxidophosphate)(2-) IUPAC hydrogenphosphate IUPAC hydrogentetraoxophosphate(2-) IUPAC hydrogentetraoxophosphate(V) IUPAC hydroxidotrioxidophosphate(2-) IUPAC HPO4(2-) IUPAC HYDROGENPHOSPHATE ION PDBeChem INORGANIC PHOSPHATE GROUP PDBeChem [P(OH)O3](2-) MolBase [PO3(OH)](2-) IUPAC hydrogen phosphate ChEBI phosphate UniProt -1 HO4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-1 QAOWNCQODCNURD-UHFFFAOYSA-M 97.07154 96.96010 [H]OS([O-])(=O)=O CHEBI:29199 CHEBI:45693 Gmelin:2121 hydrogen(tetraoxidosulfate)(1-) hydrogensulfate hydrogensulfate(1-) hydrogentetraoxosulfate(1-) hydrogentetraoxosulfate(VI) hydroxidotrioxidosulfate(1-) chebi_ontology HSO4(-) HYDROGEN SULFATE [SO3(OH)](-) CHEBI:45696 hydrogensulfate Gmelin:2121 Gmelin hydrogen(tetraoxidosulfate)(1-) IUPAC hydrogensulfate IUPAC hydrogensulfate(1-) IUPAC hydrogentetraoxosulfate(1-) IUPAC hydrogentetraoxosulfate(VI) IUPAC hydroxidotrioxidosulfate(1-) IUPAC HSO4(-) IUPAC HYDROGEN SULFATE PDBeChem [SO3(OH)](-) IUPAC 0 O 15.99940 15.99491 O=* CHEBI:29353 CHEBI:44607 PDBeChem:O OXO GROUP oxo chebi_ontology =O CHEBI:46629 oxo group OXO GROUP PDBeChem oxo IUPAC =O IUPAC In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals'). mineral Minerale minerales minerals mineraux mineral A liquid that can dissolve other substances (solutes) without any change in their chemical composition. Wikipedia:Solvent chebi_ontology Loesungsmittel solvant solvents CHEBI:46787 solvent Loesungsmittel ChEBI solvant ChEBI solvents ChEBI 0 CHO2 45.01744 44.99765 *C(=O)O CHEBI:23025 CHEBI:41420 PDBeChem:FMT CARBOXY GROUP carboxy chebi_ontology -C(O)OH -CO2H -COOH carboxyl group CHEBI:46883 carboxy group CARBOXY GROUP PDBeChem carboxy IUPAC -C(O)OH IUPAC -CO2H ChEBI -COOH IUPAC carboxyl group ChEBI Any carboxylic ester where the carboxylic acid component is acetic acid. 0 C2H3O2R 59.04400 59.01330 CC(=O)O[*] CHEBI:13244 CHEBI:13799 CHEBI:22189 CHEBI:2406 KEGG:C01883 Wikipedia:Acetate#Esters chebi_ontology Acetic ester Acetyl ester acetate acetate esters acetates acetyl esters an acetyl ester CHEBI:47622 acetate ester Acetic ester KEGG_COMPOUND Acetyl ester KEGG_COMPOUND acetate ChEBI acetate esters ChEBI acetates ChEBI acetyl esters ChEBI an acetyl ester UniProt Any steroid substituted by at least one carboxy group. chebi_ontology steroid acids CHEBI:47891 steroid acid steroid acids ChEBI chebi_ontology Schwefeloxide oxides of sulfur sulfur oxides CHEBI:48154 sulfur oxide Schwefeloxide ChEBI oxides of sulfur ChEBI sulfur oxides ChEBI A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds. polar solvent chebi_ontology polar solvents CHEBI:48354 polar solvent polar solvent IUPAC polar solvents ChEBI A polar solvent that is capable of acting as a hydron (proton) donor. protogenic solvent chebi_ontology CHEBI:48356 protic solvent protogenic solvent IUPAC Any drug that acts on an alpha-adrenergic receptor. chebi_ontology alpha-adrenergic drugs CHEBI:48539 alpha-adrenergic drug alpha-adrenergic drugs ChEBI Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own. agonist chebi_ontology agonista agoniste agonists CHEBI:48705 agonist agonist IUPAC agonista ChEBI agoniste ChEBI agonists ChEBI 0 Ar InChI=1S/Ar XKRFYHLGVUSROY-UHFFFAOYSA-N 39.94800 39.96238 [Ar] CHEBI:33311 CAS:7440-37-1 WebElements:Ar argon chebi_ontology 18Ar Ar argon CHEBI:49475 argon atom CAS:7440-37-1 ChemIDplus argon IUPAC 18Ar IUPAC Ar IUPAC argon ChEBI A metallic element predicted as eka-aluminium by Mendeleev in 1870 and discovered by Paul-Emile Lecoq de Boisbaudran in 1875. Named in honour of France (Latin Gallia) and perhaps also from the Latin gallus cock, a translation of Lecoq. 0 Ga InChI=1S/Ga GYHNNYVSQQEPJS-UHFFFAOYSA-N 69.72300 68.92557 [Ga] CHEBI:33326 CHEBI:49630 CAS:7440-55-3 WebElements:Ga gallium chebi_ontology 31Ga Ga galio gallium CHEBI:49631 gallium atom CAS:7440-55-3 ChemIDplus CAS:7440-55-3 NIST Chemistry WebBook gallium IUPAC 31Ga IUPAC Ga IUPAC galio ChEBI gallium ChEBI 0 H InChI=1S/H YZCKVEUIGOORGS-UHFFFAOYSA-N 1.00794 1.00783 [H] CHEBI:24634 CHEBI:49636 WebElements:H hydrogen chebi_ontology 1H H Wasserstoff hidrogeno hydrogen hydrogene CHEBI:49637 hydrogen atom hydrogen IUPAC 1H IUPAC H IUPAC Wasserstoff ChEBI hidrogeno ChEBI hydrogen ChEBI hydrogene ChEBI 0 Ho InChI=1S/Ho KJZYNXUDTRRSPN-UHFFFAOYSA-N 164.93032 164.93033 [Ho] CHEBI:33378 CHEBI:49647 CAS:7440-60-0 Gmelin:16291 WebElements:Ho holmium chebi_ontology 67Ho Ho holmio holmium CHEBI:49648 holmium atom CAS:7440-60-0 ChemIDplus CAS:7440-60-0 NIST Chemistry WebBook Gmelin:16291 Gmelin holmium IUPAC 67Ho IUPAC Ho IUPAC holmio ChEBI holmium ChEBI 0 Ir InChI=1S/Ir GKOZUEZYRPOHIO-UHFFFAOYSA-N 192.21700 192.96292 [Ir] CHEBI:33360 CHEBI:49665 CAS:7439-88-5 WebElements:Ir iridium chebi_ontology 77Ir Ir iridio iridium CHEBI:49666 iridium atom CAS:7439-88-5 ChemIDplus CAS:7439-88-5 NIST Chemistry WebBook iridium IUPAC 77Ir IUPAC Ir IUPAC iridio ChEBI iridium ChEBI 0 Kr InChI=1S/Kr DNNSSWSSYDEUBZ-UHFFFAOYSA-N 83.80000 83.91150 [Kr] CHEBI:33312 CAS:7439-90-9 WebElements:Kr krypton chebi_ontology 36Kr Kr cripton kripton krypton CHEBI:49696 krypton atom CAS:7439-90-9 ChemIDplus CAS:7439-90-9 NIST Chemistry WebBook krypton IUPAC 36Kr IUPAC Kr IUPAC cripton ChEBI kripton ChEBI krypton ChEBI 0 Pr InChI=1S/Pr PUDIUYLPXJFUGB-UHFFFAOYSA-N 140.90765 140.90766 [Pr] CHEBI:33370 CHEBI:49827 CAS:7440-10-0 WebElements:Pr praseodymium chebi_ontology 59Pr Pr Praseodym praseodimio praseodyme praseodymium CHEBI:49828 praseodymium atom CAS:7440-10-0 ChemIDplus CAS:7440-10-0 NIST Chemistry WebBook praseodymium IUPAC 59Pr IUPAC Pr IUPAC Praseodym ChEBI praseodimio ChEBI praseodyme ChEBI praseodymium ChEBI 0 Re InChI=1S/Re WUAPFZMCVAUBPE-UHFFFAOYSA-N 186.20700 186.95575 [Re] CHEBI:33354 CHEBI:49879 CAS:7440-15-5 WebElements:Re rhenium chebi_ontology 75Re Re Rhenium renio rhenium CHEBI:49882 rhenium atom CAS:7440-15-5 ChemIDplus CAS:7440-15-5 NIST Chemistry WebBook rhenium IUPAC 75Re IUPAC Re ChEBI Rhenium ChEBI renio ChEBI rhenium ChEBI 0 Xe InChI=1S/Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N 131.29000 131.90416 [Xe] CHEBI:32305 CAS:7440-63-3 Gmelin:16318 KEGG:C13373 WebElements:Xe xenon chebi_ontology 54Xe Xe Xenon xenon CHEBI:49957 xenon atom CAS:7440-63-3 ChemIDplus CAS:7440-63-3 KEGG COMPOUND CAS:7440-63-3 NIST Chemistry WebBook Gmelin:16318 Gmelin xenon IUPAC 54Xe IUPAC Xe IUPAC Xenon ChEBI Xenon KEGG_COMPOUND xenon ChEBI A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. chebi_ontology organic amino compounds CHEBI:50047 organic amino compound organic amino compounds ChEBI A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. 0 [51Cr] InChI=1S/Cr/i1-1 VYZAMTAEIAYCRO-BJUDXGSMSA-N 50.945 50.94477 [51Cr] CAS:14392-02-0 chromium-51 chebi_ontology (51)24Cr (51)Cr 51Cr Chromium, isotope of mass 51 CHEBI:50076 chromium-51 CAS:14392-02-0 ChemIDplus chromium-51 IUPAC (51)24Cr IUPAC (51)Cr IUPAC 51Cr ChemIDplus Chromium, isotope of mass 51 ChemIDplus Any anion formed by loss of a proton from a steroid acid. chebi_ontology steroid acid anions CHEBI:50160 steroid acid anion steroid acid anions ChEBI chebi_ontology canonical nucleotide residues CHEBI:50297 canonical nucleotide residue canonical nucleotide residues ChEBI chebi_ontology canonical deoxyribonucleotide residues CHEBI:50298 canonical deoxyribonucleotide residue canonical deoxyribonucleotide residues ChEBI chebi_ontology canonical ribonucleotide residues CHEBI:50299 canonical ribonucleotide residue canonical ribonucleotide residues ChEBI chebi_ontology CHEBI:50312 onium compound Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. onium cations chebi_ontology onium cations onium ion onium ions CHEBI:50313 onium cation onium cations IUPAC onium cations ChEBI onium ion ChEBI onium ions ChEBI chebi_ontology nucleotide residues CHEBI:50319 nucleotide residue nucleotide residues ChEBI chebi_ontology nucleoside residues CHEBI:50320 nucleoside residue nucleoside residues ChEBI Drug used to cause constriction of the blood vessels. chebi_ontology CHEBI:50514 vasoconstrictor agent Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 chebi_ontology organic compounds organic entity organic molecular entities CHEBI:50860 organic molecular entity organic compounds ChEBI organic entity ChEBI organic molecular entities ChEBI A role is particular behaviour which a material entity may exhibit. chebi_ontology CHEBI:50906 role A poison that interferes with the functions of the nervous system. CHEBI:50911 Wikipedia:Neurotoxin chebi_ontology agente neurotoxico nerve poison nerve poisons neurotoxic agent neurotoxic agents neurotoxicant neurotoxins CHEBI:50910 neurotoxin agente neurotoxico ChEBI nerve poison ChEBI nerve poisons ChEBI neurotoxic agent ChEBI neurotoxic agents ChEBI neurotoxicant ChEBI neurotoxins ChEBI A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group. chebi_ontology primary amino compounds CHEBI:50994 primary amino compound primary amino compounds ChEBI A role played by the molecular entity or part thereof within a chemical context. chebi_ontology CHEBI:51086 chemical role CHEBI:25556 CHEBI:7594 KEGG:C06061 chebi_ontology Nitrogenous compounds nitrogen compounds nitrogen molecular entities CHEBI:51143 nitrogen molecular entity Nitrogenous compounds KEGG_COMPOUND nitrogen compounds ChEBI nitrogen molecular entities ChEBI An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case. chebi_ontology dipolar compounds CHEBI:51151 dipolar compound dipolar compounds ChEBI Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s). chebi_ontology organodiyl groups CHEBI:51422 organodiyl group organodiyl groups ChEBI chebi_ontology CHEBI:51446 organic divalent group chebi_ontology CHEBI:51447 organic univalent group chebi_ontology organic polycyclic compounds CHEBI:51958 organic polycyclic compound organic polycyclic compounds ChEBI A biological role played by the molecular entity or part thereof within a biochemical context. chebi_ontology CHEBI:52206 biochemical role A role played by the molecular entity or part thereof which causes the development of a pathological process. chebi_ontology etiopathogenetic agent etiopathogenetic role CHEBI:52209 aetiopathogenetic role etiopathogenetic agent ChEBI etiopathogenetic role ChEBI A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties. chebi_ontology CHEBI:52210 pharmacological role chebi_ontology CHEBI:52211 physiological role Any substance introduced into a living organism with therapeutic or diagnostic purpose. CHEBI:33293 CHEBI:33294 chebi_ontology farmaco medicament pharmaceuticals CHEBI:52217 pharmaceutical farmaco ChEBI medicament ChEBI pharmaceuticals ChEBI The stable isotope of tin with relative atomic mass 118.903311, 8.59 atom percent natural abundance and nuclear spin (1)/2. 0 [119Sn] InChI=1S/Sn/i1+0 ATJFFYVFTNAWJD-IGMARMGPSA-N 118.903 118.90331 [119Sn] tin-119 chebi_ontology (119)50Sn (119)Sn tin-119 CHEBI:52230 tin-119 atom tin-119 IUPAC (119)50Sn IUPAC (119)Sn IUPAC tin-119 ChEBI The stable isotope of tin with relative atomic mass 119.902199 and 32.58 atom percent natural abundance. 0 [120Sn] InChI=1S/Sn/i1+1 ATJFFYVFTNAWJD-OUBTZVSYSA-N 119.902 119.90220 [120Sn] tin-120 chebi_ontology (120)50Sn (120)Sn tin-120 CHEBI:52231 tin-120 atom tin-120 IUPAC (120)50Sn IUPAC (120)Sn IUPAC tin-120 ChEBI The stable isotope of tin with relative atomic mass 117.901609 and 24.22 atom percent natural abundance. 0 [118Sn] InChI=1S/Sn/i1-1 ATJFFYVFTNAWJD-BJUDXGSMSA-N 117.902 117.90161 [118Sn] tin-118 chebi_ontology (118)50Sn (118)Sn tin-118 CHEBI:52232 tin-118 atom tin-118 IUPAC (118)50Sn IUPAC (118)Sn IUPAC tin-118 ChEBI The stable isotope of tin with relative atomic mass 115.901747 and 14.54 atom percent natural abundance. 0 [116Sn] InChI=1S/Sn/i1-3 ATJFFYVFTNAWJD-OIOBTWANSA-N 115.902 115.90174 [116Sn] tin-116 chebi_ontology (116)50Sn (116)Sn tin-116 CHEBI:52233 tin-116 atom tin-116 IUPAC (116)50Sn IUPAC (116)Sn IUPAC tin-116 ChEBI The stable isotope of tin with relative atomic mass 116.902956, 7.68 atom percent natural abundance and nuclear spin (1)/2. 0 [117Sn] InChI=1S/Sn/i1-2 ATJFFYVFTNAWJD-YPZZEJLDSA-N 116.903 116.90295 [117Sn] tin-117 chebi_ontology (117)50Sn (117)Sn tin-117 CHEBI:52234 tin-117 atom tin-117 IUPAC (117)50Sn IUPAC (117)Sn IUPAC tin-117 ChEBI The stable isotope of tin with relative atomic mass 114.903348, 0.34 atom percent natural abundance and nuclear spin (1)/2. 0 [115Sn] InChI=1S/Sn/i1-4 ATJFFYVFTNAWJD-AHCXROLUSA-N 114.903 114.90334 [115Sn] tin-115 chebi_ontology (115)50Sn (115)Sn tin-115 CHEBI:52235 tin-115 atom tin-115 IUPAC (115)50Sn IUPAC (115)Sn IUPAC tin-115 ChEBI The stable isotope of boron with relative atomic mass 11.009306, 80.1 atom percent natural abundance and nuclear spin 3/2. 0 [11B] InChI=1S/B/i1+0 ZOXJGFHDIHLPTG-IGMARMGPSA-N 11.009 11.00930 [11B] boron-11 chebi_ontology (11)5B (11)B CHEBI:52451 boron-11 atom boron-11 IUPAC (11)5B IUPAC (11)B IUPAC The stable isotope of tellurium with relative atomic mass 124.904425, 71.4 atom percent natural abundance and nuclear spin 1/2. 0 [125Te] InChI=1S/Te/i1-3 PORWMNRCUJJQNO-OIOBTWANSA-N 124.904 124.90443 [125Te] tellurium-125 chebi_ontology (125)52Te (125)Te tellurium-125 CHEBI:52452 tellurium-125 atom tellurium-125 IUPAC (125)52Te IUPAC (125)Te IUPAC tellurium-125 ChEBI The stable isotope of xenon with relative atomic mass 128.904780, 26.4 atom percent natural abundance and nuclear spin 1/2. 0 [129Xe] InChI=1S/Xe/i1-2 FHNFHKCVQCLJFQ-YPZZEJLDSA-N 128.905 128.90478 [129Xe] xenon-129 chebi_ontology (129)54Xe (129)Xe xenon-129 CHEBI:52453 xenon-129 atom xenon-129 IUPAC (129)54Xe IUPAC (129)Xe IUPAC xenon-129 ChEBI A stable isotope of selenium with relative atomic mass 76.919915, 7.60 atom percent natural abundance and nuclear spin 1/2. 0 [77Se] InChI=1S/Se/i1-2 BUGBHKTXTAQXES-YPZZEJLDSA-N 76.920 76.91991 [77Se] Chemspider:9507361 PMID:16158304 PMID:23159557 PMID:25848959 PMID:25923042 PMID:27129100 PMID:30828921 PMID:32453871 PMID:34153173 ((77)Se)selenium chebi_ontology (77)34Se (77)Se Se-77 selenium, isotope of mass 77 selenium-(77)Se selenium-77 CHEBI:52457 selenium-77 atom PMID:16158304 Europe PMC PMID:23159557 Europe PMC PMID:25848959 Europe PMC PMID:25923042 Europe PMC PMID:27129100 Europe PMC PMID:30828921 Europe PMC PMID:32453871 Europe PMC PMID:34153173 Europe PMC ((77)Se)selenium IUPAC (77)34Se IUPAC (77)Se IUPAC Se-77 ChEBI selenium, isotope of mass 77 ChEBI selenium-(77)Se ChEBI selenium-77 ChEBI The stable isotope of lithium with relative atomic mass 7.016004, 92.5 atom percent natural abundance and nuclear spin 3/2. 0 [7Li] InChI=1S/Li/i1+0 WHXSMMKQMYFTQS-IGMARMGPSA-N 7.016 7.01600 [7Li] lithium-7 chebi_ontology (7)3Li (7)Li lithium-7 CHEBI:52458 lithium-7 atom lithium-7 IUPAC (7)3Li IUPAC (7)Li IUPAC lithium-7 ChEBI The stable isotope of rubidium with relative atomic mass 86.909184, 27.9 atom percent natural abundance and nuclear spin 3/2. 0 [87Rb] InChI=1S/Rb/i1+2 IGLNJRXAVVLDKE-NJFSPNSNSA-N 86.909 86.90918 [87Rb] rubidium-87 chebi_ontology (87)37Rb (87)Rb rubidium-87 CHEBI:52459 rubidium-87 atom rubidium-87 IUPAC (87)37Rb IUPAC (87)Rb IUPAC rubidium-87 ChEBI The stable isotope of niobium with relative atomic mass 92.906378, 100 atom percent natural abundance and nuclear spin 9/2. 0 [93Nb] InChI=1S/Nb/i1+0 GUCVJGMIXFAOAE-IGMARMGPSA-N 92.906 92.90637 [93Nb] niobium-93 chebi_ontology (93)41Nb (93)Nb niobium-93 CHEBI:52460 niobium-93 atom niobium-93 IUPAC (93)41Nb IUPAC (93)Nb IUPAC niobium-93 ChEBI The stable isotope of niobium with relative atomic mass 182.950225, 14.3 atom percent natural abundance and nuclear spin 1/2. 0 [183W] InChI=1S/W/i1-1 WFKWXMTUELFFGS-BJUDXGSMSA-N 182.950 182.95022 [183W] tungsten-183 chebi_ontology (183)74W (183)W CHEBI:52462 tungsten-183 tungsten-183 IUPAC (183)74W IUPAC (183)W IUPAC The stable isotope of cadmium with relative atomic mass 110.904182, 12.8 atom percent natural abundance and nuclear spin 1/2. 0 [111Cd] InChI=1S/Cd/i1-1 BDOSMKKIYDKNTQ-BJUDXGSMSA-N 110.904 110.90418 [111Cd] cadmium-111 chebi_ontology (111)48Cd (111)Cd CHEBI:52619 cadmium-111 cadmium-111 IUPAC (111)48Cd IUPAC (111)Cd IUPAC The isotope of cadmium with relative atomic mass 112.904401, 12.2 atom percent natural abundance and nuclear spin 1/2. 0 [113Cd] InChI=1S/Cd/i1+1 BDOSMKKIYDKNTQ-OUBTZVSYSA-N 112.904 112.90441 [113Cd] cadmium-113 chebi_ontology (113)48Cd (113)Cd CHEBI:52620 cadmium-113 cadmium-113 IUPAC (113)48Cd IUPAC (113)Cd IUPAC The stable isotope of lithium with relative atomic mass 6.015122, 7.5 atom percent natural abundance and nuclear spin 1. 0 [6Li] InChI=1S/Li/i1-1 WHXSMMKQMYFTQS-BJUDXGSMSA-N 6.015 6.01512 [6Li] lithium-6 chebi_ontology (6)3Li (6)Li lithium-6 CHEBI:52621 lithium-6 atom lithium-6 IUPAC (6)3Li IUPAC (6)Li IUPAC lithium-6 ChEBI The stable isotope of yttrium with relative atomic mass 88.905848, 100 atom percent natural abundance and nuclear spin 1/2. 0 [89Y] InChI=1S/Y/i1+0 VWQVUPCCIRVNHF-IGMARMGPSA-N 88.906 88.90584 [89Y] yttrium-89 chebi_ontology (89)39Y (89)Y yttrium-89 CHEBI:52622 yttrium-89 atom yttrium-89 IUPAC (89)39Y IUPAC (89)Y IUPAC yttrium-89 ChEBI The stable isotope of iron with relative atomic mass 56.935399, 2.1 atom percent natural abundance and nuclear spin 1/2. 0 [57Fe] InChI=1S/Fe/i1+1 XEEYBQQBJWHFJM-OUBTZVSYSA-N 56.935 56.93539 [57Fe] iron-57 chebi_ontology (57)26Fe (57)Fe CHEBI:52623 iron-57 atom iron-57 IUPAC (57)26Fe IUPAC (57)Fe IUPAC The stable isotope of antimony with relative atomic mass 120.903818, 57.2 atom percent natural abundance and nuclear spin 5/2. 0 [121Sb] InChI=1S/Sb/i1-1 WATWJIUSRGPENY-BJUDXGSMSA-N 120.904 120.90381 [121Sb] antimony-121 chebi_ontology (121)51Sb (121)Sb antimony-121 CHEBI:52624 antimony-121 atom antimony-121 IUPAC (121)51Sb IUPAC (121)Sb IUPAC antimony-121 ChEBI inorganic hydroxy compound The stable isotope of antimony with relative atomic mass 122.904216, 42.8 atom percent natural abundance and nuclear spin 7/2. 0 [123Sb] InChI=1S/Sb/i1+1 WATWJIUSRGPENY-OUBTZVSYSA-N 122.904 122.90421 [123Sb] antimony-123 chebi_ontology (123)51Sb (123)Sb antimony-123 CHEBI:52626 antimony-123 atom antimony-123 IUPAC (123)51Sb IUPAC (123)Sb IUPAC antimony-123 ChEBI The stable isotope of lanthanum with relative atomic mass 138.906348, 99.9 atom percent natural abundance and nuclear spin 7/2. 0 [139La] InChI=1S/La/i1+0 FZLIPJUXYLNCLC-IGMARMGPSA-N 138.906 138.90636 [139La] lanthanum-139 chebi_ontology (139)57La (139)La lanthanum-139 CHEBI:52627 lanthanum-139 atom lanthanum-139 IUPAC (139)57La IUPAC (139)La IUPAC lanthanum-139 ChEBI The stable isotope of iodine with relative atomic mass 126.904468, 100 atom percent natural abundance and nuclear spin 5/2. 0 [127I] InChI=1S/I/i1+0 ZCYVEMRRCGMTRW-IGMARMGPSA-N 126.904 126.90447 [127I] iodine-127 chebi_ontology (127)53I (127)I iodine-127 CHEBI:52631 iodine-127 atom iodine-127 IUPAC (127)53I IUPAC (127)I IUPAC iodine-127 ChEBI The stable isotope of potassium with relative atomic mass 38.963707, 93.3 atom percent natural abundance and nuclear spin 3/2. 0 [39K] InChI=1S/K/i1+0 ZLMJMSJWJFRBEC-IGMARMGPSA-N 38.964 38.96371 [39K] potassium-39 chebi_ontology (39)19K (39)K potassium-39 CHEBI:52632 potassium-39 atom potassium-39 IUPAC (39)19K IUPAC (39)K IUPAC potassium-39 ChEBI The stable isotope of molybdenum with relative atomic mass 94.905842, 15.9 atom percent natural abundance and nuclear spin 5/2. 0 [95Mo] InChI=1S/Mo/i1-1 ZOKXTWBITQBERF-BJUDXGSMSA-N 94.906 94.90584 [95Mo] molybdenum-95 chebi_ontology (95)42Mo (95)Mo CHEBI:52633 molybdenum-95 molybdenum-95 IUPAC (95)42Mo IUPAC (95)Mo IUPAC The stable isotope of sodium with relative atomic mass 22.989770, 100 atom percent natural abundance and nuclear spin 3/2. 0 [23Na] InChI=1S/Na/i1+0 KEAYESYHFKHZAL-IGMARMGPSA-N 22.990 22.98977 [23Na] sodium-23 chebi_ontology (23)11Na (23)Na sodium-23 CHEBI:52634 sodium-23 atom sodium-23 IUPAC (23)11Na IUPAC (23)Na IUPAC sodium-23 ChEBI The stable isotope of scandium with relative atomic mass 44.955910, 100 atom percent natural abundance and nuclear spin 7/2. 0 [45Sc] InChI=1S/Sc/i1+0 SIXSYDAISGFNSX-IGMARMGPSA-N 44.956 44.95591 [45Sc] scandium-45 chebi_ontology (45)21Sc (45)Sc scandium-45 CHEBI:52635 scandium-45 atom scandium-45 IUPAC (45)21Sc IUPAC (45)Sc IUPAC scandium-45 ChEBI The isotope of iodine with relative atomic mass 128.904988, and nuclear spin 7/2. 0 [129I] InChI=1S/I/i1+2 ZCYVEMRRCGMTRW-NJFSPNSNSA-N 128.905 128.90499 [129I] iodine-129 chebi_ontology (129)53I (129)I iodine-129 CHEBI:52636 iodine-129 atom iodine-129 IUPAC (129)53I IUPAC (129)I IUPAC iodine-129 ChEBI The stable isotope of europium with relative atomic mass 150.919846, 47.8 atom percent natural abundance and nuclear spin 5/2. 0 [151Eu] InChI=1S/Eu/i1-1 OGPBJKLSAFTDLK-BJUDXGSMSA-N 150.920 150.91986 [151Eu] europium-151 chebi_ontology (151)63Eu (151)Eu europium-151 CHEBI:52637 europium-151 atom europium-151 IUPAC (151)63Eu IUPAC (151)Eu IUPAC europium-151 ChEBI The stable isotope of bromine with relative atomic mass 78.918338, 50.69 atom percent natural abundance and nuclear spin 3/2. 0 [79Br] InChI=1S/Br/i1-1 WKBOTKDWSSQWDR-BJUDXGSMSA-N 78.918 78.91834 [79Br] chebi_ontology (79)35Br (79)Br bromine-79 CHEBI:52743 bromine-79 atom (79)35Br IUPAC (79)Br IUPAC bromine-79 ChEBI The stable isotope of germanium with relative atomic mass 72.923459, 7.73 atom percent natural abundance and nuclear spin 9/2. 0 [73Ge] InChI=1S/Ge/i1+0 GNPVGFCGXDBREM-IGMARMGPSA-N 72.923 72.92346 [73Ge] chebi_ontology (73)32Ge (73)Ge germanium-73 CHEBI:52758 germanium-73 atom (73)32Ge IUPAC (73)Ge IUPAC germanium-73 ChEBI The stable isotope of magnesium with relative atomic mass 24.985837, 10.0 atom percent natural abundance and nuclear spin 5/2. 0 [25Mg] InChI=1S/Mg/i1+1 FYYHWMGAXLPEAU-OUBTZVSYSA-N 24.986 24.98584 [25Mg] chebi_ontology (25)12Mg (25)Mg magnesium-25 CHEBI:52763 magnesium-25 atom (25)12Mg IUPAC (25)Mg IUPAC magnesium-25 ChEBI An organic group that consists of a closed ring. It may be a substituent or a skeleton. chebi_ontology cyclic organic groups CHEBI:52845 cyclic organic group cyclic organic groups ChEBI The biological role played by a material entity when bound by a receptor of the adaptive immune system. Specific site on an antigen to which an antibody binds. chebi_ontology antigenic determinant epitope function epitope role CHEBI:53000 epitope antigenic determinant ChEBI epitope function ChEBI epitope role ChEBI A polymer carrying multiple negative charges. chebi_ontology polyanion polyanions CHEBI:53309 polyanionic macromolecule polyanion ChEBI polyanions SUBMITTER A macromolecule containing ionic groups. chebi_ontology ionic polymer polyionic macromolecule CHEBI:53368 ionic macromolecule ionic polymer ChEBI polyionic macromolecule ChEBI A 29-amino acid peptide hormone consisting of His, Ser, Gln, Gly, Thr, Phe, Thr, Ser, Asp, Tyr, Ser, Lys, Tyr, Leu, Asp, Ser, Arg, Arg, Ala, Gln, Asp, Phe, Val, Gln, Trp, Leu, Met, Asn and Thr residues joined in sequence. 0 C153H225N43O49S InChI=1S/C153H225N43O49S/c1-72(2)52-97(133(226)176-96(47-51-246-11)132(225)184-104(60-115(159)209)143(236)196-123(78(10)203)151(244)245)179-137(230)103(58-83-64-167-89-29-19-18-28-87(83)89)183-131(224)95(43-46-114(158)208)177-148(241)120(74(5)6)194-141(234)101(54-79-24-14-12-15-25-79)182-138(231)105(61-117(211)212)185-130(223)94(42-45-113(157)207)171-124(217)75(7)170-127(220)91(31-22-49-165-152(160)161)172-128(221)92(32-23-50-166-153(162)163)174-146(239)110(69-199)191-140(233)107(63-119(215)216)186-134(227)98(53-73(3)4)178-135(228)99(56-81-33-37-85(204)38-34-81)180-129(222)90(30-20-21-48-154)173-145(238)109(68-198)190-136(229)100(57-82-35-39-86(205)40-36-82)181-139(232)106(62-118(213)214)187-147(240)111(70-200)192-150(243)122(77(9)202)195-142(235)102(55-80-26-16-13-17-27-80)188-149(242)121(76(8)201)193-116(210)66-168-126(219)93(41-44-112(156)206)175-144(237)108(67-197)189-125(218)88(155)59-84-65-164-71-169-84/h12-19,24-29,33-40,64-65,71-78,88,90-111,120-123,167,197-205H,20-23,30-32,41-63,66-70,154-155H2,1-11H3,(H2,156,206)(H2,157,207)(H2,158,208)(H2,159,209)(H,164,169)(H,168,219)(H,170,220)(H,171,217)(H,172,221)(H,173,238)(H,174,239)(H,175,237)(H,176,226)(H,177,241)(H,178,228)(H,179,230)(H,180,222)(H,181,232)(H,182,231)(H,183,224)(H,184,225)(H,185,223)(H,186,227)(H,187,240)(H,188,242)(H,189,218)(H,190,229)(H,191,233)(H,192,243)(H,193,210)(H,194,234)(H,195,235)(H,196,236)(H,211,212)(H,213,214)(H,215,216)(H,244,245)(H4,160,161,165)(H4,162,163,166)/t75-,76+,77+,78+,88-,90-,91-,92-,93-,94-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,107-,108-,109-,110-,111-,120-,121-,122-,123-/m0/s1 MASNOZXLGMXCHN-ZLPAWPGGSA-N 3482.74700 3480.61570 CSCC[C@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(O)=O)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](C)NC(=O)[C@H](CCCNC(N)=N)NC(=O)[C@H](CCCNC(N)=N)NC(=O)[C@H](CO)NC(=O)[C@H](CC(O)=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CO)NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)[C@H](CC(O)=O)NC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](NC(=O)CNC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@@H](N)Cc1cnc[nH]1)[C@@H](C)O)[C@@H](C)O)C(C)C)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H]([C@@H](C)O)C(O)=O CAS:16941-32-5 CAS:9007-92-5 DrugBank:DB00040 Drug_Central:2994 KEGG:C01501 KEGG:D00116 PMID:21940356 PMID:22014161 PMID:22154917 PMID:22166985 PMID:22167521 PMID:22214853 PMID:22227186 PMID:22286080 PMID:22294753 PMID:22318544 PMID:22334714 PMID:22399501 PMID:22438981 PMID:22454291 Reaxys:13191924 Wikipedia:Glucagon Glucagon L-histidyl-L-seryl-L-glutaminylglycyl-L-threonyl-L-phenylalanyl-L-threonyl-L-seryl-L-alpha-aspartyl-L-tyrosyl-L-seryl-L-lysyl-L-tyrosyl-L-leucyl-L-alpha-aspartyl-L-seryl-L-arginyl-L-arginyl-L-alanyl-L-glutaminyl-L-alpha-aspartyl-L-phenylalanyl-L-valyl-L-glutaminyl-L-tryptophyl-L-leucyl-L-methionyl-L-asparaginyl-L-threonine chebi_ontology Glucagone HSQGTFTSDYSKYLDSRRAQDFVQWLMNT His-Ser-Gln-Gly-Thr-Phe-Thr-Ser-Asp-Tyr-Ser-Lys-Tyr-Leu-Asp-Ser-Arg-Arg-Ala-Gln-Asp-Phe-Val-Gln-Trp-Leu-Met-Asn-Thr His-ser-glu(nh2)-gly-thr-phe-thr-ser-asp-tyr-ser-lys-tyr-leu-asp-ser-arg-arg-ala-glu(NH2)-asp-phe-val-glu(NH2)-trp-leu-met-asp(NH2)-thr glucagon glucagonum CHEBI:5391 glucagon CAS:16941-32-5 ChemIDplus CAS:9007-92-5 ChemIDplus CAS:9007-92-5 KEGG COMPOUND Drug_Central:2994 DrugCentral PMID:21940356 Europe PMC PMID:22014161 Europe PMC PMID:22154917 Europe PMC PMID:22166985 Europe PMC PMID:22167521 Europe PMC PMID:22214853 Europe PMC PMID:22227186 Europe PMC PMID:22286080 Europe PMC PMID:22294753 Europe PMC PMID:22318544 Europe PMC PMID:22334714 Europe PMC PMID:22399501 Europe PMC PMID:22438981 Europe PMC PMID:22454291 Europe PMC Reaxys:13191924 Reaxys Glucagon KEGG_COMPOUND L-histidyl-L-seryl-L-glutaminylglycyl-L-threonyl-L-phenylalanyl-L-threonyl-L-seryl-L-alpha-aspartyl-L-tyrosyl-L-seryl-L-lysyl-L-tyrosyl-L-leucyl-L-alpha-aspartyl-L-seryl-L-arginyl-L-arginyl-L-alanyl-L-glutaminyl-L-alpha-aspartyl-L-phenylalanyl-L-valyl-L-glutaminyl-L-tryptophyl-L-leucyl-L-methionyl-L-asparaginyl-L-threonine IUPAC Glucagone ChemIDplus HSQGTFTSDYSKYLDSRRAQDFVQWLMNT ChEBI His-Ser-Gln-Gly-Thr-Phe-Thr-Ser-Asp-Tyr-Ser-Lys-Tyr-Leu-Asp-Ser-Arg-Arg-Ala-Gln-Asp-Phe-Val-Gln-Trp-Leu-Met-Asn-Thr ChEBI His-ser-glu(nh2)-gly-thr-phe-thr-ser-asp-tyr-ser-lys-tyr-leu-asp-ser-arg-arg-ala-glu(NH2)-asp-phe-val-glu(NH2)-trp-leu-met-asp(NH2)-thr ChemIDplus glucagon ChemIDplus glucagonum ChemIDplus Any metal that is characterized by its rather high atomic mass and density. Although typically occurring in low concentrations, they can be found all throughout the Earth's crust (Commonly, a density of at least 5 g cm(3) is used to define a heavy metal and to differentiate it from other, ''light'' metals). Wikipedia:Heavy_metals chebi_ontology heavy metals CHEBI:5631 heavy metal heavy metals ChEBI A cyclic compound having as ring members atoms of at least two different elements. Heterocyclic compound chebi_ontology compuesto heterociclico compuestos heterociclicos heterocycle heterocyclic compounds CHEBI:5686 heterocyclic compound Heterocyclic compound KEGG_COMPOUND compuesto heterociclico IUPAC compuestos heterociclicos IUPAC heterocycle ChEBI heterocyclic compounds ChEBI An ammonium ion that is the conjugate acid of tryptamine arising from protonation of the primary amino group; major species at pH 7.3. +1 C10H13N2 InChI=1S/C10H12N2/c11-6-5-8-7-12-10-4-2-1-3-9(8)10/h1-4,7,12H,5-6,11H2/p+1 APJYDQYYACXCRM-UHFFFAOYSA-O 161.22310 161.10732 [NH3+]CCc1c[nH]c2ccccc12 Gmelin:533978 2-(1H-indol-3-yl)ethanaminium chebi_ontology tryptamine tryptaminium cation tryptaminium(1+) CHEBI:57887 tryptaminium Gmelin:533978 Gmelin 2-(1H-indol-3-yl)ethanaminium IUPAC tryptamine UniProt tryptaminium cation ChEBI tryptaminium(1+) ChEBI A dicarboxylic acid dianion obtained by deprotonation of the two carboxy groups of bilirubin; major species at pH 7.3. -2 C33H34N4O6 InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/p-2/b26-13-,27-14- BPYKTIZUTYGOLE-IFADSCNNSA-L 582.64630 582.24893 CC1=C(C=C)\C(NC1=O)=C\c1[nH]c(Cc2[nH]c(\C=C3NC(=O)C(C=C)=C/3C)c(C)c2CCC([O-])=O)c(CCC([O-])=O)c1C Beilstein:4083310 chebi_ontology 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoate bilirubin IXalpha bilirubin dianion CHEBI:57977 bilirubin(2-) Beilstein:4083310 Beilstein 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoate ChEBI bilirubin IXalpha UniProt bilirubin dianion ChEBI An organic anion of general formula RS(=O)2O(-) where R is an organyl group. -1 O4SR 96.06300 95.95173 [O-]S(=O)(=O)O[*] chebi_ontology organosulfate oxoanions CHEBI:58958 organosulfate oxoanion organosulfate oxoanions ChEBI An organic anion arising from deprotonation of a acyclic tetrapyrrole compound. chebi_ontology acyclic tetrapyrrole anion acyclic tetrapyrrole anions linear tetrapyrrole anions CHEBI:59252 linear tetrapyrrole anion acyclic tetrapyrrole anion ChEBI acyclic tetrapyrrole anions ChEBI linear tetrapyrrole anions ChEBI Compounds containing one or more phosphoric acid units. chebi_ontology CHEBI:59698 phosphoric acids A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons. chebi_ontology nucleophile nucleophiles nucleophilic reagents CHEBI:59740 nucleophilic reagent nucleophile ChEBI nucleophiles ChEBI nucleophilic reagents ChEBI A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. chebi_ontology Chemische Substanz CHEBI:59999 chemical substance Chemische Substanz ChEBI A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. chebi_ontology Mischung CHEBI:60004 mixture Mischung ChEBI A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc.. Wikipedia:Polymer Polymer chebi_ontology Kunststoff CHEBI:60027 polymer Polymer ChEBI Kunststoff ChEBI An ionic polymer is a polymer, composed of ionic macromolecules. chebi_ontology polyionic polymer CHEBI:60164 ionic polymer polyionic polymer ChEBI An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one. chebi_ontology a monovalent cation CHEBI:60242 monovalent inorganic cation a monovalent cation UniProt Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged. 0 C2H4NO2R(C2H2NOR)n chebi_ontology a peptide peptide zwitterions CHEBI:60466 peptide zwitterion a peptide UniProt peptide zwitterions ChEBI Any compound that has a nucleobase as a part. chebi_ontology nucleobase-containing compound nucleobase-containing compounds nucleobase-containing molecular entities CHEBI:61120 nucleobase-containing molecular entity nucleobase-containing compound SUBMITTER nucleobase-containing compounds ChEBI nucleobase-containing molecular entities ChEBI A polymer, composed of polyanion macromolecules. chebi_ontology polyanion polyanions CHEBI:61469 polyanionic polymer polyanion ChEBI polyanions ChEBI A substance that removes electrons from another reactant in a redox reaction. chebi_ontology oxidant oxidants oxidiser oxidisers oxidising agents oxidizer oxidizers oxidizing agent oxidizing agents CHEBI:63248 oxidising agent oxidant ChEBI oxidants ChEBI oxidiser ChEBI oxidisers ChEBI oxidising agents ChEBI oxidizer ChEBI oxidizers ChEBI oxidizing agent ChEBI oxidizing agents ChEBI Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds. chebi_ontology carbohydrate derivatives derivatised carbohydrate derivatised carbohydrates derivatized carbohydrate derivatized carbohydrates CHEBI:63299 carbohydrate derivative carbohydrate derivatives ChEBI derivatised carbohydrate ChEBI derivatised carbohydrates ChEBI derivatized carbohydrate ChEBI derivatized carbohydrates ChEBI A carbohydrate derivative that is formally obtained from a carbohydrate acid. chebi_ontology carbohydrate acid derivatives CHEBI:63436 carbohydrate acid derivative carbohydrate acid derivatives ChEBI An aralylamino compound which contains one amino group connected to an aromatic ring by a two-carbon chain. Monoamines are derived from aromatic amino acids like phenylalanine, tyrosine, tryptophan, and the thyroid hormones by the action of aromatic amino acid decarboxylase enzymes. PMID:21822758 PMID:21993877 PMID:22005599 PMID:22082101 PMID:22153577 PMID:22213370 PMID:22218931 PMID:22342987 PMID:22371656 chebi_ontology monoamines naturally occurring monoamine naturally occurring monoamines CHEBI:63534 monoamine PMID:21822758 Europe PMC PMID:21993877 Europe PMC PMID:22005599 Europe PMC PMID:22082101 Europe PMC PMID:22153577 Europe PMC PMID:22213370 Europe PMC PMID:22218931 Europe PMC PMID:22342987 Europe PMC PMID:22371656 Europe PMC monoamines ChEBI naturally occurring monoamine ChEBI naturally occurring monoamines ChEBI A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative. chebi_ontology carbohydrate acid anion derivative carbohydrate acid anion derivatives carbohydrate acid derivative anions CHEBI:63551 carbohydrate acid derivative anion carbohydrate acid anion derivative ChEBI carbohydrate acid anion derivatives ChEBI carbohydrate acid derivative anions ChEBI Any substance which is added to food to preserve or enhance its flavour and/or appearance. Wikipedia:Food_additive chebi_ontology food additives CHEBI:64047 food additive food additives ChEBI A food additive that is used to change or otherwise control the acidity or alkalinity of foods. They may be acids, bases, neutralising agents or buffering agents. Wikipedia:Acidity_regulator chebi_ontology acidity regulator acidity regulators food acidity regulators pH control agent pH control agents CHEBI:64049 food acidity regulator acidity regulator ChEBI acidity regulators ChEBI food acidity regulators ChEBI pH control agent ChEBI pH control agents ChEBI An organic amino compound in which an aminoalkyl group is linked to an arene. chebi_ontology aralkylamino compounds CHEBI:64365 aralkylamino compound aralkylamino compounds ChEBI A fourteen-membered heterodetic cyclic peptide comprising the sequence Ala-Gly-Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys cyclised by a disulfide bridge between the two Cys residues at positions 3 and 14. 0 C76H104N18O19S2 InChI=1S/C76H104N18O19S2/c1-41(79)64(100)82-37-61(99)83-58-39-114-115-40-59(76(112)113)92-72(108)57(38-95)91-75(111)63(43(3)97)94-71(107)54(33-46-23-11-6-12-24-46)90-74(110)62(42(2)96)93-66(102)51(28-16-18-30-78)84-69(105)55(34-47-36-81-49-26-14-13-25-48(47)49)88-68(104)53(32-45-21-9-5-10-22-45)86-67(103)52(31-44-19-7-4-8-20-44)87-70(106)56(35-60(80)98)89-65(101)50(85-73(58)109)27-15-17-29-77/h4-14,19-26,36,41-43,50-59,62-63,81,95-97H,15-18,27-35,37-40,77-79H2,1-3H3,(H2,80,98)(H,82,100)(H,83,99)(H,84,105)(H,85,109)(H,86,103)(H,87,106)(H,88,104)(H,89,101)(H,90,110)(H,91,111)(H,92,108)(H,93,102)(H,94,107)(H,112,113)/t41-,42+,43+,50-,51-,52-,53-,54-,55-,56-,57-,58-,59-,62-,63-/m0/s1 NHXLMOGPVYXJNR-ATOGVRKGSA-N 1637.87800 1636.71666 C[C@@H](O)[C@@H]1NC(=O)[C@H](CCCCN)NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CSSC[C@H](NC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)[C@H](Cc2ccccc2)NC1=O)[C@@H](C)O)C(O)=O)NC(=O)CNC(=O)[C@H](C)N CAS:38916-34-6 Drug_Central:2997 HMDB:HMDB0013072 KEGG:C16022 KEGG:D07431 LINCS:LSM-5326 PMID:21922516 PMID:22129035 PMID:22147011 PMID:22251942 PMID:22483686 PMID:22509294 Reaxys:10148626 Wikipedia:Somatostatin L-alanyl-N-[(4R,7S,10S,13S,16S,19S,22S,25S,28S,31S,34S,37R)-19,34-bis(4-aminobutyl)-31-(2-amino-2-oxoethyl)-13,25,28-tribenzyl-4-carboxy-10,16-bis[(1R)-1-hydroxyethyl]-7-(hydroxymethyl)-22-(1H-indol-3-ylmethyl)-6,9,12,15,18,21,24,27,30,33,36-undecaoxo-1,2-dithia-5,8,11,14,17,20,23,26,29,32,35-undecaazacyclooctatriacontan-37-yl]glycinamide chebi_ontology Ala-Gly-cyclo-[Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys] L-alanylglycyl-L-cysteinyl-L-lysyl-L-asparaginyl-L-phenylalanyl-L-phenylalanyl-L-tryptophyl-L-lysyl-L-threonyl-L-phenylalanyl-L-threonyl-L-seryl-L-cysteine cyclic (3-14) disulfide Somatostatin-1 Somatostatin-14 Synthetic growth hormone release-inhibiting hormone somatostatin somatostatina somatostatine somatostatinum CHEBI:64628 somatostatin CAS:38916-34-6 ChemIDplus CAS:38916-34-6 KEGG DRUG Drug_Central:2997 DrugCentral PMID:21922516 Europe PMC PMID:22129035 Europe PMC PMID:22147011 Europe PMC PMID:22251942 Europe PMC PMID:22483686 Europe PMC PMID:22509294 Europe PMC Reaxys:10148626 Reaxys L-alanyl-N-[(4R,7S,10S,13S,16S,19S,22S,25S,28S,31S,34S,37R)-19,34-bis(4-aminobutyl)-31-(2-amino-2-oxoethyl)-13,25,28-tribenzyl-4-carboxy-10,16-bis[(1R)-1-hydroxyethyl]-7-(hydroxymethyl)-22-(1H-indol-3-ylmethyl)-6,9,12,15,18,21,24,27,30,33,36-undecaoxo-1,2-dithia-5,8,11,14,17,20,23,26,29,32,35-undecaazacyclooctatriacontan-37-yl]glycinamide IUPAC Ala-Gly-cyclo-[Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys] ChEBI L-alanylglycyl-L-cysteinyl-L-lysyl-L-asparaginyl-L-phenylalanyl-L-phenylalanyl-L-tryptophyl-L-lysyl-L-threonyl-L-phenylalanyl-L-threonyl-L-seryl-L-cysteine cyclic (3-14) disulfide ChemIDplus Somatostatin-1 KEGG_COMPOUND Somatostatin-14 KEGG_COMPOUND Synthetic growth hormone release-inhibiting hormone ChemIDplus somatostatin KEGG_DRUG somatostatina ChemIDplus somatostatine ChemIDplus somatostatinum ChemIDplus An organic molecular entity containing a single carbon atom (C1). chebi_ontology one-carbon compounds CHEBI:64708 one-carbon compound one-carbon compounds ChEBI Any organic molecular entity that is acidic and contains carbon in covalent linkage. chebi_ontology organic acids CHEBI:64709 organic acid organic acids ChEBI Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism. Wikipedia:Poison chebi_ontology poisonous agent poisonous agents poisonous substance poisonous substances poisons toxic agent toxic agents toxic substance toxic substances CHEBI:64909 poison poisonous agent ChEBI poisonous agents ChEBI poisonous substance ChEBI poisonous substances ChEBI poisons ChEBI toxic agent ChEBI toxic agents ChEBI toxic substance ChEBI toxic substances ChEBI A carbohydrate derivative that is any derivative of a polysaccharide. chebi_ontology polysaccharide derivatives CHEBI:65212 polysaccharide derivative polysaccharide derivatives ChEBI Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes. chebi_ontology food preservatives CHEBI:65255 food preservative food preservatives ChEBI A food preservative which prevents decomposition of food by preventing the growth of fungi or bacteria. In European countries, E-numbers for permitted food preservatives are from E200 to E299, divided into sorbates (E200-209), benzoates (E210-219), sulfites (E220-229), phenols and formates (E230-239), nitrates (E240-259), acetates (E260-269), lactates (E270-279), propionates (E280-289) and others (E290-299). chebi_ontology antimicrobial food preservatives antimicrobial preservative antimicrobial preservatives CHEBI:65256 antimicrobial food preservative antimicrobial food preservatives ChEBI antimicrobial preservative ChEBI antimicrobial preservatives ChEBI An ammonium ion derivative resulting from the protonation of the nitrogen atom of a primary amino compound. Major species at pH 7.3. +1 H3NR 17.031 17.02655 [NH3+][*] chebi_ontology a primary amine substituted ammonium CHEBI:65296 primary ammonium ion a primary amine UniProt substituted ammonium ChEBI Any compound that has anti-inflammatory effects. chebi_ontology anti-inflammatory agents antiinflammatory agent antiinflammatory agents CHEBI:67079 anti-inflammatory agent anti-inflammatory agents ChEBI antiinflammatory agent ChEBI antiinflammatory agents ChEBI An organic cation that is the conjugate acid of (R)-noradrenaline, obtained by protonation of the priamry amino group; major species at pH 7.3. +1 C8H12NO3 InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/p+1/t8-/m0/s1 SFLSHLFXELFNJZ-QMMMGPOBSA-O 170.187 170.08117 C=1(C=CC(=CC1O)[C@H](C[NH3+])O)O PDBeChem:E5E (2R)-2-(3,4-dihydroxyphenyl)-2-hydroxyethanaminium chebi_ontology (R)-noradrenaline (R)-noradrenaline cation (R)-noradrenalinium cation (R)-noradrenalinium(1+) CHEBI:72587 (R)-noradrenaline(1+) (2R)-2-(3,4-dihydroxyphenyl)-2-hydroxyethanaminium IUPAC (R)-noradrenaline UniProt (R)-noradrenaline cation ChEBI (R)-noradrenalinium cation ChEBI (R)-noradrenalinium(1+) ChEBI Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. chebi_ontology organic compound organic compounds organic molecules CHEBI:72695 organic molecule organic compound ChEBI organic compounds ChEBI organic molecules ChEBI A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment. MetaCyc:Exopolysaccharides PMID:11160795 PMID:11785425 PMID:1444258 PMID:15738217 PMID:16075348 PMID:17440912 PMID:18097339 PMID:19453747 PMID:20172021 PMID:20631870 PMID:20718297 PMID:2688547 PMID:6354590 Wikipedia:Exopolysaccharide Wikipedia:Extracellular_polymeric_substance chebi_ontology exopolysaccharides extracellular polymeric substance extracellular polymeric substances CHEBI:72813 exopolysaccharide PMID:11160795 Europe PMC PMID:11785425 Europe PMC PMID:1444258 Europe PMC PMID:15738217 Europe PMC PMID:16075348 Europe PMC PMID:17440912 Europe PMC PMID:18097339 Europe PMC PMID:19453747 Europe PMC PMID:20172021 Europe PMC PMID:20631870 Europe PMC PMID:20718297 Europe PMC PMID:2688547 Europe PMC PMID:6354590 Europe PMC exopolysaccharides ChEBI extracellular polymeric substance ChEBI extracellular polymeric substances ChEBI A mancude heterobicyclic organic group consisting of a benzene ring fused to a pyrrole ring. 0 C8N 110.09230 110.00307 C1(=C(C(=C2C(=C1*)N(C(=C2*)*)*)*)*)* chebi_ontology CHEBI:73398 indole skeleton A bicyclic organic group that contains both carbon and hetero atoms. chebi_ontology organic heterobicyclic rings CHEBI:73541 organic heterobicyclic ring organic heterobicyclic rings ChEBI Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms. chebi_ontology eukaryotic metabolites CHEBI:75763 eukaryotic metabolite eukaryotic metabolites ChEBI Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals. CHEBI:77721 CHEBI:77743 chebi_ontology animal metabolites CHEBI:75767 animal metabolite animal metabolites ChEBI Any animal metabolite produced during a metabolic reaction in mammals. CHEBI:77464 CHEBI:77744 chebi_ontology mammalian metabolites CHEBI:75768 mammalian metabolite mammalian metabolites ChEBI Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). chebi_ontology Mus musculus metabolite Mus musculus metabolites mouse metabolites CHEBI:75771 mouse metabolite Mus musculus metabolite ChEBI Mus musculus metabolites ChEBI mouse metabolites ChEBI Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae). CHEBI:76949 CHEBI:76951 chebi_ontology S. cerevisiae metabolite S. cerevisiae metabolites S. cerevisiae secondary metabolite S. cerevisiae secondary metabolites Saccharomyces cerevisiae metabolites Saccharomyces cerevisiae secondary metabolites baker's yeast metabolite baker's yeast metabolites baker's yeast secondary metabolite baker's yeast secondary metabolites CHEBI:75772 Saccharomyces cerevisiae metabolite S. cerevisiae metabolite ChEBI S. cerevisiae metabolites ChEBI S. cerevisiae secondary metabolite ChEBI S. cerevisiae secondary metabolites ChEBI Saccharomyces cerevisiae metabolites ChEBI Saccharomyces cerevisiae secondary metabolites ChEBI baker's yeast metabolite ChEBI baker's yeast metabolites ChEBI baker's yeast secondary metabolite ChEBI baker's yeast secondary metabolites ChEBI Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. chebi_ontology prokaryotic metabolites CHEBI:75787 prokaryotic metabolite prokaryotic metabolites ChEBI Any metabolite produced by metabolism of a xenobiotic compound. chebi_ontology xenobiotic metabolites CHEBI:76206 xenobiotic metabolite xenobiotic metabolites ChEBI envoPolar greenhouse gas Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*). Wikipedia:Hydrolase chebi_ontology EC 3.* (hydrolase) inhibitors EC 3.* inhibitor EC 3.* inhibitors EC 3.*.*.* inhibitor EC 3.*.*.* inhibitors hydrolase (EC 3.*) inhibitor hydrolase (EC 3.*) inhibitors hydrolase inhibitor hydrolase inhibitors CHEBI:76759 EC 3.* (hydrolase) inhibitor EC 3.* (hydrolase) inhibitors ChEBI EC 3.* inhibitor ChEBI EC 3.* inhibitors ChEBI EC 3.*.*.* inhibitor ChEBI EC 3.*.*.* inhibitors ChEBI hydrolase (EC 3.*) inhibitor ChEBI hydrolase (EC 3.*) inhibitors ChEBI hydrolase inhibitor ChEBI hydrolase inhibitors ChEBI Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*). chebi_ontology EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors EC 3.5.* inhibitor EC 3.5.* inhibitors CHEBI:76764 EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor ChEBI EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors ChEBI EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor ChEBI EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors ChEBI EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors ChEBI EC 3.5.* inhibitor ChEBI EC 3.5.* inhibitors ChEBI An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*). chebi_ontology EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors EC 3.5.1.* inhibitor EC 3.5.1.* inhibitors non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors CHEBI:76807 EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors ChEBI EC 3.5.1.* inhibitor ChEBI EC 3.5.1.* inhibitors ChEBI non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor ChEBI non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors ChEBI Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms. CHEBI:75766 CHEBI:76925 chebi_ontology plant metabolites plant secondary metabolites CHEBI:76924 plant metabolite plant metabolites ChEBI plant secondary metabolites ChEBI Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds. CHEBI:75765 CHEBI:76947 chebi_ontology fungal metabolites CHEBI:76946 fungal metabolite fungal metabolites ChEBI Any human metabolite produced by metabolism of a xenobiotic compound in humans. chebi_ontology human xenobiotic metabolites CHEBI:76967 human xenobiotic metabolite human xenobiotic metabolites ChEBI Any prokaryotic metabolite produced during a metabolic reaction in bacteria. CHEBI:75760 CHEBI:76970 chebi_ontology CHEBI:76969 bacterial metabolite Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. chebi_ontology E.coli metabolite E.coli metabolites Escherichia coli metabolites CHEBI:76971 Escherichia coli metabolite E.coli metabolite ChEBI E.coli metabolites ChEBI Escherichia coli metabolites ChEBI A stable isotope of boron with relative atomic mass 10.0129370, 19.9 atom percent natural abundance and nuclear spin 3+. 0 [10B] InChI=1S/B/i1-1 ZOXJGFHDIHLPTG-BJUDXGSMSA-N 10.013 10.01294 [10B] boron-10 chebi_ontology (10)B CHEBI:77014 boron-10 atom boron-10 IUPAC (10)B SUBMITTER Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens). CHEBI:75770 CHEBI:77123 chebi_ontology H. sapiens metabolite H. sapiens metabolites Homo sapiens metabolite Homo sapiens metabolites CHEBI:77746 human metabolite H. sapiens metabolite ChEBI H. sapiens metabolites ChEBI Homo sapiens metabolite ChEBI Homo sapiens metabolites ChEBI An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4). Wikipedia:Amidase chebi_ontology EC 3.5.1.4 (amidase) inhibitors EC 3.5.1.4 inhibitor EC 3.5.1.4 inhibitors N-acetylaminohydrolase inhibitor N-acetylaminohydrolase inhibitors acylamidase inhibitor acylamidase inhibitors acylamide amidohydrolase inhibitor acylamide amidohydrolase inhibitors amidase (EC 3.5.1.4) inhibitor amidase (EC 3.5.1.4) inhibitors amidase inhibitor amidase inhibitors amidohydrolase inhibitor amidohydrolase inhibitors deaminase inhibitor deaminase inhibitors fatty acylamidase inhibitor fatty acylamidase inhibitors CHEBI:77941 EC 3.5.1.4 (amidase) inhibitor EC 3.5.1.4 (amidase) inhibitors ChEBI EC 3.5.1.4 inhibitor ChEBI EC 3.5.1.4 inhibitors ChEBI N-acetylaminohydrolase inhibitor ChEBI N-acetylaminohydrolase inhibitors ChEBI acylamidase inhibitor ChEBI acylamidase inhibitors ChEBI acylamide amidohydrolase inhibitor ChEBI acylamide amidohydrolase inhibitors ChEBI amidase (EC 3.5.1.4) inhibitor ChEBI amidase (EC 3.5.1.4) inhibitors ChEBI amidase inhibitor ChEBI amidase inhibitors ChEBI amidohydrolase inhibitor ChEBI amidohydrolase inhibitors ChEBI deaminase inhibitor ChEBI deaminase inhibitors ChEBI fatty acylamidase inhibitor ChEBI fatty acylamidase inhibitors ChEBI A food additive that is a (generally inert) gas which is used to envelop foodstuffs during packing and so protect them from unwanted chemical reactions such as food spoilage or oxidation during subsequent transport and storage. The term includes propellant gases, used to expel foods from a container. Wikipedia:Packaging_gas chebi_ontology food packaging gases CHEBI:77974 food packaging gas food packaging gases ChEBI A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. chebi_ontology dietary component dietary components food components CHEBI:78295 food component dietary component ChEBI dietary components ChEBI food components ChEBI environmental contaminant A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure. Wikipedia:Refrigerant chebi_ontology refrigerants CHEBI:78433 refrigerant refrigerants ChEBI An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3. 0 C2H4NO2R 74.059 74.02420 [NH3+]C([*])C([O-])=O CHEBI:83409 MetaCyc:Alpha-Amino-Acids chebi_ontology an alpha-amino acid CHEBI:78608 alpha-amino acid zwitterion MetaCyc:Alpha-Amino-Acids SUBMITTER an alpha-amino acid UniProt Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. chebi_ontology carbohydrates and derivatives carbohydrates and their derivatives CHEBI:78616 carbohydrates and carbohydrate derivatives carbohydrates and derivatives ChEBI carbohydrates and their derivatives ChEBI Any metabolite produced by all living cells. chebi_ontology essential metabolite essential metabolites fundamental metabolites CHEBI:78675 fundamental metabolite essential metabolite ChEBI essential metabolites ChEBI fundamental metabolites ChEBI Any inorganic anion with a valency of three. chebi_ontology trivalent inorganic anions CHEBI:79387 trivalent inorganic anion trivalent inorganic anions ChEBI Any inorganic anion with a valency of two. chebi_ontology divalent inorganic anions CHEBI:79388 divalent inorganic anion divalent inorganic anions ChEBI Any inorganic anion with a valency of one. chebi_ontology monovalent inorganic anions CHEBI:79389 monovalent inorganic anion monovalent inorganic anions ChEBI A zinc atom in which the nucleus contains 35 neutrons. It has a half-life of 244 days, decaying by emission of a positron (beta(+) decay), and is the most abundant and stable of the 25 known radioisotopes of zinc. 0 [65Zn] InChI=1S/Zn/i1+0 HCHKCACWOHOZIP-IGMARMGPSA-N 64.929 64.92925 [65Zn] CAS:13982-39-3 PMID:11431342 PMID:13615323 PMID:13694484 PMID:13734409 PMID:13744376 PMID:13783426 PMID:13841044 PMID:14425466 PMID:1682403 PMID:17807441 PMID:19448268 ((65)Zn)zinc chebi_ontology (65)30Zn (65)Zn Zn-65 zinc, isotope of mass 65 zinc-65 CHEBI:82623 zinc-65 atom CAS:13982-39-3 ChemIDplus PMID:11431342 Europe PMC PMID:13615323 Europe PMC PMID:13694484 Europe PMC PMID:13734409 Europe PMC PMID:13744376 Europe PMC PMID:13783426 Europe PMC PMID:13841044 Europe PMC PMID:14425466 Europe PMC PMID:1682403 Europe PMC PMID:17807441 Europe PMC PMID:19448268 Europe PMC ((65)Zn)zinc IUPAC (65)30Zn IUPAC (65)Zn IUPAC Zn-65 ChEBI zinc, isotope of mass 65 ChemIDplus zinc-65 ChemIDplus An animal metabolite produced by arthropods such as crabs, lobsters, crayfish, shrimps and krill. chebi_ontology crustacean metabolites CHEBI:83039 crustacean metabolite crustacean metabolites ChEBI A Daphnia metabolite produced by the species Daphnia magna. chebi_ontology Daphnia magna metabolites CHEBI:83056 Daphnia magna metabolite Daphnia magna metabolites ChEBI A crustacean metabolite produced by the genus of small planktonic arthropods, Daphnia Wikipedia:Daphnia chebi_ontology Daphnia metabolites CHEBI:83057 Daphnia metabolite Daphnia metabolites ChEBI Any member of the class of indoles carrying at least one hydroxy group. chebi_ontology CHEBI:84729 hydroxyindoles Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae. chebi_ontology algal metabolites CHEBI:84735 algal metabolite algal metabolites ChEBI Any metal which causes the onset of an allergic reaction. chebi_ontology allergenic metal allergenic metals metal allergens CHEBI:88184 metal allergen allergenic metal ChEBI allergenic metals ChEBI metal allergens ChEBI An independent material continuant that is self-connected and retains its identity over time. CHMO:0000993 portion of material An independent material continuant that is self-connected and retains its identity over time. https://orcid.org/0000-0001-5985-7429 A piece of apparatus that is used to measure a physical quantity. CHMO:0002793 sensor A piece of apparatus that is used to measure a physical quantity. https://orcid.org/0000-0001-5985-7429 Measurement of the dose of a substance taken up by an object. CHMO:0002796 dosimetry Measurement of the dose of a substance taken up by an object. https://doi.org/10.1039/9781847559753-00013 A sensor that is used to measure the dose of a substance taken by up an object. CHMO:0002797 dosimeter A sensor that is used to measure the dose of a substance taken by up an object. https://doi.org/10.1039/9781847559753-00013 cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. A material entity that has a plasma membrane and results from cellular division. CALOHA:TS-2035 CALOHA:TS-2035 FBbt:00007002 FMA:68646 FMA:68646 GO:0005623 GO:0005623 KUPO:0000002 KUPO:0000002 MESH:D002477 NCIt:C12508 NCIt:C48694 VHOG:0001533 VHOG:0001533 WBbt:0004017 WBbt:0004017 XAO:0003012 XAO:0003012 CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CARO:mah Any fibroblast that is deriived from the neural crest. fibroblast neural crest derived Any fibroblast that is deriived from the neural crest. https://orcid.org/0000-0001-5208-3432 neuronal receptor cell (sensu Animalia) neuronal receptor cell A cell found in the embryo before the formation of all the gem layers is complete. early embryonic cell (metazoa) A cell found in the embryo before the formation of all the gem layers is complete. GOC:tfm Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. migratory cranial neural crest cell Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. ZFA:0007091 https://orcid.org/0000-0001-5208-3432 Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination. migratory trunk neural crest cell Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination. ZFA:0007095 https://orcid.org/0000-0001-5208-3432 A stem cell that is the precursor of gametes. FBbt:00004861 germline stem cell germ line stem cell true A stem cell that is the precursor of gametes. doi:10.1016/j.stem.2012.05.016 Female germ cell is a germ cell that supports female gamete production. MA:0000388 VHOG:0001530 ncithesaurus:Egg female germ cell true Female germ cell is a germ cell that supports female gamete production. GOC:tfm PMID:11023867 PMID:20454446 A stem cell that is the precursor of female gametes. FBbt:00004873 female germ line stem cell true true A stem cell that is the precursor of female gametes. doi:10.1016/j.stem.2012.05.016 A female germ cell that has entered meiosis. BTO:0000964 CALOHA:TS-0711 FBbt:00004886 FMA:18644 MESH:D009865 WBbt:0006797 oogonium oocyte true A female germ cell that has entered meiosis. GOC:tfm ISBN:0721662544 An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. FMA:83673 oogonial cell true An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. GOC:tfm ISBN:0721662544 A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization. BTO:0000369 BTO:0003801 CALOHA:TS-2191 FBbt:00057012 FMA:67343 MESH:D010063 mature oocyte ovum egg cell https://www.swissbiopics.org/api/image/Egg_cell.svg true A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization. GOC:tfm ISBN:0721662544 A smooth muscle cell derived from the neural crest. smooth muscle cell neural crest derived true A smooth muscle cell derived from the neural crest. https://orcid.org/0000-0001-5208-3432 neuron neural crest derived neural crest derived neuron true A cell that will develop into a neuron often after a migration phase. BTO:0000930 FMA:70563 neuroblast neuroblast (sensu Vertebrata) A cell that will develop into a neuron often after a migration phase. GOC:NV http://en.wikipedia.org/wiki/Neuroblast A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CALOHA:TS-2086 FMA:63368 animal stem cell This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. GOC:tfm MESH:D013234 A stem cell that self-renews as well as give rise to a single mature cell type. FMA:70569 unipotent stem cell unipotential stem cell single fate stem cell A stem cell that self-renews as well as give rise to a single mature cell type. GOC:tfm A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. BTO:0000725 CALOHA:TS-0448 FMA:86475 MESH:D006412 VHOG:0001485 blood forming stem cell hemopoietic stem cell HSC colony forming unit hematopoietic Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. GOC:add GOC:dsd GOC:tfm PMID:19022770 http://en.wikipedia.org/wiki/Hematopoietic_stem_cell HSC A progenitor cell committed to the erythroid lineage. BTO:0004911 BFU-E CFU-E blast forming unit erythroid burst forming unit erythroid colony forming unit erythroid erythroid stem cell erythroid progenitor cell true A progenitor cell committed to the erythroid lineage. GOC:add ISBN:0721601464 BFU-E CFU-E A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. Originally this term had some plant germ line cell children. germ line cell A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. GOC:tfm ISBN:0721662544 A stem cell that can give rise to multiple lineages of cells. FMA:84789 multi-fate stem cell multifate stem cell multipotent cell multipotent stem cell multi fate stem cell A stem cell that can give rise to multiple lineages of cells. GOC:add A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. BTO:0004730 common myeloid precursor CFU-GEMM CFU-S CMP colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor true A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. GOC:add ISBN:0878932437 MESH:D023461 CFU-GEMM ISBN:0878932437 CFU-S ISBN:0878932437 CMP ISBN:0878932437 colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte ISBN:0878932437 multipotential myeloid stem cell ISBN:0878932437 myeloid stem cell ISBN:0878932437 pluripotent stem cell (bone marrow) ISBN:0878932437 A progenitor cell committed to the megakaryocyte and erythroid lineages. CFU-EM CFU-MegE MEP Meg/E progenitor colony forming unit erythroid megakaryocyte megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell true A progenitor cell committed to the megakaryocyte and erythroid lineages. GOC:add GOC:dsd GOC:tfm MESH:D055015 PMID:16647566 http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell A stem cell from which all cells of the body can form. FMA:84790 MESH:D039901 totipotential stem cell totipotent stem cell A stem cell from which all cells of the body can form. GOC:add GOC:tfm A precursor cell with a limited number of potential fates. BTO:0000125 FMA:84782 blast cell define using PATO mulit-potent or oligopotent? non-terminally differentiated cell A precursor cell with a limited number of potential fates. SANBI:mhl A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. BTO:0000222 CALOHA:TS-0650 FBbt:00005083 FMA:70335 VHOG:0001529 myoblast A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. GOC:tfm MESH:D032446 PMID:21849021 A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 CALOHA:TS-0362 FMA:63877 NCIT:C12482 VHOG:0001482 These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. ISBN:0517223651 MESH:D005347 http://en.wikipedia.org/wiki/Fibroblast Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell. BTO:0003607 FMA:66783 chrondoplast chondroblast Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell. GOC:tfm GO_REF:0000034 ISBN:0618947256 A cell that has a filiform extrusion of the cell surface. VHOG:0001532 XAO:0000031 ciliated cell A cell that has a filiform extrusion of the cell surface. GOC:tfm A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 epitheliocyte epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. FB:ma GOC:tfm MESH:D004847 An epithelial cell that has a cilia. FMA:70605 ciliated epithelial cell An epithelial cell that has a cilia. GOC:tfm An epithelial cell that is part of a duct. duct epithelial cell An epithelial cell that is part of a duct. https://orcid.org/0000-0001-5208-3432 branched duct epithelial cell An endothelial cell that lines the vasculature. cuboidal endothelial cell of vascular tree blood vessel endothelial cell true An endothelial cell that lines the vasculature. GOC:tfm A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. columnar/cuboidal epithelial cell A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. GO:0002065 https://orcid.org/0000-0001-5208-3432 CALOHA:TS-1249 squamous epithelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. FMA:66773 mesotheliocyte mesothelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. GOC:tfm ISBN:0721662544 A cell which moves among different tissues of the body, via blood, lymph, or other medium. circulating cell A cell which moves among different tissues of the body, via blood, lymph, or other medium. GOC:add A cell found predominately in the blood. FMA:62844 MESH:D001773 blood cell true A cell found predominately in the blood. GOC:add GOC:tfm An epithelial cell of the lung. BTO:0004299 lung epithelial cell epithelial cell of lung An epithelial cell of the lung. https://orcid.org/0000-0001-5208-3432 An epithelial cell of the pancreas. BTO:0000028 pancreas epithelial cell pancreatic epithelial cell epithelial cell of pancreas An epithelial cell of the pancreas. GOC:tfm neuron associated cell A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. neuroepithelial cell BTO:0004301 The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). sensory epithelial cell A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. GOC:tfm ISBN:0517223651 ISBN:0721662544 Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 FBbt:00005125 FMA:67313 WBbt:0005113 interneuron Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. GOC:tfm MESH:D007395 An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. BTO:0000312 FBbt:00005123 FMA:83617 WBbt:0005409 motoneuron motor neuron An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. MESH:D009046 PMID:16875686 Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 FBbt:00005124 FMA:84649 MESH:D011984 WBbt:0005759 sensory neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. ISBN:0721662544 A neuron whose cell body is within an autonomic ganglion. FMA:80121 autonomic neuron A neuron whose cell body is within an autonomic ganglion. GOC:tfm A neuron that uses acetylcholine as a vesicular neurotransmitter. BTO:0004902 FBbt:00007173 FMA:84796 MESH:D059329 WBbt:0006840 cholinergic neuron A neuron that uses acetylcholine as a vesicular neurotransmitter. GOC:tfm An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 CALOHA:TS-0278 FMA:66772 endotheliocyte From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. GOC:tfm MESH:D042783 PMID:21275341 http://en.wikipedia.org/wiki/Endothelial_cell https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855 CNS neuron (sensu Vertebrata) A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. BTO:0002606 CALOHA:TS-0415 FBbt:00005144 FMA:54536 neuroglial cell neuroglia Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571 glial cell A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. MESH:D009457 Ectoderm destined to be nervous tissue. neurectoderm cell neurectodermal cell Ectoderm destined to be nervous tissue. GOC:tfm ISBN:068340007X A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. BTO:0002625 BTO:0003298 FMA:70546 bone marrow stromal cells colony-forming unit-fibroblast marrow stromal cells BMSC CFU-F MSC mesenchymal precursor cell mesenchymal progenitor cells mesenchymal stem cell mesenchymal stromal cell mesenchymal stromal cells stem cells, mesenchymal Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 true A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. FB:ma GOC:dsd PMCID:PMC2613570 PMID:10102814 PMID:16923606 PMID:17986482 PMID:19960544 http://en.wikipedia.org/wiki/Mesenchymal_stem_cell http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells marrow stromal cells PMID:11378515 BMSC CFU-F MSC PMID:11378515 mesenchymal progenitor cells MESH:D044982 mesenchymal stromal cells stem cells, mesenchymal MESH:D044982 A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. BTO:0000443 CALOHA:TS-0012 FMA:63880 adipose cell fat cell adipocyte A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. MESH:D017667 Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell. BTO:0000249 CALOHA:TS-0138 FMA:66782 cartilage cell chondrocyte Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell. GO_REF:0000034 MESH:D019902 A pigment cell is a cell that contains pigment granules. VHOG:0001678 chromatocyte chromatophore pigment cell A pigment cell is a cell that contains pigment granules. GOC:tfm pigment cell visual pigment cell A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. CALOHA:TS-2085 FMA:86494 glandular epithelial cell A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. GOC:tfm A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 secretory cell A cell that specializes in controlled release of one or more substances. GOC:tfm ISBN:0721662544 A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 exocrine cell A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. ISBN:0198547684 A cell that secretes glycosaminoglycans. GAG secreting cell hyaluronic acid secreting cell glycosaminoglycan secreting cell A cell that secretes glycosaminoglycans. GOC:tfm protein secreting cell seromucus secreting cell A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. FMA:83809 endocrinocyte endocrine cell A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. MESH:D055098 An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. BTO:0003865 FMA:62930 MESH:D019858 enteroendocrine cell An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. GOC:tfm SANBI:mhl A neuron that is capable of some hormone secretion in response to neuronal signals. BTO:0002691 FBbt:00005130 FMA:83810 neurosecretory cell neurosecretory neuron The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron. neuroendocrine cell A neuron that is capable of some hormone secretion in response to neuronal signals. MESH:D055099 The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron. PMID:5342440 https://www.clinicalkey.com/#!/content/book/3-s2.0-B9780323555968000073 peptide hormone secreting cell BTO:0000783 insulin secreting cell A cell that secretes insulin and is located towards the center of the islets of Langerhans. beta cell BTO:0000783 EV:0200009 FMA:70586 MA:0002419 ncithesaurus:Beta_Cell B-cell of pancreatic islet beta cell of pancreatic islet insulin-secreting cell pancreatic B cell pancreatic B-cell pancreatic beta cell pancreatic islet core type B enteroendocrine cell beta cell islet Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression. type B pancreatic cell true A cell that secretes insulin and is located towards the center of the islets of Langerhans. GOC:tfm ISBN:0517223651 http://en.wikipedia.org/wiki/Pancreatic_b_cell beta cell ZFA:0009102 B-cell of pancreatic islet FMA:70586 beta cell of pancreatic islet FMA:70586 insulin-secreting cell FMA:70586 pancreatic B-cell FMA:70586 pancreatic beta cell FMA:70586 pancreatic islet core MA:0002419 type B enteroendocrine cell FMA:70586 beta cell islet MA:0002419 A cell that secretes glucagon. FMA:84045 glucagon-secreting cell glucagon secreting cell A cell that secretes glucagon. GOC:tfm A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. BTO:0000990 FMA:70585 MESH:D050416 alpha cell of islet of Langerhans pancreatic alpha cell pancreatic A cell A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. GOC:tfm ISBN:0721662544 somatostatin secreting cell A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. BTO:0000803 FMA:70587 D-cell of pancreatic islet delta cell of islet delta cell of pancreatic islet pancreatic D-cell pancreatic delta cell somatostatin-secreting pancreatic cell pancreatic D cell A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. FMA:0517223651 GOC:tfm steroid hormone secreting cell The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. BTO:0000575 CALOHA:TS-0454 FMA:14515 Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. hepatocyte The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. GOC:tfm ISBN:0412046911 MESH:D022781 PMID:19717280 http://en.wikipedia.org/wiki/Hepatocyte A cell whose primary function is to shorten. contractile cell A cell whose primary function is to shorten. FB:ma A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. BTO:0000888 BTO:0000902 CALOHA:TS-2032 FBbt:00005074 FMA:67328 WBbt:0003675 muscle fiber myocyte muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. MESH:D032342 A somatic cell located in skeletal muscle. BTO:0004392 CALOHA:TS-2158 FMA:9727 skeletal muscle cell cell of skeletal muscle A somatic cell located in skeletal muscle. GOC:tfm A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 SMCs myocytes, smooth muscle smooth muscle fiber smooth muscle cell A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). MESH:D032389 PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell SMCs PMID:9315361 myocytes, smooth muscle MESH:D032389 A cell that is capable of detection of a stimulus involved in sensory perception. MESH:D011984 receptor cell sensory receptor cell A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. chemoreceptor cell A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. MESH:D002628 A cell specialized to detect and transduce light. BTO:0001060 CALOHA:TS-0868 FMA:86740 photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg true A cell specialized to detect and transduce light. MESH:D010786 A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell A cell whose function is determined by the generation or the reception of an electric signal. FB:ma A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. boundary cell lining cell A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. JB:jb A cell located in the synovial joint. CALOHA:TS-0995 synoviocyte synovial cell true A cell whose primary function is to prevent the transport of stuff across compartments. barrier cell A cell whose primary function is to prevent the transport of stuff across compartments. JB:jb A cell that moves by its own activities. motile cell A cell that moves by its own activities. FB:ma A cell of the outer of the three germ layers of the embryo. FMA:72549 ectoderm cell ectodermal cell A cell of the outer of the three germ layers of the embryo. MESH:D004475 A cell of the middle germ layer of the embryo. FMA:72554 mesoblast mesoderm cell mesodermal cell A cell of the middle germ layer of the embryo. MESH:D008648 A cell of the inner of the three germ layers of the embryo. FMA:72555 endoderm cell endodermal cell A cell of the inner of the three germ layers of the embryo. MESH:D004707 A cell that lacks a nucleus. FMA:68647 non-nucleated cell anucleate cell A cell that lacks a nucleus. FB:ma A cell with a single nucleus. single nucleate cell A cell with a single nucleus. FB:ma GOC:tfm binucleate cell A cell with more than one nucleus. AEO:0000203 WBbt:0008074 syncitium syncytial cell syncytium multinucleate cell A cell with more than one nucleus. FB:ma A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. BTO:0000424 CALOHA:TS-0290 FMA:81100 RBC red blood cell erythrocyte true A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. GOC:tfm MESH:D004912 MESH:D005057 eukaryotic cell Eumycetozoan cell eye photoreceptor cell A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. structural cell A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. TAIR:sr A mature sexual reproductive cell having a single set of unpaired chromosomes. CALOHA:TS-0395 FBbt:00005412 FMA:18649 haploid nucleated cell haploid germ cell gamete true A mature sexual reproductive cell having a single set of unpaired chromosomes. GOC:tfm ISBN:0721662544 lens cell crystallin accumulating cell Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid. BTO:0003687 FMA:62511 serous cell serous secreting cell Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid. GOC:tfm ISBN:0517223651 ISBN:0721662544 BTO:0003689 mucous cell mucus secreting cell A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell A cell that is specialised to accumulate a particular substance(s). FB:ma extracellular matrix secreting cell oxygen accumulating cell A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 migratory neural crest cell A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. doi:10.1016/j.stem.2015.02.017 A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. mesenchyme condensation cell A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. GOC:tfm PMID:5025404 A cell of the sclera of the eye. scleral cell A cell of the sclera of the eye. GOC:add A structural cell that is part of optic choroid. choroidal cell of the eye A structural cell that is part of optic choroid. GOC:add extraembryonic cell A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. FMA:83028 trophoblastic cell trophoblast cell true A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. GOC:tfm MESH:D014327 A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. epiblast cell A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. GOC:tfm ISBN:0618947256 An undifferentiated cell produced by early cleavages of the fertilized egg (zygote). BTO:0001473 FMA:72551 blastomere blastoderm cell An undifferentiated cell produced by early cleavages of the fertilized egg (zygote). MESH:D001756 A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. FMA:86767 Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. multi-potent skeletal muscle stem cell true A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. PMID:18282570 A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. sphincter associated smooth muscle cell true A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. GOC:cjm A smooth muscle cell associated with the vasculature. VSMC vascular smooth muscle cell vascular associated smooth muscle cell true A smooth muscle cell associated with the vasculature. GOC:dsd GOC:tfm An epithelial cell of the integument (the outer layer of an organism). BTO:0001470 CALOHA:TS-0283 FMA:62411 MESH:D000078404 cell of epidermis epithelial cell of skin epidermal cell An epithelial cell of the integument (the outer layer of an organism). Flybase:dsj MA:ma cell of epidermis FMA:62411 epithelial cell of skin FMA:62411 Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 EHDAA2:0004546 FMA:72395 animal zygote Diploid cell produced by the fusion of sperm cell nucleus and egg cell. ISBN:0471245208 A cell whose function is determined by its response to an electric signal. electrically responsive cell A cell whose function is determined by its response to an electric signal. FB:ma ganglion interneuron true An interneuron that has its cell body in a central nervous system. Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. CNS interneuron An interneuron that has its cell body in a central nervous system. doi:10.1016/B978-0-12-817424-1.00001-X A cell that initiates an electrical signal and passes that signal to another cell. electrically signaling cell A cell that initiates an electrical signal and passes that signal to another cell. FB:ma A cell that contains more than two haploid sets of chromosomes. polyploid cell A cell that contains more than two haploid sets of chromosomes. FB:ma PMID:32646579 https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy A cell whose nucleus contains a single haploid genome. haploid cell A cell whose nucleus contains a single haploid genome. FB:ma GOC:tfm endopolyploid cell carbohydrate secreting cell biogenic amine secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). 5-HT secreting cell 5-Hydroxytryptamine secreting cell serotonin secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). GOC:tfm PMID:19630576 A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme. noradrenaline secreting cell norepinephrin secreting cell norepinephrine secreting cell noradrenergic cell A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme. GOC:tfm ISBN:068340007X A photoreceptor cell that detects visible light. visible light photoreceptor cell A photoreceptor cell that detects visible light. GOC:tfm A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. BTO:0002064 FMA:83624 stromal cell A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. GOC:tfm MESH:D017154 A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. FMA:62935 D cell type D enteroendocrine cell A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. MESH:D019864 An endorphine cell that secretes enkephalin. enkephalin secreting cell An endorphine cell that secretes enkephalin. GO:tfm A peptide hormone secreting cell that secretes endorphin. endorphin secreting cell A peptide hormone secreting cell that secretes endorphin. GO:tfm An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. BTO:0004108 FMA:67609 G cell type G enteroendocrine cell An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. GOC:tfm ISBN:0517223651 MESH:D019863 A peptide hormone secreting cell that secretes gastrin. gastrin secreting cell A peptide hormone secreting cell that secretes gastrin. GO:tfm A precursor cell destined to differentiate into cardiac muscle cell. FMA:84797 cardiac muscle progenitor cell cardiomyocyte progenitor cell cardiac muscle myoblast A precursor cell destined to differentiate into cardiac muscle cell. GOC:tfm MESH:D032386 A precursor cell destined to differentiate into smooth muscle myocytes. FMA:84798 myoblast, smooth muscle satellite cell smooth muscle myoblast A precursor cell destined to differentiate into smooth muscle myocytes. GOC:tfm MESH:D032390 myoblast, smooth muscle MESH:D032390 A myoblast that differentiates into skeletal muscle fibers. FMA:84799 skeletal myoblast skeletal muscle myoblast A myoblast that differentiates into skeletal muscle fibers. SANBI:mhl fungal cell A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy. FMA:83043 syncytial trophoblast cell syncytiotrophoblastic cell plasmidotrophoblast cell syntrophoblast cell syncytiotrophoblast cell https://github.com/obophenotype/cell-ontology/issues/2100 A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy. GOC:tfm ISBN:0323052908 syncytial trophoblast cell PMID:11787150 syncytiotrophoblastic cell PMID:21733368 A neuron which conveys sensory information centrally from the periphery. FMA:87653 input neuron afferent neuron A neuron which conveys sensory information centrally from the periphery. GOC:tfm MESH:D009475 A neuron which sends impulses peripherally to activate muscles or secretory cells. output neuron efferent neuron A neuron which sends impulses peripherally to activate muscles or secretory cells. MESH:D009476 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 nerve cell These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron https://www.swissbiopics.org/api/image/Neuron_cells.svg The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. MESH:D009474 http://en.wikipedia.org/wiki/Neuron An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. FMA:83518 rubriblast pronormoblast proerythroblast true An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. ISBN:0721601464 PMID:1638021 rubriblast ISBN:0721601464 A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83505 basophilic normoblast early erythroblast early normoblast prorubricyte basophilic erythroblast true A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. GOC:tfm ISBN:0721601464 basophilic normoblast ISBN:0721601464 early erythroblast ISBN:0721601464 early normoblast ISBN:0721601464 prorubricyte ISBN:0721601464 A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83506 intermediate erythroblast intermediate normoblast polychromatic erythroblast polychromatic normoblast polychromatophilic normoblast rubricyte polychromatophilic erythroblast true A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. ISBN:0721601464 intermediate erythroblast ISBN:0721601464 intermediate normoblast ISBN:0721601464 polychromatic erythroblast ISBN:0721601464 polychromatic normoblast ISBN:0721601464 polychromatophilic normoblast ISBN:0721601464 rubricyte ISBN:0721601464 The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. FMA:84646 acidophilic erythroblast eosinophilic erythroblast late erythoblast orthochromatic normoblast pyknotic eto enrythroblast orthochromatic erythroblast true The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. ISBN:0721601464 acidophilic erythroblast ISBN:0721601464 eosinophilic erythroblast ISBN:0721601464 orthochromatic normoblast ISBN:0721601464 pyknotic eto enrythroblast ISBN:0721601464 The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). BTO:0001164 CALOHA:TS-0610 FMA:84235 MESH:D055016 CFU-Meg Meg-CFC MkP colony-forming unit-megakaryocyte megacaryoblast megacaryocyte progenitor cell megakaryoblast megakaryocytic progenitor cell promegacaryocyte promegakaryocyte Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell true The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). GOC:dsd GOC:tfm ISBN:0721601464 CFU-Meg PMID:11722431 PMID:12482498 Meg-CFC PMCID:PMC1794060 MkP PMID:21116988 megakaryocytic progenitor cell PMID:12482498 A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. BTO:0000843 CALOHA:TS-0611 FMA:83555 megacaryocyte megalocaryocyte megalokaryocyte Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte true A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. ISBN:0721601464 MESH:D008533 PMID:31043076 http://en.wikipedia.org/wiki/Megakaryocyte An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. BTO:0001173 CALOHA:TS-0864 MESH:D012156 reticulocyte true An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. GOC:add GOC:tfm PMID:15946868 PMID:2037622 An erythrocyte having a nucleus. RBC red blood cell nucleate erythrocyte true An erythrocyte having a nucleus. GOC:add GOc:tfm A mesenchymal stem cell capable of developing into blood vessel endothelium. angioblast chondroplast These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell true A mesenchymal stem cell capable of developing into blood vessel endothelium. GOC:dsd GOC:tfm PMID:12768659 A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field. cardiac mesenchymal cell A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field. PMID:18816864 One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. BTO:0001036 CALOHA:TS-0866 FMA:67748 cone retinal cone cell One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. MESH:D017949 cone doi:10.1038/s41598-020-66092-9 An epithelial cell of the cornea. BTO:0004298 CALOHA:TS-0173 FMA:70551 epithelial cell of cornea corneal epithelial cell An epithelial cell of the cornea. GOC:tfm epithelial cell of cornea FMA:70551 The reproductive cell in multicellular organisms. BTO:0000535 NCIT:C12597 VHOG:0001534 WBbt:0006796 germ cell true The reproductive cell in multicellular organisms. MESH:D005854 A steroid hormone secreting cell that secretes androgen. androgen secreting cell A steroid hormone secreting cell that secretes androgen. GOC:tfm An erythrocyte lacking a nucleus. red blood cell RBC enucleate erythrocyte true An erythrocyte lacking a nucleus. GOC:add GOC:tfm RBC One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision. BTO:0001024 CALOHA:TS-0870 FMA:67747 rod retinal rod cell One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision. MESH:D017948 rod doi:10.1038/s41598-020-66092-9 A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). FMA:83625 MESH:D061354 acinic cell acinous cell acinar cell A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). GOC:tfm http://www.copewithcytokines.de A cell whose primary function is to support other cell types. BTO:0002315 supportive cell supporting cell A cell whose primary function is to support other cell types. FB:ma GOC:tfm An extracellular matrix secreting cell that secretes collagen. collagen secreting cell An extracellular matrix secreting cell that secretes collagen. GOC:tfm A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. FMA:70567 gonocyte primitive germ cell primordial germ cell true true A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. GOC:tfm PMID:1381289 A mature sexual reproductive cell of the female germline. female gamete true A mature sexual reproductive cell of the female germline. GOC:tfm A non-terminally differentiated cell that is capable of developing into a muscle cell. muscle precursor cell A non-terminally differentiated cell that is capable of developing into a muscle cell. GOC:add A cell that stores and secretes pancreatic polypeptide hormone. FMA:62938 FMA:83409 type F enteroendocrine cell PP cell A cell that stores and secretes pancreatic polypeptide hormone. GOC:tfm JB:jb PMID:15153415 Epithelial cells derived from neural plate and neural crest. neuroepithelial cell BTO:0004301 FMA:70557 The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). neurecto-epithelial cell Epithelial cells derived from neural plate and neural crest. GOC:tfm A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 MESH:D053687 somatic stem cell A stem cell that can give rise to cell types of the body other than those of the germ-line. GO:0048103 Muscle cell which has as its direct parts myofilaments organized into sarcomeres. BTO:0002916 CALOHA:TS-2157 FMA:86936 striated muscle cell Muscle cell which has as its direct parts myofilaments organized into sarcomeres. GOC:tfm ISBN:0721662544 An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 CALOHA:TS-0549 FMA:62852 MESH:D007962 NCIT:C12529 leucocyte white blood cell immune cell leukocyte true An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. GOC:add GOC:tfm ISBN:978-0-323-05290-0 The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve. BTO:0001800 FMA:67765 MESH:D012165 gangliocyte ganglion cell of retina RGC RGCs retinal ganglion cell The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve. GOC:dph RGC doi:10.1038/s41598-020-66092-9 RGCs doi:10.1038/s41598-020-66092-9 Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. FMA:83808 cardiocyte BTO:0001539 CALOHA:TS-0115 FMA:14067 MESH:D032383 cardiac muscle fiber cardiac myocyte cardiomyocyte heart muscle cell This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. cardiac muscle cell Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. GOC:mtg_cardiacconduct_nov11 GOC:tfm ISBN:0323052908 PMID:22426062 PMID:4711263 cardiac muscle fiber GO:0048739 A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. BTO:0001441 CALOHA:TS-0647 MESH:D022423 myeloid cell true A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. GOC:add A immature or mature cell in the lineage leading to and including erythrocytes. CALOHA:TS-0290 FMA:62845 FMA:83516 erythropoietic cell Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell A immature or mature cell in the lineage leading to and including erythrocytes. GOC:add GOC:tfm A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. BTO:0001571 CALOHA:TS-0289 FMA:83504 MESH:D004900 normoblast erythroblast true A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. GOC:add ISBN:0721601464 PMID:18174176 A cell of the monocyte, granulocyte, or mast cell lineage. myeloid leukocyte true A cell of the monocyte, granulocyte, or mast cell lineage. GOC:add A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. BTO:0000725 CALOHA:TS-0448 MPP hemopoietic progenitor cell Markers differ between mouse and human. hematopoietic multipotent progenitor cell A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. GOC:add GOC:tfm PMID:19022770 A progenitor cell restricted to the myeloid lineage. myeloid progenitor cell BTO:0004730 CALOHA:TS-2099 FMA:70339 Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell true A progenitor cell restricted to the myeloid lineage. GOC:add GOC:tfm PMID:19022770 A leukocyte with a single non-segmented nucleus in the mature form. BTO:0000878 CALOHA:TS-0768 FMA:86713 mononuclear leukocyte peripheral blood mononuclear cell mononuclear cell true A leukocyte with a single non-segmented nucleus in the mature form. GOC:add A neuron that releases serotonin as a neurotransmitter. FBbt:00005133 MESH:D059326 WBbt:0006837 5-HT neuron 5-hydroxytryptamine neuron serotinergic neuron serotonergic neuron A neuron that releases serotonin as a neurotransmitter. SANBI:mhl A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 haematopoietic cell haemopoietic cell hemopoietic cell hematopoietic cell A cell of a hematopoietic lineage. GOC:add GO_REF:0000031 A connective tissue cell found in bone. 2011-11-16T04:28:16Z bone cell A connective tissue cell found in bone. GOC:add GO_REF:0000034 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. 2010-01-06T03:43:27Z hematopoietic oligopotent progenitor cell, lineage-negative A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. GOC:tfm PMID:19022770 A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). BTO:0004911 BFU-E CFU-E blast forming unit erythroid burst forming unit erythroid colony forming unit erythroid erythroid stem cell erythroid progenitor cell, mammalian A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). GOC:add ISBN:0721601464 BFU-E CFU-E A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. GOC:tfm PMID:19022770 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. GOC:tfm PMID:19022770 https://orcid.org/0000-0001-5208-3432 A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. 2010-06-24T03:16:29Z BTO:0000028 CALOHA:TS-0737 FMA:63032 acinar cell of pancreas pancreatic acinar cell true A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. GOC:tfm ISBN:0517223651 PMID:20395539 http://www.copewithcytokines.de/cope.cgi?key=pancreatic%20acinar%20cells An enteroendocrine cell that produces glucagon. 2010-09-10T10:48:54Z FMA:62939 type A enteroendocrine cell An enteroendocrine cell that produces glucagon. GOC:tfm ISBN:0412046911 Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter. 2010-06-28T08:36:15Z BTO:0001032 FMA:14146 Purkinje cell fiber Purkinje muscle cell myocytus conducens cardiacus Purkinje myocyte Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter. FMA:0412046911 GOC:tfm PMID:19939742 A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery. 2010-06-29T11:41:37Z pacemaker cell BTO:0004190 FMA:67101 P cell cardiac pacemaker cell myocytus nodalis nodal myocyte A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery. FMA:67101 GOC:tfm cardiac pacemaker cell GOC:pr Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes. 2010-06-29T02:39:32Z FMA:67142 transitional myocyte Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes. FMA:67142 GOC:tfm The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides). 2010-06-29T11:50:47Z FMA:67111 myocardial endocrine cell The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides). FMA:67111 GOC:tfm An epithelial cell derived from endoderm. 2010-06-29T03:38:14Z FMA:69075 endo-epithelial cell An epithelial cell derived from endoderm. FMA:69075 GOC:tfm An epithelial cell derived from ectoderm. 2010-06-29T03:38:22Z FMA:69074 ecto-epithelial cell An epithelial cell derived from ectoderm. FMA:69074 GOC:tfm Epithelial cell derived from mesoderm or mesenchyme. 2010-06-29T03:49:14Z FMA:69076 epithelial mesenchymal cell meso-epithelial cell Epithelial cell derived from mesoderm or mesenchyme. FMA:69076 GOC:tfm Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. 2010-06-30T08:49:43Z FMA:63099 pancreatic ductal cell Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. FMA:63099 GOC:tfm PMID:14740223 A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types. 2010-06-30T08:49:52Z FMA:62455 centroacinar cell of Langerhans pancreatic centroacinar cell pancreatic centro-acinar cell A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types. GOC:tfm PMID:12142741 PMID:20018761 PMID:8185160 A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart. 2010-07-21T01:33:38Z FMA:67968 specialized cardiac myocyte A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart. FMA:67968 GOC:tfm A leukocyte that lacks granules. 2010-07-22T11:30:33Z FMA:62855 agranular leukocyte nongranular leukocyte true A leukocyte that lacks granules. GOC:tfm This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise. 2010-07-22T03:26:00Z BTO:0003914 FMA:86573 ICC intestinal pacemaker cell Some argue this cell type is of mesenchymal origin. interstitial cell of Cajal true This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise. GOC:tfm PMID:16460275 PMID:19520112 intestinal pacemaker cell GOC:pr A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 MESH:D001854 MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell true A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. GOC:tfm ISBN:0618947256 A cell in the hilum of the ovary that produces androgens. 2010-08-23T11:18:18Z FMA:18710 hilar cell of ovary hilus cell of ovary A cell in the hilum of the ovary that produces androgens. GOC:tfm ISBN:068340007X A stomal cell of the ovary 2010-08-23T12:10:31Z FMA:72299 ovarian stromal cell stromal cell of ovary A stomal cell of the ovary GOC:tfm ovarian stromal cell GOC:cjm An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 vascular endothelial cell cubodial endothelial cell of vascular tree These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. GOC:dsd GOC:tfm PMID:12768659 An endothelial cell found in capillaries. 2010-08-24T10:15:00Z BTO:0004956 CALOHA:TS-0112 FMA:67756 capillary endothelial cell An endothelial cell found in capillaries. GOC:tfm Epithelial cells derived from general body ectoderm and ectoderm placodes. 2010-08-26T08:31:08Z FMA:70556 general ecto-epithelial cell Epithelial cells derived from general body ectoderm and ectoderm placodes. GOC:tfm An epithelial cell found in the lining of the stomach. 2010-08-25T03:22:08Z FMA:62948 epithelial cell of stomach true An epithelial cell found in the lining of the stomach. GOC:tfm A mucous cell in the epithelium of the stomach. 2010-08-25T03:38:51Z FMA:63464 mucous cell of stomach A mucous cell in the epithelium of the stomach. GOC:tfm A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. 2010-08-25T03:57:08Z FMA:62953 stem cell of gastric gland true A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. GOC:tfm ISBN:0517223651 A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes). 2010-08-30T02:00:42Z FMA:86577 HpSC hepatic stem cell https://github.com/obophenotype/cell-ontology/issues/800 true A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes). GOC:tfm PMID:26798363 HpSC PMID:18442648 A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. 2010-09-07T10:38:03Z FMA:70950 vertebrate lens cell A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. GOC:tfm ISBN:0721662544 A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. 2010-09-07T10:45:47Z FMA:67559 lens epithelial cell true A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. GOC:tfm ISBN:0721662544 http://en.wikipedia.org/wiki/Lens_%28anatomy%29#Lens_epithelium A fibroblast in the bone marrow. 2010-09-07T02:25:18Z FMA:84377 marrow fibroblast A fibroblast in the bone marrow. GOC:tfm A cell containing at least one nucleus. 2010-09-07T03:32:33Z FMA:67513 nucleate cell A cell containing at least one nucleus. GOC:tfm A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells. 2010-09-08T08:53:42Z FMA:70611 smooth muscle fiber of sphincter of pupil smooth muscle fibre of sphincter of pupil smooth muscle cell of sphincter of pupil true A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells. GOC:tfm ISBN:0721662544 ISBN:0721694128 A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). 2010-09-07T03:57:09Z BTO:0002669 FMA:86711 MESH:D000072916 PBSC peripheral blood stem cell true A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). GOC:tfm An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. 2010-09-08T09:26:53Z epithelial cell of alimentary canal An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. GOC:tfm ISBN:0721662544 An epithelial cell of the esophagus. 2010-09-08T09:28:20Z FMA:63071 epithelial cell of esophagus true An epithelial cell of the esophagus. GOC:tfm An epithelial cell of the large intestine. 2010-09-08T09:28:22Z BTO:0004297 FMA:256157 epithelial cell of colon epithelial cell of large intestine true An epithelial cell of the large intestine. GOC:tfm An epithelial cell of the small intestine. 2010-09-08T09:41:46Z FMA:256159 epithelial cell of small intestine true An epithelial cell of the small intestine. GOC:tfm An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. 2010-09-14T10:57:26Z FMA:63134 endothelial cell of sinusoid An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. GOC:tfm ISBN:0618947256 A type of enteroendocrine cell found in the stomach that secretes glucagon. 2010-09-10T10:54:42Z FMA:83411 type A cell of stomach A type of enteroendocrine cell found in the stomach that secretes glucagon. GOC:tfm A D cell located in the colon. 2010-09-10T11:37:35Z FMA:268744 colon D-cell colonic delta cell delta cell of colon type D cell of colon A D cell located in the colon. GOC:tfm A type D cell of the small intestine. 2010-09-10T01:34:22Z FMA:268736 delta cell of small intestine small intestine D-cell small intestine delta cell type D cell of small intestine A type D cell of the small intestine. GOC:tfm A type D cell found in the stomach. 2010-09-10T01:36:03Z FMA:83410 delta cell of stomach stomach D-cell stomach delta cell type D cell of stomach A type D cell found in the stomach. GOC:tfm A PP cell located in the islets of the pancreas. 2010-09-10T03:30:31Z BTO:0000805 FMA:70588 MESH:D050418 PP cell of pancreatic islet PP-cell of pancreatic islet pancreatic polypeptide-secreting cell The term PP cell of pancreatic acinus was obsoleted due to a lack of evidence, making PP cell of pancreatic islets synonymous with pancreatic PP cell. pancreatic PP cell A PP cell located in the islets of the pancreas. GOC:tfm An epithelial cell of a skin gland. 2010-09-14T12:00:07Z FMA:70657 epithelial cell of gland of skin epithelial cell of skin gland An epithelial cell of a skin gland. GOC:tfm A cell that is part of the nervous system. 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 neural cell A cell that is part of the nervous system. GOC:tfm ISBN:0618947256 A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 connective tissue cell A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. GOC:tfm ISBN:0618947256 A cell of the embryo. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 embryonic cell (metazoa) A cell of the embryo. FMA:0618947256 An adipocyte derived from a neural crest cell. 2010-09-20T02:25:25Z neural crest derived adipocyte An adipocyte derived from a neural crest cell. GOC:tfm PMID:17507398 An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. 2010-09-21T04:33:05Z FMA:75621 endocardial endothelial cell endothelial cell of endocardium endocardial cell An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. GOC:tfm ISSN:0452-3458 endothelial cell of endocardium FMA:75621 A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. 2010-09-21T04:41:06Z pancreatic endocrine progenitor pancreatic islet progenitor cell progenitor cell of endocrine pancreas A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. GOC:tfm PMID:20025937 PMID:20217494 PMID:22728667 A hematopoietic stem cell that exists during embryogenesis. 2010-09-22T09:05:13Z gestational hematopoietic stem cell A hematopoietic stem cell that exists during embryogenesis. GOC:tfm ISBN:978-60327-246-6 A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate. 2010-09-22T01:57:40Z corneal fibroblast corneal keratocyte keratocyte A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate. GOC:tfm ISBN:9780702029585 An endo-epithelial cell of the respiratory tract. 2010-09-23T04:38:49Z BTO:0004533 airway epithelial cell respiratory epithelial cell true An endo-epithelial cell of the respiratory tract. GOC:tfm A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. 2010-09-24T01:13:01Z FBbt:00005812 myotubule single cell sarcomere myotube A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. GOC:dos GOC:tfm ISBN:0323052908 PMID:22274696 A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles. 2010-10-15T09:24:05Z nucleated reticulocyte true A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles. GOC:tfm PMID:18182572 PMID:9011180 PMID:9046052 A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes. 2010-10-15T09:24:08Z CALOHA:TS-0864 FMA:66785 enucleated reticulocyte true A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes. GOC:tfm ISBN:0-12203-052-4 ISBN:0721601464 A cell located in the heart, including both muscle and non muscle cells. 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 FMA:84791 heart cell From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte A cell located in the heart, including both muscle and non muscle cells. GOC:tfm A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc 2010-12-07T04:03:56Z BTO:0002441 FMA:84639 adventitial cell A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc GOC:tfm A smooth muscle cell of the intestine. 2011-01-17T03:39:38Z intestinal smooth muscle cell enteric smooth muscle cell true A smooth muscle cell of the intestine. GOC:tfm An adipocyte that is part of subcutaneous adipose tissue. 2011-02-21T02:51:22Z subcutaneous fat cell subcutaneous adipocyte true An adipocyte that is part of subcutaneous adipose tissue. GOC:tfm An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. 2011-02-28T01:20:20Z small bile duct cholangiocyte intrahepatic cholangiocyte true An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. GOC:tfm PMID:23720296 small bile duct cholangiocyte PMID:23720296 A smooth muscle cell of the aorta. 2011-02-28T01:42:12Z BTO:0004577 aortic smooth muscle cell A smooth muscle cell of the aorta. GOC:tfm A mesenchymal stem cell that is part of the bone marrow. 2011-02-28T01:47:47Z mesenchymal stem cell of the bone marrow A mesenchymal stem cell that is part of the bone marrow. GOC:tfm An endothelial cell that is part of the vein. 2011-02-28T03:48:11Z FMA:62104 KUPO:0001099 endothelial cell of vein venous endothelial cell vein endothelial cell true An endothelial cell that is part of the vein. GOC:tfm An endothelial progenitor cell that participates in angiogenesis during development. 2011-02-28T04:20:39Z See CL:0002619. embryonic blood vessel endothelial progenitor cell An endothelial progenitor cell that participates in angiogenesis during development. GOC:tfm A fibroblast of the aortic adventitia. 2011-02-28T04:43:41Z fibroblast of the aortic adventitia true A fibroblast of the aortic adventitia. GOC:tfm A fibroblast that is part of the heart. 2011-02-28T04:57:44Z cardiac fibroblast fibroblast of cardiac tissue true true A fibroblast that is part of the heart. GOC:tfm 2011-02-28T05:05:33Z fibroblast of dermis true A fibroblast that is part of lung. 2011-02-28T05:11:03Z BTO:0000764 CALOHA:TS-0575 fibroblast of lung true A fibroblast that is part of lung. GOC:tfm A fibroblast of pulmonary artery. 2011-02-28T05:22:27Z fibroblast of pulmonary artery true A fibroblast of pulmonary artery. GOC:tfm An epithelial cell of the intestine. 2011-03-01T05:18:31Z intestinal epithelial cell An epithelial cell of the intestine. GOC:tfm A mesenchymal stem cell of adipose tissue. 2011-03-01T09:57:17Z mesenchymal stem cell of adipose mesenchymal stem cell of adipose tissue A mesenchymal stem cell of adipose tissue. GOC:tfm A mesenchymal stem cell of liver. 2011-03-01T09:58:51Z hepatic mesenchymal stem cell true A mesenchymal stem cell of liver. GOC:tfm A mesenchymal stem cell of the vertebrae. 2011-03-01T10:40:27Z vertebral mesenchymal stem cell true A mesenchymal stem cell of the vertebrae. GOC:tfm A stromal cell of the pancreas. 2011-03-02T02:40:41Z stromal cell of pancreas true A stromal cell of the pancreas. GOC:tfm A blood vessel endothelial cell that is part of the retina. 2011-03-06T03:28:27Z retinal blood vessel endothelial cell true A blood vessel endothelial cell that is part of the retina. GOC:tfm A smooth muscle cell of the bachiocephalic vasculature. 2011-03-06T05:00:58Z smooth muscle cell of the brachiocephalic vasculature A smooth muscle cell of the bachiocephalic vasculature. GOC:tfm A vascular associated smooth muscle cell of the brain vasculature. 2011-03-06T05:01:20Z smooth muscle cell of the brain vasculature true A vascular associated smooth muscle cell of the brain vasculature. GOC:tfm A smooth muscle of the pulmonary artery. 2011-03-06T05:01:28Z BTO:0003336 smooth muscle cell of the pulmonary artery A smooth muscle of the pulmonary artery. GOC:tfm A smooth muscle cell of the subclavian artery. 2011-03-06T05:01:52Z smooth muscle cell of the subclavian artery A smooth muscle cell of the subclavian artery. GOC:tfm Smooth muscle cell of the carotid artery. 2011-03-06T05:01:56Z smooth muscle cell of the carotid artery Smooth muscle cell of the carotid artery. GOC:tfm A smooth muscle cell of the esophagus. 2011-03-06T05:48:17Z smooth muscle cell of the esophagus true A smooth muscle cell of the esophagus. GOC:tfm A neuron of the raphe nuclei. 2011-03-06T07:42:06Z raphe nuclei neuron true A neuron of the raphe nuclei. GOC:tfm A neuron of the ventral spinal cord. 2011-03-06T07:46:03Z neuron of the ventral spinal cord true A neuron of the ventral spinal cord. GOC:tfm A fibroblast of skin. 2011-03-14T12:31:49Z BTO:0001255 CALOHA:TS-0935 skin fibroblast true A fibroblast of skin. GOC:tfm 2011-06-21T12:29:31Z epithelial cell of lower respiratory tract true A glandular epithelial cell of the esophagus. 2011-07-08T03:55:57Z FMA:86548 glandular cell of esophagus true true A glandular epithelial cell of the esophagus. GOC:tfm A glandular epithelial cell of the large intestine. 2011-07-08T04:03:01Z FMA:87194 glandular cell of the large intestine true A glandular epithelial cell of the large intestine. GOC:tfm A glandular epithelial cell that is part of the stomach. 2011-07-11T01:20:35Z CALOHA:TS-1284 FMA:86554 glandular cell of stomach true A glandular epithelial cell that is part of the stomach. GOC:tfm A myocardial endocrine cell that is part of the atrium. 2011-07-11T02:45:39Z FMA:83389 myocardial endocrine cell of atrium true A myocardial endocrine cell that is part of the atrium. GOC:tfm A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart. 2011-07-11T03:15:38Z cardiovascular progenitor cell CPC Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell. cardioblast A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart. GOC:tfm PMID:19745164 cardiovascular progenitor cell PMID:17519333 PMID:19745164 CPC PMID:19745164 A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. 2011-08-16T02:38:01Z retinal progenitor cell A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. GOC:tfm PMID:20959166 PMID:21148186 A neuroblast derived from a neural crest cell. 2011-08-22T09:24:15Z neural crest derived neuroblast A neuroblast derived from a neural crest cell. GOC:tfm PMID:17407019 A PP cell found in intestine. 2011-09-27T11:59:01Z PP cell of intestine true A PP cell found in intestine. GOC:tfm PMID:2420136 PMID:728970 A CNS interneuron located in the spinal cord. Is_a interneuron, part_of UBERON:0002240. spinal cord interneuron true A CNS interneuron located in the spinal cord. CL:CVS A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic. somatic motor neuron somatomotor neuron A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic. ZFIN:CVS Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation. hepatoblast https://github.com/obophenotype/cell-ontology/issues/800 Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation. GOC:CVS PMID:18356246 PMID:20483998 PMID:26798363 https://orcid.org/0000-0003-1940-6740 Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). 2012-06-15T02:51:27Z scleroblast Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). GO_REF:0000034 scleroblast GO_REF:0000034 Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. 2012-06-27T08:27:35Z premigratory neural crest cell Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. UBERONREF:0000002 Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. 2012-06-27T10:44:01Z prechondroblast Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. GO_REF:0000034 Any muscle cell in which the fibers are not organised into sarcomeres. non-striated muscle cell Any muscle cell in which the fibers are not organised into sarcomeres. GOC:DOS Any hematopoietic cell that is a precursor of some other hematopoietic cell type. hematopoietic precursor cell Any hematopoietic cell that is a precursor of some other hematopoietic cell type. GOC:dos A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. MESH:D018485 skeletal muscle fiber A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. GOC:tfm ISBN:0323052908 A muscle cell that is part of some visceral muscle. FBbt:00005070 visceral muscle cell A muscle cell that is part of some visceral muscle. GOC:dos A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods. striated visceral muscle cell A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods. GOC:dos A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods. transversely striated visceral muscle cell A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods. GOC:dos A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers. myogenic precursor cell The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins. adult skeletal muscle myoblast A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers. PMID:23303905 myogenic precursor cell PMID:23303905 A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration. mesenchyme cell mesenchymal cell A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves. endocardial cushion cell A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves. PMID:18816864 An endocrine cell that is part of the pancreas. pancreatic endocrine cell An endocrine cell that is part of the pancreas. GOC:dos A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter. noradrenergic neuron A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter. GOC:dos 2017-07-09T19:12:36Z visual system neuron Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation. 2020-02-29T17:33:55Z mural cell Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation. Wiki:Mural_cell&oldid=930603194 2020-02-29T17:37:00Z microcirculation associated smooth muscle cell A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord. spinal sensory neuron sensory neuron of spinal nerve A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord. GOC:nv GOC:pr Any cell in the compound eye, a light sensing organ composed of ommatidia. GOC:pr PMID:12021768 compound eye retinal cell Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 retinal cell Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. GOC:pr An enteroendocrine cell that is located in the small intestine. small intestine enteroendocrine cell enteroendocrine cell of small intestine An enteroendocrine cell that is located in the small intestine. http://orcid.org/0000-0003-3440-1876 A stromal cell found in the lamina propria of the large intestine. stromal cell of lamina propria of large intestine A stromal cell found in the lamina propria of the large intestine. http://orcid.org/0000-0003-4183-8865 A stromal cell found in the lamina propria of the small intestine. stromal cell of lamina propria of small intestine A stromal cell found in the lamina propria of the small intestine. http://orcid.org/0000-0003-4183-8865 A mesothelial cell that is part of the small intestine. mesothelial cell of small intestine A mesothelial cell that is part of the small intestine. http://orcid.org/0000-0003-4183-8865 A mesothelial cell that is part of the colon. mesothelial cell of large intestine mesothelial cell of colon A mesothelial cell that is part of the colon. http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865 A stromal cell found in the lamina propria of the colon. stromal cell of colon lamina propria stromal cell of lamina propria of colon A stromal cell found in the lamina propria of the colon. http://orcid.org/0000-0003-3440-1876 An enteroendocrine cell that is located in the colon. colon enteroendocrine cell enteroendocrine cell of colon An enteroendocrine cell that is located in the colon. http://orcid.org/0000-0003-3440-1876 A smooth muscle cell that is located in the anorectum. anorectum smooth muscle cell smooth muscle cell of anorectum A smooth muscle cell that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 A stromal cell found in the lamina propria of the anorectum. stromal cell of anorectum lamina propria A stromal cell found in the lamina propria of the anorectum. http://orcid.org/0000-0003-3440-1876 An enteroendocrine cell that is located in the anorectum. anorectum enteroendocrine cell enteroendocrine cell of anorectum An enteroendocrine cell that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 An endothelial cell that is part of a hepatic portal vein. 2021-12-13T14:01:05Z portal endothelial cell EFO:0010704 endothelial cell of hepatic portal vein An endothelial cell that is part of a hepatic portal vein. PMID:30348985 https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development. 2022-02-21T15:39:10Z embryonic skeletal muscle fiber A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development. PMID:32094117 PMID:7196501 http://orcid.org/0000-0003-2034-601X A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen. 2022-03-17T12:00:44Z portal fibroblast hepatic portal fibroblast A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen. PMID:20209607 PMID:24814904 https://orcid.org/0000-0001-7655-4833 A stromal cell that is part_of a bone marrow. bone marrow stromal cell stromal cell of bone marrow A mononuclear cell that is part_of a bone marrow. bone marrow mononuclear cell mononuclear cell of bone marrow cardiac blood vessel endothelial cell His-Purkinje system cell cardiac endothelial cell camera type eye photoreceptor cell camera-type eye photoreceptor cell A zygote in a plant or an animal. MESH:D015053 zygote cardiac glial cell MESH:D032386 cardiac myoblast A neuron that has its soma in the heart. This term is used in 3 GO terms that were created as part of the heart development focus project. cardiac neuron https://github.com/obophenotype/cell-ontology/pull/1488 A neuron that has its soma in the heart. PMID:12486170 PMID:29265764 A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement. spinal cord motor neuron true A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement. GOC:nv A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites. paraxial mesoderm cell somitic mesoderm cell presomitic mesoderm cell paraxial cell A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites. GOC:NV PMID:11687492 A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. neural crest cell A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 A mesothelial cell that is part of the epicardium. mesothelial cell of epicardium A fibroblast that is part of upper back skin. fibroblast of upper back skin A fibroblast that is part of skin of back. fibroblast of skin of back A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. progenitor cell A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. ISBN:978-1-62808-994-3 https://doi.org/10.1016/B978-0-12-409503-8.00002-0 Any fibroblast that is part of skeletal muscle tissue. skeleton muscle fibroblast skeletal muscle fibroblast Any fibroblast that is part of skeletal muscle tissue. PMID:28369879 https://orcid.org/0000-0001-6164-0667 Any microvascular endothelial cell that is part of the dermis. DMEC cell dermal microvascular endothelium cell dermal microvascular endothelial cell Any microvascular endothelial cell that is part of the dermis. BTO:0004574 CL:patterns/cellPartOfAnatomicalEntity Epithelial cell that is part of the colon epithelium. colonic epithelial cell colon epithelial cell Epithelial cell that is part of the colon epithelium. GOC:NV A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell A cell that, by division or terminal differentiation, can give rise to other cell types. GOC:dos Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. GOC:add Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. 2009-12-22T04:24:54Z basophilic cytoplasm Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. GOC:tfm Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. 2009-12-28T04:25:23Z polychromatophilic cytoplasm Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. GOC:tfm A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. 2009-12-23T10:53:24Z increased nucleus size A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. GOC:tfm A smooth muscle cell that is part of any blood vessel. 2020-07-21T12:42:48Z smooth muscle cell of blood vessel blood vessel smooth muscle cell A smooth muscle cell that is part of any blood vessel. PMID:9108778 An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes. 2020-09-03T12:24:24Z large bile duct cholangiocyte extrahepatic cholangiocyte An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes. PMID:23720296 large bile duct cholangiocyte PMID:23720296 An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid. 2020-09-09T13:56:47Z EFO:0010705 periportal LSEC periportal hepatic sinusoidal endothelial cell endothelial cell of periportal hepatic sinusoid An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid. PMID:27423426 periportal LSEC PMID:28287163 periportal hepatic sinusoidal endothelial cell PMID:30348985 An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid. 2020-09-10T12:38:29Z EFO:0010706 central venous hepatic sinusoidal endothelial cell pericentral LSEC endothelial cell of pericentral hepatic sinusoid An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid. PMID:27423426 central venous hepatic sinusoidal endothelial cell PMID:30348985 pericentral LSEC PMID:28287163 stomach neuroendocrine cell A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. pulmonary neuroendocrine cell PNEC lung neuroendocrine cell A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. PMID:33355253 doi:10.3109/01902148209069653 doi:10.7554/eLife.78216 pulmonary neuroendocrine cell PMID:33355253 PNEC PMID:33355253 lung ciliated cell lung secretory cell trophectoderm cell trophectodermal cell A smooth muscle cell that is part of the small intestine. FMA:15050 non-striated muscle fiber of small intestine smooth muscle cell of small intestine true A smooth muscle cell that is part of the small intestine. GOC:tfm non-striated muscle fiber of small intestine FMA:15050 A smooth muscle cell that is part of the duodenum. FMA:15058 non-striated muscle fiber of duodenum smooth muscle fiber of duodenum true A smooth muscle cell that is part of the duodenum. GOC:tfm non-striated muscle fiber of duodenum FMA:15058 A smooth muscle cell that is part of the large intestine. FMA:15653 non-striated muscle fiber of large intestine smooth muscle cell of large intestine true A smooth muscle cell that is part of the large intestine. GOC:tfm non-striated muscle fiber of large intestine FMA:15653 A smooth muscle cell that is part of the colon. FMA:15663 non-striated muscle fiber of colon smooth muscle cell of colon A smooth muscle cell that is part of the colon. GOC:tfm non-striated muscle fiber of colon FMA:15663 A smooth muscle cell that is part of the sigmoid colon. FMA:17521 non-striated muscle fiber of sigmoid colon smooth muscle cell of sigmoid colon true A smooth muscle cell that is part of the sigmoid colon. GOC:tfm non-striated muscle fiber of sigmoid colon FMA:17521 A smooth muscle cell that is part of the rectum. FMA:17522 non-striated muscle fiber of rectum smooth muscle fiber of rectum smooth muscle cell of rectum A smooth muscle cell that is part of the rectum. GOC:tfm non-striated muscle fiber of rectum FMA:17522 A fibroblast that is part of the areolar connective tissue. FMA:261279 fibroblast of areolar connective tissue true A fibroblast that is part of the areolar connective tissue. GOC:tfm A fibroblast that is part of the tunica adventitia of artery. FMA:261285 fibroblast of tunica adventitia of artery true A fibroblast that is part of the tunica adventitia of artery. GOC:tfm A fibroblast that is part of the dense regular elastic tissue. FMA:261287 fibroblast of dense regular elastic tissue A fibroblast that is part of the dense regular elastic tissue. GOC:tfm An adipocyte that is part of the epicardial fat. FMA:261293 adipocyte of epicardial fat epicardial fat cell epicardial adipocyte An adipocyte that is part of the epicardial fat. GOC:tfm adipocyte of epicardial fat FMA:261293 epicardial fat cell FMA:261293 An adipocyte that is part of the epicardial fat of right ventricle. FMA:261297 epicardial adipocyte of right ventricle epicardial fat cell of right ventricle adipocyte of epicardial fat of right ventricle An adipocyte that is part of the epicardial fat of right ventricle. GOC:tfm epicardial adipocyte of right ventricle FMA:261297 epicardial fat cell of right ventricle FMA:261297 An adipocyte that is part of the epicardial fat of left ventricle. FMA:261300 epicardial adipocyte of left ventricle epicardial fat cell of left ventricle adipocyte of epicardial fat of left ventricle An adipocyte that is part of the epicardial fat of left ventricle. GOC:tfm epicardial adipocyte of left ventricle FMA:261300 epicardial fat cell of left ventricle FMA:261300 A transitional myocyte that is part of the interatrial septum. FMA:263152 transitional myocyte of interatrial septum true A transitional myocyte that is part of the interatrial septum. GOC:tfm A transitional myocyte that is part of the interventricular septum. FMA:263154 transitional myocyte of interventricular septum true A transitional myocyte that is part of the interventricular septum. GOC:tfm A Purkinje myocyte that is part of the interventricular septum. FMA:263182 Purkinje myocyte of interventricular septum true A Purkinje myocyte that is part of the interventricular septum. GOC:tfm An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates. BTO:000125 FMA:62911 LSEC endotheliocyte of hepatic sinusoid liver sinusoidal endothelial cell endothelial cell of hepatic sinusoid An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates. GOC:tfm PMID:3926620 LSEC PMID:30348985 endotheliocyte of hepatic sinusoid FMA:62911 liver sinusoidal endothelial cell PMID:30348985 A muscle cell that is part of the sinoatrial node. FMA:67102 SA nodal myocyte SA node cardiac muscle cell sinoatrial node cell sinoatrial node myocyte sinuatrial node myocyte myocyte of sinoatrial node A muscle cell that is part of the sinoatrial node. FMA:67102 GOC:tfm SA nodal myocyte FMA:67102 SA node cardiac muscle cell GOC:pr sinoatrial node cell GOC:pr sinuatrial node myocyte FMA:67102 A muscle cell that is part of the atrioventricular node. FMA:67106 AV nodal myocyte AV node cardiac muscle cell AV node cell atrioventricular node cell atrioventricular node myocyte myocyte of atrioventricular node A muscle cell that is part of the atrioventricular node. FMA:67106 GOC:tfm AV nodal myocyte FMA:67106 AV node cardiac muscle cell GOC:pr AV node cell GOC:pr atrioventricular node cell GOC:pr atrioventricular node myocyte FMA:67106 An endothelial cell that is part of the arteriole. FMA:67760 KUPO:0001097 endothelial cell of arteriole true An endothelial cell that is part of the arteriole. GOC:tfm A blood vessel endothelial cell that is part of an arterial endothelium. BTO:0004758 FMA:67761 KUPO:0001095 arterial endothelial cell endothelial cell of artery A blood vessel endothelial cell that is part of an arterial endothelium. GOC:tfm An endothelial cell that is part of the venule. FMA:67762 endothelial cell of venule true An endothelial cell that is part of the venule. GOC:tfm An epithelial cell that is part of the gallbladder. FMA:67780 epithelial cell of gallbladder An epithelial cell that is part of the gallbladder. GOC:tfm A somatic stem cell that is part of the epidermis. FMA:70541 epidermal stem cell stem cell of epidermis true A somatic stem cell that is part of the epidermis. GOC:tfm epidermal stem cell FMA:70541 A smooth muscle cell that is part of the ciliary body. FMA:70610 smooth muscle cell of ciliary body ciliary muscle cell true A smooth muscle cell that is part of the ciliary body. GOC:tfm smooth muscle cell of ciliary body FMA:70610 A mesothelial cell that is part of the anterior chamber of eyeball. FMA:70615 mesothelial cell of anterior chamber of eye A mesothelial cell that is part of the anterior chamber of eyeball. GOC:tfm A mesothelial cell that is part of the parietal peritoneum. FMA:72142 mesothelial cell of parietal peritoneum A mesothelial cell that is part of the parietal peritoneum. GOC:tfm A mesothelial cell that is part of the visceral peritoneum. FMA:72143 mesothelial cell of visceral peritoneum A mesothelial cell that is part of the visceral peritoneum. GOC:tfm A transitional myocyte that is part of the sinoatrial node. FMA:83384 transitinal myocyte of sinuatrial node transitional myocyte of sinoatrial node true A transitional myocyte that is part of the sinoatrial node. GOC:tfm A Purkinje myocyte that is part of the atrioventricular node. FMA:83386 Purkinje myocyte of atrioventricular node true A Purkinje myocyte that is part of the atrioventricular node. GOC:tfm A myocardial endocrine cell that is part of the interventricular septum. FMA:83390 myocardial endocrine cell of interventricular septum true A myocardial endocrine cell that is part of the interventricular septum. GOC:tfm An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. FMA:86481 epithelial cell of bile duct cholangiocyte true An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. GOC:tfm PMID:16550043 PMID:18356246 A mesothelial cell that is part of the peritoneum. FMA:86736 peritoneal mesothelial cell mesothelial cell of peritoneum A mesothelial cell that is part of the peritoneum. GOC:tfm peritoneal mesothelial cell FMA:86736 A mesothelial cell that is part of the pleura. FMA:86737 pleural mesothelial cell mesothelial cell of pleura A mesothelial cell that is part of the pleura. GOC:tfm pleural mesothelial cell FMA:86737 A mesothelial cell that is part of the parietal pleura. FMA:86738 mesothelial cell of parietal pleura A mesothelial cell that is part of the parietal pleura. GOC:tfm A mesothelial cell that is part of the visceral pleura. FMA:86739 mesothelial cell of visceral pleura A mesothelial cell that is part of the visceral pleura. GOC:tfm An epithelial cell of the exocrine pancreas. FMA:70986 exocrine pancreas cell epithelial cell of exocrine pancreas An epithelial cell of the exocrine pancreas. GOC:tfm The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. intestinal enteroendocrine cell The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. MP:0010802 endothelial cell of lung pulmonary vessel endothelial cell lung endothelial cell BTO:0001141 PAEC cell pulmonary artery endothelial cell PAEC cell BTO:0001141 A vascular endothelial cell found in colon blood vessels. CALOHA:TS-2397 colon endothelial cells colonic endothelial cell colon endothelial cell A vascular endothelial cell found in colon blood vessels. NPX:PDR https://orcid.org/0000-0001-5208-3432 colon endothelial cells CALOHA:TS-2397 colonic endothelial cell CALOHA:TS-2397 Squamous cell of oral epithelium. CALOHA:TS-1252 oral cavity mucosa squamous cell oral cavity mucosa squamous epithelial cell oral mucosa squamous epithelial cell oral mucosa squamous epithelial cells oral mucosa squamous cell Squamous cell of oral epithelium. NPX:PDR oral cavity mucosa squamous cell CALOHA:TS-1252 oral cavity mucosa squamous epithelial cell CALOHA:TS-1252 oral mucosa squamous epithelial cell CALOHA:TS-1252 oral mucosa squamous epithelial cells CALOHA:TS-1252 Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1274 colon glandular cells colon glandular cell Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. NPX:PDR colon glandular cells CALOHA:TS-1274 Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell. CALOHA:TS-1275 duodenum glandular cells duodenum glandular cell Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell. NPX:PDR duodenum glandular cells CALOHA:TS-1275 Glandular cell of gallbladder epithelium. CALOHA:TS-1278 gall bladder glandular cell gall bladder glandular cells gallbladder glandular cells gallbladder glandular cell Glandular cell of gallbladder epithelium. NPX:PDR gall bladder glandular cell FMA:7202 gall bladder glandular cells CALOHA:TS-1278 gallbladder glandular cells CALOHA:TS-1278 Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1281 rectal glandular cell rectum glandular cells rectum glandular cell Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells. NPX:PDR rectal glandular cell CALOHA:TS-1281 rectum glandular cells CALOHA:TS-1281 A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) . CALOHA:TS-1286 FMA:86928 small bowel glandular cell small intestinal glandular cell small intestine glandular cells small intestine glandular cell A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) . NCI_Thesaurus:Small_Intestinal_Glandular_Cell NPX:PDR small bowel glandular cell CALOHA:TS-1286 small intestinal glandular cell CALOHA:TS-1286 small intestine glandular cells CALOHA:TS-1286 Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. BTO:0000028 CALOHA:TS-1242 exocrine pancreas glandular cell pancreas exocrine glandular cells pancreas exocrine glandular cell Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. HPA:HPA NPX:PDR exocrine pancreas glandular cell CALOHA:TS-1242 pancreas exocrine glandular cells CALOHA:TS-1242 Fibroblast from muscle organ. CALOHA:TS-0643 muscle fibroblast Fibroblast from muscle organ. NPX:PDR Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells bone marrow hematopoietic cell Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. NPX:PDR bone marrow hematopoietic cells CALOHA:TS-2109 bone marrow poietic cells CALOHA:TS-2109 A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. 2014-02-11T17:29:04Z CL:2000001 peripheral blood mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. GOC:TermGenie Any blood vessel endothelial cell that is part of a microvascular endothelium. 2014-06-04T15:07:42Z CL:2000008 microvascular endothelial cell Any blood vessel endothelial cell that is part of a microvascular endothelium. GOC:TermGenie Any blood vessel endothelial cell that is part of a dermis. 2014-06-04T15:12:06Z CL:2000010 dermis blood vessel endothelial cell Any blood vessel endothelial cell that is part of a dermis. GOC:TermGenie Any skin fibroblast that is part of a skin of abdomen. 2014-06-04T15:18:16Z CL:2000013 fibroblast of skin of abdomen Any skin fibroblast that is part of a skin of abdomen. GOC:TermGenie Any lung endothelial cell that is part of a microvascular endothelium. 2014-06-04T16:00:56Z CL:2000016 lung microvascular endothelial cell Any lung endothelial cell that is part of a microvascular endothelium. GOC:TermGenie Any photoreceptor cell that is part of a compound eye. 2014-06-24T23:16:45Z FBbt:00004211 CL:2000019 compound eye photoreceptor cell Any photoreceptor cell that is part of a compound eye. GOC:TermGenie Any native cell that is part of a inner cell mass. 2014-06-24T23:16:53Z CL:2000020 inner cell mass cell Any native cell that is part of a inner cell mass. GOC:TermGenie Any native cell that is part of a cardiac septum. 2014-06-24T23:17:07Z CL:2000022 cardiac septum cell Any native cell that is part of a cardiac septum. GOC:TermGenie Any neuron that is part of a central nervous system. 2014-06-25T01:17:43Z CL:2000029 central nervous system neuron Any neuron that is part of a central nervous system. GOC:TermGenie A neuron that is part of a peripheral nervous system. 2014-06-25T02:28:17Z FMA:84664 PNS neuron peripheral neuron CL:2000032 peripheral nervous system neuron A neuron that is part of a peripheral nervous system. GOC:TermGenie ISBN:0721662544 Any fibroblast that is part of a embryo. 2014-07-09T00:12:00Z CL:2000042 embryonic fibroblast Any fibroblast that is part of a embryo. GOC:TermGenie Any microvascular endothelial cell that is part of a brain. 2014-07-09T00:24:53Z CL:2000044 brain microvascular endothelial cell Any microvascular endothelial cell that is part of a brain. GOC:TermGenie Any cardiac muscle cell that is part of a cardiac ventricle. 2014-08-12T20:50:28Z CL:2000046 ventricular cardiac muscle cell Any cardiac muscle cell that is part of a cardiac ventricle. GOC:TermGenie Any motor neuron that is part of a brainstem. 2014-10-02T23:52:53Z CL:2000047 brainstem motor neuron Any motor neuron that is part of a brainstem. GOC:TermGenie Any fibroblast that is part of a spleen. 2014-10-06T18:58:47Z CL:2000051 splenic fibroblast Any fibroblast that is part of a spleen. GOC:TermGenie Any endothelial cell that is part of a spleen. 2014-10-06T19:06:04Z CL:2000053 http://www.sciencellonline.com/site/productInformation.php?keyword=5500 splenic endothelial cell Any endothelial cell that is part of a spleen. GOC:TermGenie Any fibroblast that is part of a female gonad. 2014-10-07T17:57:42Z CL:2000063 http://www.sciencellonline.com/site/productInformation.php?keyword=7330 ovarian fibroblast Any fibroblast that is part of a female gonad. GOC:TermGenie Any epithelial cell that is part of a female gonad. 2014-10-07T17:59:13Z CL:2000064 http://www.sciencellonline.com/site/productInformation.php?keyword=7310 ovarian surface epithelial cell Any epithelial cell that is part of a female gonad. GOC:TermGenie Any fibroblast that is part of a cardiac ventricle. 2014-10-07T18:35:38Z CL:2000066 http://www.sciencellonline.com/site/productInformation.php?keyword=6310 cardiac ventricle fibroblast Any fibroblast that is part of a cardiac ventricle. GOC:TermGenie Any fibroblast that is part of a cardiac atrium. 2014-10-07T18:36:54Z CL:2000067 http://www.sciencellonline.com/site/productInformation.php?keyword=6320 cardiac atrium fibroblast Any fibroblast that is part of a cardiac atrium. GOC:TermGenie Any fibroblast that is part of a pericardium. 2014-10-07T18:38:06Z CL:2000068 http://www.sciencellonline.com/site/productInformation.php?keyword=6430 pericardium fibroblast Any fibroblast that is part of a pericardium. GOC:TermGenie Any fibroblast that is part of a gallbladder. 2014-10-07T18:41:43Z CL:2000069 http://www.sciencellonline.com/site/productInformation.php?keyword=5430 gallbladder fibroblast Any fibroblast that is part of a gallbladder. GOC:TermGenie Any fibroblast that is part of a optic choroid. 2014-10-07T18:50:43Z CL:2000070 http://www.sciencellonline.com/site/productInformation.php?keyword=6620 optic choroid fibroblast Any fibroblast that is part of a optic choroid. GOC:TermGenie Any microvascular endothelial cell that is part of a adipose tissue. 2014-10-07T22:13:45Z CL:2000072 http://www.sciencellonline.com/site/productInformation.php?keyword=7200 adipose microvascular endothelial cell Any microvascular endothelial cell that is part of a adipose tissue. GOC:TermGenie Any migratory neural crest cell that is part of a cardiac neural crest. 2014-11-05T01:18:43Z cardiac neural crest cell CL:2000073 migratory cardiac neural crest cell Any migratory neural crest cell that is part of a cardiac neural crest. GOC:TermGenie cardiac neural crest cell PMID:33060096 Any leukocyte that is part of a spleen. 2014-11-05T01:26:50Z CL:2000074 Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology. splenocyte Any leukocyte that is part of a spleen. GOC:TermGenie Any mesenchymal stem cell of adipose tissue that is part of an abdomen. 2014-12-02T19:10:34Z mesenchymal stem cell of abdominal adipose CL:2000080 mesenchymal stem cell of abdominal adipose tissue Any mesenchymal stem cell of adipose tissue that is part of an abdomen. GOC:TermGenie A ciliated epithelial cell of the esophagus. 2019-02-09T16:40:30Z CL:3000000 ciliated epithelial cell of esophagus A ciliated epithelial cell of the esophagus. GOC:CellBLAST PMID:29802404 Peripheral sensory neuron. 2019-02-25T19:34:33Z CL:3000004 peripheral sensory neuron Peripheral sensory neuron. GOC:CellBLAST PMID:30096314 A cell that is part of the brain vasculature. brain vascular cell A cell that is part of the brain vasculature. DOI:10.1101/2022.10.12.511898 A GABAergic inhibitory neuron that is derived from the midbrain. midbrain-derived inhibitory neuron A GABAergic inhibitory neuron that is derived from the midbrain. DOI:10.1101/2022.10.12.511898 A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli. somatosensory neuron A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli. PMID:22865660 Any capillary endothelial cell that is part of a lung. 2021-11-23T02:31:40Z lung capillary endothelial cell pulmonary capillary endothelial cell A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium. 2023-01-25T11:06:01Z ciliated cell of the respiratory tract respiratory ciliated cell A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium. PMID:18757316 PMID:21364219 A(n) vein endothelial cell that is part of a(n) respiratory system. vein endothelial cell of respiratory system A(n) vein endothelial cell that is part of a(n) respiratory system. PMID:34030460 A megakaryocyte that is resident in the lung connective tissue. 2023-03-16T11:31:23Z lung resident megakaryocyte lung-resident megakaryocyte MKL lung MKs lung megakaryocyte A megakaryocyte that is resident in the lung connective tissue. PMID:33351116 lung resident megakaryocyte PMID:36524131 lung-resident megakaryocyte PMID:36524131 MKL PMID:36524131 lung MKs PMID:33351116 A neuron that releases catecholamine as a neurotransmitter. 2023-05-18T12:07:45Z Frequently used when describing the developing nervous system in zebrafish. A catecholaminergic neuron expresses tyrosine hydroxylase (TH), tyrosine hydroxylase 2 (TH2), aromatic amino acid decarboxylase (AADC), dopamine b-hydroxylase (DBH), and phenylethanolamine-N-methyl transferase (PEMT), which are enzymes necessary for catecholamine synthesis. catecholaminergic neuron A neuron that releases catecholamine as a neurotransmitter. ISBN:0521442516 PMID:12094209 Frequently used when describing the developing nervous system in zebrafish. A catecholaminergic neuron expresses tyrosine hydroxylase (TH), tyrosine hydroxylase 2 (TH2), aromatic amino acid decarboxylase (AADC), dopamine b-hydroxylase (DBH), and phenylethanolamine-N-methyl transferase (PEMT), which are enzymes necessary for catecholamine synthesis. PMID:10191060 PMID:12128258 PMID:34880760 https://orcid.org/0000-0002-2244-7917 A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics. 2023-08-22T13:40:28Z perivascular cell A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics. PMID:24928499 PMID:27889329 An endothelial cell that is part of a central vein of liver. endothelial cell of central vein endothelial cell of central vein of liver An endothelial cell that is part of a central vein of liver. PMID:28287163 endothelial cell of central vein PMID:28287163 Any mesenchymal stem cell of adipose tissue that is part of an orbital region. 2023-09-18T10:43:00Z OAMSC Orbital ASCs orbital adipose-derived mesenchymal stem cell mesenchymal stem cell of orbital adipose tissue Any mesenchymal stem cell of adipose tissue that is part of an orbital region. OAMSC PMID:31377878 Orbital ASCs PMID:30210548 orbital adipose-derived mesenchymal stem cell PMID:31377878 1 A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom action specification A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. planned process http://purl.obolibrary.org/obo/IAO_0000015 Pier 'representational entity' This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc information representation physical information carrier A respiratory system disease which involves the lower respiratory tract. ICD9CM:478.19 SNOMEDCT_US_2021_09_01:195823002 UMLS_CUI:C0029581 disease_ontology DOID:0050161 lower respiratory tract disease A respiratory system disease which involves the lower respiratory tract. url:http://en.wikipedia.org/wiki/lower_respiratory_tract A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle. lschriml 2012-01-03T02:54:11Z ICD10CM:I42 ICD9CM:425 ICD9CM:425.9 MESH:D009202 NCI:C34830 NCI:C53654 SNOMEDCT_US_2021_09_01:266301006 SNOMEDCT_US_2021_09_01:89461002 SNOMEDCT_US_2021_09_01:89600009 UMLS_CUI:C0033141 UMLS_CUI:C0036529 UMLS_CUI:C0878544 Cardiomyopathies disease_ontology DOID:0050700 MESH:D009202 added from NeuroDevNet [WAK]. cardiomyopathy A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle. url:http://en.wikipedia.org/wiki/Cardiomyopathy url:http://www.nhlbi.nih.gov/health/health-topics/topics/cm/ A glomerulonephritis that is characterized by hardening of the glomerulus in the kidney. lschriml 2014-04-15T03:40:31Z disease_ontology DOID:0050851 glomerulosclerosis A glomerulonephritis that is characterized by hardening of the glomerulus in the kidney. url:http://en.wikipedia.org/wiki/Glomerulosclerosis An infratentorial cancer that is located_in the lower part of the brain and is a type of primitive neuroectodermal tumor. lschriml 2014-10-06T14:36:37Z DOID:0060105 DOID:168 DOID:3858 DOID:4981 GARD:7005 ICDO:9470/3 MESH:D008527 MESH:D018242 NCI:C27294 NCI:C3222 NCI:C3716 OMIM:155255 SNOMEDCT_US_2021_09_01:189925001 SNOMEDCT_US_2021_09_01:443333004 UMLS_CUI:C0025149 UMLS_CUI:C0206663 UMLS_CUI:C1334410 CNS PNET CPNET brain medulloblastoma infratentorial primitive neuroectodermal tumor localized primitive neuroectodermal tumor disease_ontology DOID:0050902 OMIM mapping confirmed by DO. [SN]. medulloblastoma An infratentorial cancer that is located_in the lower part of the brain and is a type of primitive neuroectodermal tumor. url:http://en.wikipedia.org/wiki/Medulloblastoma url:http://www.cancer.gov/dictionary?CdrID=45780 url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306779/ A disease of mental health that occur during a child's developmental period between birth and age 18 resulting in retarding of the child's psychological or physical development. disease_ontology DOID:0060037 developmental disorder of mental health A disease of mental health that occur during a child's developmental period between birth and age 18 resulting in retarding of the child's psychological or physical development. url:http://en.wikipedia.org/wiki/Developmental_disorders A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs. DOID:1033 DOID:353 ICD10CM:C85.9 ICDO:9590/3 MESH:D008223 NCI:C3208 NCI:C7065 SNOMEDCT_US_2021_09_01:118600007 SNOMEDCT_US_2021_09_01:414628006 UMLS_CUI:C0024299 UMLS_CUI:C0598798 lymphoid cancer disease_ontology DOID:0060058 lymphoma A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs. url:http://en.wikipedia.org/wiki/Lymphoma url:http://www.lymphoma.org/site/pp.asp?c=bkLTKaOQLmK8E&b=6300161 url:http://www.nlm.nih.gov/medlineplus/lymphoma.html A disease of cellular proliferation that results in abnormal growths in the body, which do not invade or destroy the surrounding tissue but, given enough time, will transform into a cancer. lschriml 2011-05-11T12:18:41Z disease_ontology DOID:0060071 pre-malignant neoplasm A disease of cellular proliferation that results in abnormal growths in the body, which do not invade or destroy the surrounding tissue but, given enough time, will transform into a cancer. url:http://en.wikipedia.org/wiki/Neoplasm A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize. lschriml 2011-05-11T12:18:41Z disease_ontology DOID:0060072 benign neoplasm A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize. url:http://en.wikipedia.org/wiki/Benign_neoplasm url:http://www.nlm.nih.gov/medlineplus/benigntumors.html An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction. DOID:2284 ICD10CM:H18.9 ICD9CM:371.9 MESH:D003316 NCI:C26731 SNOMEDCT_US_2021_09_01:15250008 UMLS_CUI:C0010034 disease_ontology DOID:10124 corneal disease An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction. url:https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C26731 A cardiovascular system disease that involves the heart's electrical conduction system. ICD9CM:426.6 SNOMEDCT_US_2021_09_01:195053008 UMLS_CUI:C0029630 heart rhythm disease disease_ontology DOID:10273 heart conduction disease A cardiovascular system disease that involves the heart's electrical conduction system. url:http://en.wikipedia.org/wiki/Conduction_system_of_the_heart A prostate cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. EFO:0001663 KEGG:05215 NCI:C4863 SNOMEDCT_US_2021_09_01:254900004 UMLS_CUI:C0600139 cancer of prostate carcinoma of prostate disease_ontology DOID:10286 prostate carcinoma A prostate cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. url:http://en.wikipedia.org/wiki/Carcinoma A leukemia that has_material_basis_in a B-cell or T-cell lineage involving primarily the bone marrow and the peripheral blood. DOID:10747 ICD10CM:C91 ICD9CM:204 ICDO:9820/3 MESH:D007945 NCI:C7539 SNOMEDCT_US_2021_09_01:93170002 UMLS_CUI:C0023448 lymphoblastic leukaemia lymphoblastic leukemia lymphocytic leukaemia disease_ontology DOID:1037 lymphoid leukemia A leukemia that has_material_basis_in a B-cell or T-cell lineage involving primarily the bone marrow and the peripheral blood. url:http://www.cancer.gov/dictionary?CdrID=616067 A lymphocytic leukemia characterized by over production of B-cells and their accumulation in bone marrow and blood. EFO:0000095 GARD:6104 ICD10CM:C91.10 ICD9CM:204.1 MESH:D015451 NCI:C3163 OMIM:109543 OMIM:151400 OMIM:609630 OMIM:612557 OMIM:612558 OMIM:612559 ORDO:67038 SNOMEDCT_US_2021_09_01:51092000 UMLS_CUI:C0023434 B-cell chronic lymphocytic leukaemia B-cell chronic lymphocytic leukemia CLL chronic lymphatic leukaemia chronic lymphatic leukemia chronic lymphocytic leukaemia lymphoplasmacytic leukaemia lymphoplasmacytic leukemia disease_ontology B-cell chronic lymphoid leukemia DOID:1040 Xref MGI. chronic lymphocytic leukemia A lymphocytic leukemia characterized by over production of B-cells and their accumulation in bone marrow and blood. url:http://en.wikipedia.org/wiki/B-cell_chronic_lymphocytic_leukemia url:http://www.cancer.gov/dictionary?cdrid=346545 A gastrointestinal system cancer that is located_in the stomach. DOID:10539 DOID:10542 DOID:10543 DOID:4713 GARD:7704 ICD10CM:C16 ICD10CM:C16.2 ICD10CM:C16.5 ICD10CM:C16.6 ICD9CM:151 ICD9CM:151.4 ICD9CM:151.5 ICD9CM:151.6 MESH:D013274 NCI:C3387 NCI:C9331 OMIM:613659 SNOMEDCT_US_2021_09_01:126824007 SNOMEDCT_US_2021_09_01:269459004 SNOMEDCT_US_2021_09_01:269460009 SNOMEDCT_US_2021_09_01:93717002 SNOMEDCT_US_2021_09_01:94074003 UMLS_CUI:C0024623 UMLS_CUI:C0038356 UMLS_CUI:C0153421 UMLS_CUI:C0153422 UMLS_CUI:C0153423 gastric cancer gastric neoplasm disease_ontology DOID:10534 OMIM mapping confirmed by DO. [SN]. stomach cancer A gastrointestinal system cancer that is located_in the stomach. url:http://cancergenome.nih.gov/cancersselected/stomach-esophagealcancer url:http://en.wikipedia.org/wiki/Stomach A tauopathy that is characterized by memory lapses, confusion, emotional instability and progressive loss of mental ability and results in progressive memory loss, impaired thinking, disorientation, and changes in personality and mood starting and leads in advanced cases to a profound decline in cognitive and physical functioning and is marked histologically by the degeneration of brain neurons especially in the cerebral cortex and by the presence of neurofibrillary tangles and plaques containing beta-amyloid. EFO:0000249 GARD:10254 ICD10CM:G30 ICD9CM:331.0 KEGG:05010 MESH:D000544 NCI:C2866 SNOMEDCT_US_2021_09_01:73768007 UMLS_CUI:C0002395 Alzheimer disease Alzheimers dementia disease_ontology DOID:10652 Xref MGI. OMIM mapping confirmed by DO. [SN]. Alzheimer's disease A tauopathy that is characterized by memory lapses, confusion, emotional instability and progressive loss of mental ability and results in progressive memory loss, impaired thinking, disorientation, and changes in personality and mood starting and leads in advanced cases to a profound decline in cognitive and physical functioning and is marked histologically by the degeneration of brain neurons especially in the cerebral cortex and by the presence of neurofibrillary tangles and plaques containing beta-amyloid. url:http://en.wikipedia.org/wiki/Alzheimer%27s_disease url:http://www.merriam-webster.com/medical/alzheimer%27s%20disease url:http://www.nia.nih.gov/alzheimers/publication/alzheimers-disease-fact-sheet ls:IEDB An urinary system cancer that results_in malignant growth located_in the urinary bladder. DOID:5428 GARD:12210 ICD10CM:C67 ICD9CM:188 KEGG:05219 MESH:D001749 NCI:C2901 NCI:C9334 OMIM:109800 SNOMEDCT_US_2021_09_01:126885006 SNOMEDCT_US_2021_09_01:363455001 UMLS_CUI:C0005684 UMLS_CUI:C0005695 bladder cancer tumor of the bladder disease_ontology DOID:11054 OMIM mapping confirmed by DO. [SN]. urinary bladder cancer An urinary system cancer that results_in malignant growth located_in the urinary bladder. url:http://en.wikipedia.org/wiki/Bladder_cancer A cell type cancer that has_material_basis_in abnormally proliferating cells derives from embryonic mesoderm. DOID:3936 ICD10CM:C49 ICD9CM:171.9 ICDO:8800/3 SNOMEDCT_US_2021_09_01:93765001 UMLS_CUI:C0153519 connective and soft tissue neoplasm tumor of soft tissue and skeleton disease_ontology DOID:1115 sarcoma A cell type cancer that has_material_basis_in abnormally proliferating cells derives from embryonic mesoderm. url:http://cancergenome.nih.gov/cancersselected/Sarcoma url:http://en.wikipedia.org/wiki/Sarcoma url:http://www.cancer.gov/dictionary?CdrID=45562 A cardiovascular system disease that involves the heart. ICD10CM:I51.9 ICD9CM:429.9 MESH:D006331 NCI:C3079 SNOMEDCT_US_2021_09_01:194707003 UMLS_CUI:C0018799 disease_ontology DOID:114 heart disease A cardiovascular system disease that involves the heart. url:http://en.wikipedia.org/wiki/Heart_disease A lower respiratory tract disease that affects the airways leading into the lungs, which is caused due to inflammation of the bronchi and bronchioles, infection, or blockage. DOID:1175 DOID:12322 MESH:D001982 SNOMEDCT_US_2021_09_01:41427001 UMLS_CUI:C0006261 disease_ontology DOID:1176 bronchial disease A lower respiratory tract disease that affects the airways leading into the lungs, which is caused due to inflammation of the bronchi and bronchioles, infection, or blockage. url:https://www.ncbi.nlm.nih.gov/pubmed/11685087 A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells. DOID:9145 ICD10CM:C95.90 ICD9CM:208 ICDO:9800/3 MESH:D007938 NCI:C3161 SNOMEDCT_US_2021_09_01:255049003 UMLS_CUI:C0023418 disease_ontology DOID:1240 leukemia A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells. url:http://en.wikipedia.org/wiki/Leukemia url:http://www.cancer.gov/dictionary?CdrID=45343 A hematopoietic system disease that is characterized by abnormal blood clotting or bleeding. DOID:13997 DOID:2212 DOID:9474 ICD10CM:D68.9 ICD9CM:286 MESH:D001778 NCI:C2902 SNOMEDCT_US_2021_09_01:64779008 UMLS_CUI:C0005779 coagulation protein disease postpartum coagulation defect postpartum coagulation defect with delivery inherited blood coagulation disease disease_ontology DOID:1247 blood coagulation disease A hematopoietic system disease that is characterized by abnormal blood clotting or bleeding. url:https://www.cedars-sinai.edu/Patients/Health-Conditions/Coagulation-System-Disorders.aspx A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. DOID:73 ICD9CM:429.2 MESH:D002318 NCI:C2931 SNOMEDCT_US_2021_09_01:266275004 UMLS_CUI:C0007222 disease of subdivision of hemolymphoid system disease_ontology DOID:1287 cardiovascular system disease A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. url:http://en.wikipedia.org/wiki/Circulatory_system A cognitive disorder resulting from a loss of brain function affecting memory, thinking, language, judgement and behavior. ICD9CM:290.8 UMLS_CUI:C0154319 disease_ontology DOID:1307 dementia A cognitive disorder resulting from a loss of brain function affecting memory, thinking, language, judgement and behavior. url:http://www.nlm.nih.gov/medlineplus/ency/article/000739.htm A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain. DOID:2125 DOID:2126 DOID:3543 DOID:6649 DOID:911 ICD10CM:C71 ICD9CM:191 ICD9CM:239.6 MESH:D001932 NCI:C170814 NCI:C2907 NCI:C3568 NCI:C5115 NCI:C7710 SNOMEDCT_US_2021_09_01:126952004 SNOMEDCT_US_2021_09_01:428061005 SNOMEDCT_US_2021_09_01:93727008 UMLS_CUI:C0006118 UMLS_CUI:C0153633 UMLS_CUI:C0220624 UMLS_CUI:C0750974 UMLS_CUI:C0750979 UMLS_CUI:C1334557 BT - Brain tumour adult brain tumor adult malignant brain neoplasm brain neoplasm brain neoplasm, adult malignant brain tumour malignant primary brain neoplasm malignant primary brain tumor malignant tumor of Brain malignant tumor of adult brain neoplasm of brain primary brain neoplasm primary brain tumor primary malignant neoplasm of brain tumor of the Brain disease_ontology DOID:1319 brain cancer A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain. url:http://www.cancer.gov/dictionary?CdrID=387264 A brain disease that is characterized by loss of structure or function of neurons, including death of neurons and loss of brain tissue. GARD:6019 ICD9CM:331.9 SNOMEDCT_US_2021_09_01:52522001 UMLS_CUI:C0154671 Brain degeneration disease_ontology DOID:1443 cerebral degeneration A brain disease that is characterized by loss of structure or function of neurons, including death of neurons and loss of brain tissue. url:https://en.wikipedia.org/wiki/Neurodegeneration A disease that is characterized by abnormally rapid cell division. neoplasm DOID:0000818 cell process disease neoplasm disease_ontology DOID:14566 disease of cellular proliferation A disease that is characterized by abnormally rapid cell division. url:http://en.wikipedia.org/w/index.php?title=Cell_proliferation A disease that involves a psychological or behavioral pattern generally associated with subjective distress or disability that occurs in an individual, and which are not a part of normal development or culture. ICD10CM:F99 MESH:D001523 NCI:C2893 SNOMEDCT_US_2021_09_01:74732009 UMLS_CUI:C0004936 disease_ontology DOID:150 disease of mental health A disease that involves a psychological or behavioral pattern generally associated with subjective distress or disability that occurs in an individual, and which are not a part of normal development or culture. url:http://en.wikipedia.org/wiki/Mental_disorder A disease of mental health that involve long-term patterns of thoughts and behaviors that cause serious problems with relationships and work. ICD9CM:301.8 SNOMEDCT_US_2021_09_01:191770003 UMLS_CUI:C0029707 character disorder disease_ontology DOID:1510 personality disorder A disease of mental health that involve long-term patterns of thoughts and behaviors that cause serious problems with relationships and work. url:http://www.nlm.nih.gov/medlineplus/personalitydisorders.html A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism. DOID:1531 MESH:D010995 NCI:C26859 SNOMEDCT_US_2021_09_01:88075009 UMLS_CUI:C0032226 disorder of pleura non-neoplastic pleural disease disease_ontology DOID:1532 pleural disease A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism. url:http://en.wikipedia.org/wiki/Pleural_disease A disease of mental health that affects cognitive functions including memory processing, perception and problem solving. ICD10CM:F09 MESH:D019965 NCI:C34870 SNOMEDCT_US_2021_09_01:111479008 UMLS_CUI:C0029227 cognitive disease disease_ontology Organic Mental disorder DOID:1561 cognitive disorder A disease of mental health that affects cognitive functions including memory processing, perception and problem solving. url:http://en.wikipedia.org/wiki/Cognitive_disorder A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. DOID:3226 ICD10CM:J98 ICD9CM:519 SNOMEDCT_US_2021_09_01:155603009 UMLS_CUI:C0029582 disease_ontology DOID:1579 respiratory system disease A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. url:http://en.wikipedia.org/wiki/File:Respiratory_system_complete_en.svg url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=respiratory%20system A thoracic cancer that originates in the mammary gland. DOID:1648 DOID:4241 ICD10CM:C50 MESH:D001943 NCI:C9335 OMIM:114480 SNOMEDCT_US_2021_09_01:254837009 UMLS_CUI:C0006142 breast tumor malignant neoplasm of breast malignant tumor of the breast mammary cancer mammary tumor primary breast cancer disease_ontology mammary neoplasm DOID:1612 Xref MGI. OMIM mapping confirmed by DO. [SN]. breast cancer A thoracic cancer that originates in the mammary gland. url:http://en.wikipedia.org/wiki/Breast_cancer url:http://en.wikipedia.org/wiki/Mammary url:http://www.cancer.gov/cancertopics/types/breast url:http://www.nlm.nih.gov/medlineplus/breastcancer.html A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80.1 ICD9CM:199 ICDO:8000/3 MESH:D009369 NCI:C9305 SNOMEDCT_US_2021_09_01:269513004 UMLS_CUI:C0006826 malignant neoplasm malignant tumor primary cancer disease_ontology DOID:162 Updating out dated UMLS CUI. cancer A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. url:http://en.wikipedia.org/wiki/cancer url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cancer A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart. DOID:0000405 DOID:2403 DOID:2869 DOID:324 DOID:325 DOID:45 ICD10CM:I72.9 ICD9CM:442.9 MESH:D000783 MESH:D014652 MESH:D020758 MESH:D020760 NCI:C26693 NCI:C35117 SNOMEDCT_US_2021_09_01:27550009 SNOMEDCT_US_2021_09_01:371029002 SNOMEDCT_US_2021_09_01:432119003 UMLS_CUI:C0002940 UMLS_CUI:C0042373 UMLS_CUI:C0752127 UMLS_CUI:C0752130 vascular tissue disease disease_ontology DOID:178 vascular disease A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart. url:http://en.wikipedia.org/wiki/Vascular_disease A pericardium disease that is characterized by an inflammation of the pericardium and has_symptom chest pain. MESH:D010493 NCI:C34915 SNOMEDCT_US_2021_09_01:3238004 UMLS_CUI:C0031046 disease_ontology DOID:1787 pericarditis A pericardium disease that is characterized by an inflammation of the pericardium and has_symptom chest pain. url:http://en.wikipedia.org/wiki/Pericarditis A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from melanocytes which are found in skin, the bowel and the eye. EFO:0000756 ICDO:8720/3 KEGG:05218 MESH:D008545 NCI:C3224 SNOMEDCT_US_2021_09_01:2092003 UMLS_CUI:C0025202 Naevocarcinoma malignant melanoma disease_ontology DOID:1909 melanoma MESH:D008545 A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from melanocytes which are found in skin, the bowel and the eye. url:http://en.wikipedia.org/wiki/Melanoma url:https://www.ncbi.nlm.nih.gov/pubmed/22123420 EFO:0003914 ICD10CM:I70 ICD9CM:440 MESH:D050197 NCI:C35768 SNOMEDCT_US_2021_09_01:155414001 UMLS_CUI:C0004153 disease_ontology DOID:1936 atherosclerosis MESH:D050197 A cognitive disorder that involves an excessive, irrational dread of everyday situations. DOID:12884 ICD10CM:F41.9 MESH:D001008 NCI:C2878 OMIM:607834 SNOMEDCT_US_2021_09_01:65673007 UMLS_CUI:C0003469 anxiety anxiety state disease_ontology DOID:2030 anxiety disorder A cognitive disorder that involves an excessive, irrational dread of everyday situations. url:http://www.nimh.nih.gov/health/topics/anxiety-disorders/index.shtml A female reproductive organ cancer that is located_in the ovary. DOID:0060070 DOID:2144 DOID:9595 GARD:7295 ICD10CM:C56 ICD9CM:183.0 MESH:D010051 NCI:C4984 NCI:C7431 OMIM:167000 OMIM:607893 ORDO:213500 ORDO:213517 SNOMEDCT_US_2021_09_01:123843001 SNOMEDCT_US_2021_09_01:372117006 SNOMEDCT_US_2021_09_01:93934004 UMLS_CUI:C0919267 UMLS_CUI:C1140680 UMLS_CUI:C1299247 malignant Ovarian tumor malignant tumour of ovary ovarian neoplasm ovary neoplasm primary ovarian cancer tumor of the Ovary disease_ontology DOID:2394 Xref MGI. OMIM mapping confirmed by DO. [SN]. ovarian cancer A female reproductive organ cancer that is located_in the ovary. url:http://www.cancer.gov/dictionary?CdrID=445074 MESH:D007499 NCI:C34737 SNOMEDCT_US_2021_09_01:85478004 UMLS_CUI:C0022078 disease_ontology DOID:240 iris disease A cognitive disorder that involves abnormal thinking and perceptions resulting in a disconnection with reality. EFO:0000677 ICD9CM:298.8 UMLS_CUI:C0029516 mental or behavioural disorder disease_ontology DOID:2468 psychotic disorder A cognitive disorder that involves abnormal thinking and perceptions resulting in a disconnection with reality. url:http://www.nlm.nih.gov/medlineplus/psychoticdisorders.html A skin carcinoma affecting basal cells. DOID:4275 DOID:4276 EFO:0004193 ICDO:8090/3 KEGG:05217 MESH:D018295 NCI:C156767 NCI:C3784 NCI:C7586 SNOMEDCT_US_2021_09_01:127570002 SNOMEDCT_US_2021_09_01:154507009 SNOMEDCT_US_2021_09_01:252995000 UMLS_CUI:C0007117 UMLS_CUI:C0206710 UMLS_CUI:C1368295 Basal cell cancer Basal cell carcinoma of skin Basal cell neoplasm Basal cell tumor Epithelioma basal cell Rodent ulcer malignant Basal cell neoplasm malignant basal cell tumor disease_ontology DOID:2513 Xref MGI. basal cell carcinoma A skin carcinoma affecting basal cells. url:http://en.wikipedia.org/wiki/Basal-cell_carcinoma An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes. DOID:1034 DOID:2532 MESH:D019337 NCI:C27134 SNOMEDCT_US_2021_09_01:414388001 UMLS_CUI:C0376544 Hematologic malignancy Hematologic neoplasm Hematological tumors blood cancer hematopoietic and lymphoid system tumor hematopoietic cancer hematopoietic neoplasm hematopoietic tumors malignant hematopoietic neoplasm disease_ontology DOID:2531 hematologic cancer An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes. url:http://en.wikipedia.org/wiki/Blood_cancer url:http://www.cancer.gov/dictionary/?CdrID=45708 A brain disease that is characterized by damage to brain substance located_in cerebellum; has_symptom ataxia, has_symptom dysarthria, and has_symptom cerebellar cognitive affective syndrome. MESH:D002526 SNOMEDCT_US_2021_09_01:267691001 UMLS_CUI:C0007760 disease_ontology DOID:2786 cerebellar disease A brain disease that is characterized by damage to brain substance located_in cerebellum; has_symptom ataxia, has_symptom dysarthria, and has_symptom cerebellar cognitive affective syndrome. url:https://en.wikipedia.org/wiki/Cerebellum url:https://www.ncbi.nlm.nih.gov/pubmed/15377747 A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body. ICD10CM:E34.9 ICD9CM:259.9 MESH:D004700 NCI:C3009 SNOMEDCT_US_2021_09_01:67432001 UMLS_CUI:C0014130 disease_ontology DOID:28 endocrine system disease A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body. url:http://en.wikipedia.org/wiki/Endocrine_system A nephritis that causes inflammation of the glomeruli located_in kidney. GARD:6516 ICD10CM:N08 MESH:D005921 NCI:C26784 SNOMEDCT_US_2021_09_01:36171008 UMLS_CUI:C0017658 disease_ontology DOID:2921 glomerulonephritis A nephritis that causes inflammation of the glomeruli located_in kidney. url:http://en.wikipedia.org/wiki/Glomerulonephritis sn:IEDB A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from germ cells. DOID:2157 MESH:D009373 NCI:C3708 SNOMEDCT_US_2021_09_01:302853003 UMLS_CUI:C0205851 malignant tumor of the germ cell disease_ontology germ cell neoplasm germ cell tumour DOID:2994 germ cell cancer A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from germ cells. url:http://en.wikipedia.org/wiki/Germ_cell_tumor A disease of mental health involving the abuse or dependence on a substance that is ingested in order to produce a high, alter one's senses, or otherwise affect functioning. MESH:D019966 NCI:C92203 UMLS_CUI:C0236969 disease_ontology DOID:303 substance-related disorder A disease of mental health involving the abuse or dependence on a substance that is ingested in order to produce a high, alter one's senses, or otherwise affect functioning. url:https://www.psychologytoday.com/us/conditions/substance-related-disorders An obstructive lung disease that is characterized by irreversible airflow obstruction due to chronic bronchitis, emphysema, and/or small airways disease. DOID:11500 DOID:6144 EFO:0000341 ICD10CM:J44.9 MESH:D029424 NCI:C3199 OMIM:606963 SNOMEDCT_US_2021_09_01:13645005 UMLS_CUI:C0024117 COLD COPD chronic obstructive airway disease chronic obstructive lung disease disease_ontology DOID:3083 chronic obstructive pulmonary disease An obstructive lung disease that is characterized by irreversible airflow obstruction due to chronic bronchitis, emphysema, and/or small airways disease. url:https://pubmed.ncbi.nlm.nih.gov/28513453/ url:https://www.nhlbi.nih.gov/health-topics/copd An artery disease that is characterized by plaque building up along the inner walls of the arteries of the heart resulting in a narrowing of the arteries and a reduced blood supply to the cardiac muscles. DOID:10506 DOID:3363 DOID:3394 DOID:9420 EFO:0001645 ICD10CM:I20-I25 ICD10CM:I25 ICD10CM:I25.10 ICD9CM:410-414.99 ICD9CM:414.0 ICD9CM:414.9 MESH:D003324 MESH:D003327 MESH:D017202 NCI:C35505 NCI:C50625 OMIM:300464 OMIM:607339 OMIM:608316 OMIM:608318 OMIM:608320 OMIM:610947 OMIM:611139 OMIM:612030 OMIM:614293 SNOMEDCT_US_2021_09_01:194852007 SNOMEDCT_US_2021_09_01:233822007 SNOMEDCT_US_2021_09_01:41702007 SNOMEDCT_US_2021_09_01:53741008 UMLS_CUI:C0010054 UMLS_CUI:C0010068 UMLS_CUI:C0151744 UMLS_CUI:C0264694 CHD Coronary disease coronary arteriosclerosis coronary heart disease disease_ontology DOID:3393 Xref MGI. coronary artery disease An artery disease that is characterized by plaque building up along the inner walls of the arteries of the heart resulting in a narrowing of the arteries and a reduced blood supply to the cardiac muscles. url:http://en.wikipedia.org/wiki/Coronary_heart_disease A skin cancer that is located_in tissues of the skin and develops from epithelial cells. NCI:C4914 UMLS_CUI:C0699893 carcinoma of skin disease_ontology DOID:3451 skin carcinoma A skin cancer that is located_in tissues of the skin and develops from epithelial cells. url:http://www.cancer.gov/cancertopics/types/skin A hepatobiliary system cancer that is located_in the liver. DOID:12300 DOID:269 DOID:7330 DOID:915 DOID:919 ICD10CM:C22.0 ICD10CM:C22.9 ICD9CM:155.0 ICD9CM:155.2 MESH:D008113 NCI:C34803 NCI:C7692 SNOMEDCT_US_2021_09_01:126851005 SNOMEDCT_US_2021_09_01:187771009 SNOMEDCT_US_2021_09_01:93870000 UMLS_CUI:C0023903 UMLS_CUI:C0024620 UMLS_CUI:C0345904 UMLS_CUI:C0854795 Ca liver - primary Resectable malignant neoplasm of Liver ca liver - primary hepatic cancer hepatic neoplasm malignant hepato-biliary neoplasm malignant neoplasm of liver malignant neoplasm of liver, not specified as primary or secondary malignant neoplasm of liver, primary malignant tumor of liver neoplasm of liver non-resectable primary hepatic malignant neoplasm primary liver cancer primary malignant neoplasm of Liver primary malignant neoplasm of liver resectable malignant neoplasm of the liver disease_ontology DOID:3571 liver cancer A hepatobiliary system cancer that is located_in the liver. url:http://en.wikipedia.org/wiki/Liver An integumentary system disease that is located_in skin. DOID:1576 DOID:1698 DOID:187 DOID:6486 DOID:8948 ICD9CM:702 MESH:D012871 MESH:D012873 NCI:C156032 NCI:C3371 SNOMEDCT_US_2021_09_01:201095006 SNOMEDCT_US_2021_09_01:5613003 SNOMEDCT_US_2021_09_01:95320005 UMLS_CUI:C0029574 UMLS_CUI:C0037274 UMLS_CUI:C0037277 Genodermatosis skin and subcutaneous tissue disease disease_ontology DOID:37 skin disease An integumentary system disease that is located_in skin. url:http://en.wikipedia.org/wiki/Skin_disease A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. MESH:D004194 NCI:C2991 SNOMEDCT_US_2021_09_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ A gastrointestinal system disease that is located_in the mouth. MESH:D009059 NCI:C27641 SNOMEDCT_US_2021_09_01:118938008 UMLS_CUI:C0026636 disease_ontology DOID:403 mouth disease A gastrointestinal system disease that is located_in the mouth. url:http://en.wikipedia.org/wiki/Oral_and_maxillofacial_pathology A heart disease involving one or more of the four valves of the heart (the aortic and mitral valves on the left and the pulmonary and tricuspid valves on the right). DOID:989 MESH:D006349 MESH:D016127 NCI:C45525 SNOMEDCT_US_2021_09_01:368009 SNOMEDCT_US_2021_09_01:398995000 UMLS_CUI:C0018824 UMLS_CUI:C0079485 Valvular heart disease disease_ontology DOID:4079 heart valve disease A heart disease involving one or more of the four valves of the heart (the aortic and mitral valves on the left and the pulmonary and tricuspid valves on the right). url:http://en.wikipedia.org/wiki/Heart_valve_disease DOID:2164 DOID:2165 DOID:46 ICD10CM:K76.9 ICD9CM:573.9 MESH:D008107 NCI:C3196 SNOMEDCT_US_2021_09_01:62857009 UMLS_CUI:C0023895 disorder of liver hepatic disorder disease_ontology DOID:409 liver disease A disease of mental health that involves physical symptoms suggesting a physical illness where the biological or medical cause of the symptoms is indeterminate. DOID:10133 DOID:144 ICD10CM:F45 ICD10CM:F45.0 ICD9CM:300.8 ICD9CM:300.81 MESH:D013001 NCI:C34956 SNOMEDCT_US_2021_09_01:192430009 SNOMEDCT_US_2021_09_01:60368009 UMLS_CUI:C0037650 UMLS_CUI:C0520482 physiological malfunction arising from mental factor psychophysiologic disorder psychosomatic disorder disease_ontology DOID:4737 somatoform disorder A disease of mental health that involves physical symptoms suggesting a physical illness where the biological or medical cause of the symptoms is indeterminate. url:http://en.wikipedia.org/wiki/Somatoform_disorder MESH:D001855 NCI:C34433 SNOMEDCT_US_2021_09_01:127035006 UMLS_CUI:C0005956 bone marrow disorder disease_ontology DOID:4961 bone marrow disease A gastrointestinal system cancer that is located_in the esophagus. DOID:10291 DOID:10292 DOID:10448 DOID:1102 DOID:1104 GARD:6383 ICD10CM:C15.3 ICD10CM:C15.4 ICD10CM:C15.5 ICD9CM:150.2 ICD9CM:150.3 ICD9CM:150.4 ICD9CM:150.5 ICD9CM:150.8 MESH:D004938 NCI:C3028 NCI:C3533 NCI:C3534 NCI:C3535 NCI:C4764 OMIM:133239 SNOMEDCT_US_2021_09_01:126817006 SNOMEDCT_US_2021_09_01:187729008 SNOMEDCT_US_2021_09_01:93656003 SNOMEDCT_US_2021_09_01:93877002 SNOMEDCT_US_2021_09_01:93895004 SNOMEDCT_US_2021_09_01:94119000 UMLS_CUI:C0014859 UMLS_CUI:C0153413 UMLS_CUI:C0153414 UMLS_CUI:C0153415 UMLS_CUI:C0153416 UMLS_CUI:C0496775 Ca lower third oesophagus Ca middle third oesophagus esophagus cancer malignant neoplasm of distal third of esophagus malignant neoplasm of lower third of oesophagus malignant neoplasm of middle third of oesophagus malignant neoplasm of proximal third of esophagus malignant neoplasm of upper third esophagus malignant tumor of Distal Third of esophagus malignant tumor of Proximal Third of esophagus malignant tumor of abdominal esophagus malignant tumor of the middle Third of the esophagus disease_ontology DOID:5041 esophageal cancer A gastrointestinal system cancer that is located_in the esophagus. url:http://cancergenome.nih.gov/cancersselected/stomach-esophagealcancer url:http://en.wikipedia.org/wiki/Esophagus A disease of mental health that involves disruption of sleep patterns. DOID:9028 ICD9CM:307.4 UMLS_CUI:C0154564 Non-organic sleep disorder disease_ontology DOID:535 sleep disorder A disease of mental health that involves disruption of sleep patterns. url:http://en.wikipedia.org/wiki/Sleep_disorder A intestinal disease located in the colon. DOID:10758 MESH:D003108 SNOMEDCT_US_2021_09_01:128524007 UMLS_CUI:C0009373 colon disorder disease_ontology DOID:5353 colonic disease A intestinal disease located in the colon. url:https://www.nature.com/subjects/colonic-diseases A urinary system disease that is located_in the kidney. DOID:11705 EFO:0003086 ICD10CM:N08 MESH:D007674 NCI:C3149 SNOMEDCT_US_2021_09_01:266612003 UMLS_CUI:C0022658 impaired renal function disease nephropathy disease_ontology DOID:557 kidney disease A urinary system disease that is located_in the kidney. url:http://www.nlm.nih.gov/medlineplus/kidneydiseases.html An eye and adnexa disease that is located_in the eye. DOID:2933 ICD10CM:H44 ICD9CM:379.90 MESH:D005128 NCI:C26767 SNOMEDCT_US_2021_09_01:371409005 UMLS_CUI:C0015397 disease_ontology DOID:5614 eye disease An eye and adnexa disease that is located_in the eye. url:http://en.wikipedia.org/wiki/Eye_disease A sarcoma and hematologic cancer that derives_from follicular lymphoma. NCI:C9294 UMLS_CUI:C1334030 histiocytic and dendritic cell disease_ontology DOID:5621 histiocytic and dendritic cell cancer A sarcoma and hematologic cancer that derives_from follicular lymphoma. url:http://www.springerlink.com/content/h9wrn7p72x26q035/ DOID:12757 ICD10CM:C69.1 ICD9CM:190.4 NCI:C3565 NCI:C4361 SNOMEDCT_US_2021_09_01:126997008 SNOMEDCT_US_2021_09_01:93766000 UMLS_CUI:C0153629 UMLS_CUI:C0339304 Corneal tumor malignant Corneal tumor malignant neoplasm of cornea malignant tumor of cornea neoplasm of cornea disease_ontology DOID:6199 cornea cancer A disease that has_material_basis_in genetic variations in the human genome. MESH:D030342 NCI:C3101 SNOMEDCT_US_2021_09_01:32895009 UMLS_CUI:C0019247 disease_ontology DOID:630 genetic disease A disease that has_material_basis_in genetic variations in the human genome. url:http://ghr.nlm.nih.gov/ A cell type benign neoplasm that is composed_of epithelial tissue in which tumor cells form glands or glandlike structures. DOID:2655 ICDO:8140/0 MESH:D000236 NCI:C2855 NCI:C4196 SNOMEDCT_US_2021_09_01:443416007 SNOMEDCT_US_2021_09_01:79041005 UMLS_CUI:C0001430 UMLS_CUI:C0334389 acinar cell adenoma acinic cell adenoma adenomas disease_ontology DOID:657 adenoma MESH:D000236 A cell type benign neoplasm that is composed_of epithelial tissue in which tumor cells form glands or glandlike structures. url:http://coloncancer.about.com/od/glossaries/g/Adenoma.htm url:http://en.wikipedia.org/wiki/Adenoma A disease that manifests in a defined anatomical structure. DOID:1 DOID:2 DOID:5 DOID:71 DOID:72 DOID:8 disease_ontology DOID:7 disease of anatomical entity A disease that manifests in a defined anatomical structure. url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic An immune system disease that is located_in the lymphatic system. MESH:D008206 SNOMEDCT_US_2021_09_01:266326002 UMLS_CUI:C0024228 Adenopathy Lymphangiopathy Lymphatic disease Lymphatic disorder disease of lympoid system disorder of lymph node and lymphatics disorder of lymphatic system disorder of lymphoid system lymphatic disorder lympoid system disease disease_ontology DOID:75 lymphatic system disease An immune system disease that is located_in the lymphatic system. url:http://en.wikipedia.org/wiki/Lymphatic_disease url:http://www.nlm.nih.gov/medlineplus/lymphaticdiseases.html A leukemia that occurs in children. NCI:C4989 UMLS_CUI:C1332977 disease_ontology DOID:7757 childhood leukemia A leukemia that occurs in children. url:http://www.nlm.nih.gov/medlineplus/leukemiachildhood.html A lens disease characterized by clouding of the lens inside the eye which leads to a decrease in vision. ICD10CM:H26 ICD9CM:366.8 OMIM:601371 OMIM:PS116200 SNOMEDCT_US_2021_09_01:193620000 UMLS_CUI:C0029531 disease_ontology DOID:83 Xref MGI. cataract MESH:D002386 A lens disease characterized by clouding of the lens inside the eye which leads to a decrease in vision. url:http://en.wikipedia.org/wiki/Cataract url:https://www.ncbi.nlm.nih.gov/pubmed/10414631 A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. DOID:11894 DOID:11895 DOID:29 DOID:766 ICD10CM:J98.4 MESH:D008171 NCI:C3198 SNOMEDCT_US_2021_09_01:266374002 UMLS_CUI:C0024115 disease_ontology DOID:850 Updating out dated CUI and removing lung abscess as a synonym. lung disease A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. url:http://www.niehs.nih.gov/health/topics/conditions/lung-disease/index.cfm url:http://www.nlm.nih.gov/medlineplus/ency/article/000066.htm A myeloid leukemia that is characterized by over production of white blood cells. DOID:8551 DOID:8606 EFO:0000339 GARD:6105 ICD9CM:205.1 ICDO:9863/3 KEGG:05220 OMIM:608232 ORDO:521 SNOMEDCT_US_2021_09_01:154592009 UMLS_CUI:C0023473 CML CML - chronic Myelogenous Leukemia Myeloid Leukemia, chronic chronic granulocytic leukaemia chronic granulocytic leukemia chronic myelogenous leukaemia chronic myelogenous leukemia chronic myeloid leukaemia disease_ontology DOID:8552 OMIM mapping confirmed by DO. [SN]. chronic myeloid leukemia A myeloid leukemia that is characterized by over production of white blood cells. url:http://www.cancer.gov/dictionary?CdrID=46755 A leukemia that is located_in myeloid tissue. DOID:8878 DOID:8879 DOID:8910 DOID:9066 DOID:9126 GARD:8226 ICD10CM:C92 ICD9CM:205 ICDO:9860/3 MESH:D007951 NCI:C3172 SNOMEDCT_US_2021_09_01:269631008 UMLS_CUI:C0023470 Non-Lymphocytic Leukemia leukaemia myelogenous leukemia myelogenous myeloid granulocytic leukaemia myeloid granulocytic leukemia myeloid leukaemia disease_ontology DOID:8692 myeloid leukemia A leukemia that is located_in myeloid tissue. url:http://en.wikipedia.org/wiki/Myeloid_leukemia A carcinoma that is an early development defined by the absence of invasion of surrounding tissues. DOID:8793 DOID:8821 ICD10CM:D09.9 ICD9CM:230-234.99 MESH:D002278 NCI:C2917 SNOMEDCT_US_2021_09_01:109355002 UMLS_CUI:C0007099 disease_ontology DOID:8719 in situ carcinoma A carcinoma that is an early development defined by the absence of invasion of surrounding tissues. url:http://en.wikipedia.org/wiki/Carcinoma_in_situ An acute myeloid leukemia that derives from blood-forming tissue in which megakaryocytes proliferate in the bone marrow and circulate in the blood in large numbers. DOID:9009 GARD:524 ICD10CM:C94.2 ICD9CM:207.2 ICDO:9910/3 MESH:D007947 NCI:C3170 SNOMEDCT_US_2021_09_01:52220008 UMLS_CUI:C0023462 Megakaryocytic myelosis Thrombocytic leukaemia disease_ontology DOID:8761 acute megakaryocytic leukemia An acute myeloid leukemia that derives from blood-forming tissue in which megakaryocytes proliferate in the bone marrow and circulate in the blood in large numbers. url:https://en.wikipedia.org/wiki/Acute_megakaryoblastic_leukemia url:https://pubmed.ncbi.nlm.nih.gov/26228843/ url:https://www.orpha.net/data/patho/GB/uk-AMLM7.pdf A myeloid leukemia that is characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells. DOID:9118 DOID:9171 GARD:12757 ICD10CM:C92.0 ICD9CM:205.0 ICDO:9861/3 KEGG:05221 MESH:D015470 NCI:C3171 OMIM:601626 SNOMEDCT_US_2021_09_01:91861009 UMLS_CUI:C0023467 AML - acute Myeloid Leukemia Leukemia, Myelocytic, acute acute myeloblastic leukaemia acute myeloblastic leukemia acute myelogenous leukaemia acute myelogenous leukemia acute myeloid leukaemia disease_ontology DOID:9119 OMIM mapping confirmed by DO. [SN]. acute myeloid leukemia A myeloid leukemia that is characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells. url:http://cancergenome.nih.gov/cancersselected/acutemyeloidleukemia url:http://en.wikipedia.org/wiki/Acute_myeloid_leukemia url:http://www.cancer.gov/dictionary?cdrid=44363 url:https://www.cancer.org/cancer/acute-myeloid-leukemia/detection-diagnosis-staging/how-classified.html A large intestine cancer that is located_in the colon and/or located_in the rectum. ICD10CM:C18.9 KEGG:05210 MESH:D015179 NCI:C2956 NCI:C4978 OMIM:114500 SNOMEDCT_US_2021_09_01:126837005 SNOMEDCT_US_2021_09_01:93854002 UMLS_CUI:C0009404 UMLS_CUI:C0346629 disease_ontology DOID:9256 Xref MGI. OMIM mapping confirmed by DO. [SN]. colorectal cancer A large intestine cancer that is located_in the colon and/or located_in the rectum. url:http://www.cancer.gov/dictionary?CdrID=444983 A mouth disease that is characterized by inflammation of the mouth and lips. ICD10CM:K12.1 MESH:D013280 NCI:C26887 SNOMEDCT_US_2021_09_01:95361005 UMLS_CUI:C0038362 disease_ontology DOID:9637 stomatitis A mouth disease that is characterized by inflammation of the mouth and lips. url:https://en.wikipedia.org/wiki/Stomatitis A acute leukemia that is characterized by over production of lymphoblasts. DOID:5600 EFO:0000220 GARD:522 ICD10CM:C91.00 ICD9CM:204.0 NCI:C3167 NCI:C7055 OMIM:247640 OMIM:613065 ORDO:513 SNOMEDCT_US_2021_09_01:128822004 UMLS_CUI:C0023449 UMLS_CUI:C1335469 ALL acute lymphoblastic leukaemia acute lymphocytic leukaemia precursor lymphoblastic lymphoma/leukemia disease_ontology DOID:9952 Xref MGI. acute lymphoblastic leukemia A acute leukemia that is characterized by over production of lymphoblasts. url:http://www.cancer.gov/dictionary?CdrID=46332 An astrononmical body part which delimited by physical discontinuities with its surroundings. https://en.wikipedia.org/wiki/Geographic_feature macroscopic spatial feature envoPolar This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass. geographic feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. FTT:78 TGN:50001 man-made feature manmade feature anthropogenic geographic feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. ORCID:0000-0002-4366-3088 Mine tailings are the materials left over after the process of separating the valuable fraction from the uneconomic fraction (gangue) of an ore. tailing FTT:625 FTT:631 mine tailing Mine tailings are the materials left over after the process of separating the valuable fraction from the uneconomic fraction (gangue) of an ore. https://en.wikipedia.org/wiki/Tailings tailing ADL:FTT A construction which enables the movement of humans, their animals or their vehicles. FTT:83 transport feature A construction which enables the movement of humans, their animals or their vehicles. MA:ma A geographical feature associated with water. FTT:131 FTT:280 FTT:711 FTT:761 FTT:824 FTT:825 FTT:826 FTT:827 FTT:828 FTT:829 Geonames:H.OVF fluvial feature envoPolar hydrographic feature A geographical feature associated with water. MA:ma fluvial feature ADL:FTT A marine water body which is constitutes the majority of an astronomical body's hydrosphere. LTER:695 EcoLexicon:ocean FTT:1019 FTT:943 Geonames:H.OCN SWEETRealm:Ocean TGN:21102 https://en.wikipedia.org/wiki/Ocean ocean region envoMarine envoPolar ocean LTER:695 https://vocab.lternet.edu/vocab/vocab/index.php?tema=695&/oceans ocean region ADL:FTT A large expanse of saline water usually connected with an ocean. EcoLexicon:sea FTT:233 FTT:830 Geonames:H.SEA TGN:21103 https://en.wikipedia.org/wiki/Sea channel closed sea marginal sea open sea open sound open water envoMarine envoPolar sea A large expanse of saline water usually connected with an ocean. https://en.wikipedia.org/wiki/Sea closed sea USGS:SDTS marginal sea USGS:SDTS open sea USGS:SDTS open sound USGS:SDTS open water USGS:SDTS A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L). ENVO ENVO:00000017 saline hydrographic feature A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L). https://en.wikipedia.org/wiki/Salinity A lake whose water contains a considerable concentration of dissolved salts. FTT:221 FTT:907 Geonames:H.LKN Geonames:H.LKSN TGN:21116 https://en.wikipedia.org/wiki/Saline_lake salt lake salina soda lake saline lake A lake whose water contains a considerable concentration of dissolved salts. MA:ma salt lake USGS:SDTS salina USGS:SDTS A body of water or other liquid of considerable size contained in a depression on a landmass. LTER:278 EcoLexicon:lake FTT:221 FTT:704 FTT:909 Geonames:H.LK Geonames:H.LKS SPIRE:Lake_or_pond SWEETRealm:Lake TGN:21114 TGN:21115 catch basin open water tarn broad llyn loch lochan lough mere mortlake pasteuer lake envoPolar lake A body of water or other liquid of considerable size contained in a depression on a landmass. https://en.wikipedia.org/wiki/Lake LTER:278 https://vocab.lternet.edu/vocab/vocab/index.php?tema=278&/lakes catch basin USGS:SDTS open water USGS:SDTS tarn ADL:FTT lochan ADL:FTT mortlake USGS:SDTS pasteuer lake USGS:SDTS A quarry from which sand is extracted. https://en.wikipedia.org/wiki/Sand_pit ENVO sand pit ENVO:00000028 sand pit quarry A quarry from which sand is extracted. MA:ma An vegetated area which overlaps a wetland ecosystem. WetlandRegion wetland area An vegetated area which overlaps a wetland ecosystem. https://en.wikipedia.org/wiki/Wetland WetlandRegion NASA:earthrealm An accumulation of water of varying size. hydrographic feature EcoLexicon:waterbody FTT:131 FTT:280 FTT:827 SWEETRealm:BodyOfWater TGN:21100 TGN:21101 https://en.wikipedia.org/wiki/Water_body aquatic feature bodies of water body of water waterbody https://en.wikipedia.org/wiki/ The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water. water body An accumulation of water of varying size. https://en.wikipedia.org/wiki/Body_of_water hydrographic feature ADL:FTT bodies of water Getty:TGN body of water ADL:FTT body of water Getty:TGN A construction that has been assembled by deliberate human effort. "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference constructed feature human construction A construction that has been assembled by deliberate human effort. MA:ma A permanent walled and roofed construction. FTT:42 Geonames:S.BLDG LTER:76 TGN:51011 https://en.wikipedia.org/wiki/Building building A permanent walled and roofed construction. USGS:SDTS An excavation in the Earth for the purpose of extracting earth materials. EcoLexicon:mine FTT:14 FTT:968 Geonames:L.MNA Geonames:S.MN TGN:54211 TGN:54212 mine An excavation in the Earth for the purpose of extracting earth materials. USGS:SDTS https://en.wikipedia.org/wiki/Mine A region rendered barren or partially barren by environmental extremes, especially by low rainfall. EcoLexicon:desert FTT:1 FTT:188 Geonames:T.DSRT LTER:147 SWEETRealm:Desert TGN:21201 https://en.wikipedia.org/wiki/Desert arid region envoPolar desert area A region rendered barren or partially barren by environmental extremes, especially by low rainfall. USGS:SDTS arid region ADL:FTT A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate. EcoLexicon:valley FTT:158 FTT:166 FTT:418 FTT:761 FTT:811 FTT:949 Geonames:T.GRGE Geonames:T.VAL Geonames:T.VALS SWEETRealm:Valley TGN:21425 TGN:21451 TGN:21452 TGN:21453 chasm coulee dale glacial gorge glacial trough gulch gully median valley shelf valley glen goe gorge graben hollow lavaka moat ravine re-entrant seachannel strath trench vale water gap Valleys are typically located between hills our mountains. valley A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate. ADL:FTT https://en.wikipedia.org/wiki/Valley chasm USGS:SDTS coulee USGS:SDTS dale USGS:SDTS glacial gorge USGS:SDTS glacial trough USGS:SDTS gulch USGS:SDTS gully Getty:TGN gully USGS:SDTS median valley ADL:FTT median valley Geonames:feature shelf valley Geonames:feature glen ADL:FTT glen USGS:SDTS goe USGS:SDTS gorge Geonames:feature gorge USGS:SDTS graben USGS:SDTS hollow ADL:FTT hollow Getty:TGN hollow USGS:SDTS moat USGS:SDTS ravine USGS:SDTS re-entrant USGS:SDTS seachannel USGS:SDTS strath USGS:SDTS trench USGS:SDTS water gap USGS:SDTS An area in which grasses (Graminae) are a significant component of the vegetation. grazing area herbaceous area grassland area An area in which grasses (Graminae) are a significant component of the vegetation. https://en.wikipedia.org/wiki/Grassland grazing area Getty:TGN herbaceous area USGS:SDTS Land having a cover of trees, shrubs, or both. FTT:1083 FTT:505 FTT:506 FTT:719 FTT:774 Geonames:V.GRVPN LTER:503 SWEETRealm:Break SWEETRealm:Scrub TGN:21631 TGN:21632 TGN:21641 https://en.wikipedia.org/wiki/Woodland brigalow pine grove caatinga chanaral coniferous forest copse deciduous forest equatorial forest equatorial rain forest garique grove jungle mallee scrub monsoon forest moor mott motte mulga mulga scrub rain forest reforested area sagebrush scrub shrub silva stand taiga thicket thorn forest tropical rain forest wood wooded area woodland area Land having a cover of trees, shrubs, or both. USGS:SDTS brigalow USGS:SDTS pine grove Geonames:feature caatinga USGS:SDTS chanaral USGS:SDTS coniferous forest USGS:SDTS copse USGS:SDTS deciduous forest USGS:SDTS equatorial forest USGS:SDTS equatorial rain forest USGS:SDTS garique USGS:SDTS grove ADL:FTT grove USGS:SDTS jungle Getty:TGN jungle USGS:SDTS mallee scrub USGS:SDTS monsoon forest USGS:SDTS moor USGS:SDTS motte USGS:SDTS mulga USGS:SDTS mulga scrub USGS:SDTS rain forest ADL:FTT rain forest Getty:TGN reforested area USGS:SDTS sagebrush USGS:SDTS scrub USGS:SDTS shrub USGS:SDTS silva USGS:SDTS stand USGS:SDTS taiga USGS:SDTS thicket USGS:SDTS thorn forest USGS:SDTS tropical rain forest USGS:SDTS wood ADL:FTT wood Getty:TGN wood USGS:SDTS wooded area USGS:SDTS An area with a high density of trees. A small forest may be called a wood. EcoLexicon:forest FTT:258 FTT:506 FTT:715 FTT:717 Geonames:V.FRST LTER:2 SWEETRealm:Forest TGN:21641 TGN:21642 TGN:21645 https://en.wikipedia.org/wiki/Forest forest wood The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome. forested area An area with a high density of trees. A small forest may be called a wood. https://en.wikipedia.org/wiki/Forest forest Geonames:feature wood Getty:TGN A valley which no longer has water flowing or accumulating over its surface. https://en.wikipedia.org/wiki/Dry_valley Typically found in either Karst (limestone) or chalk terrain. dry valley A valley which no longer has water flowing or accumulating over its surface. https://en.wikipedia.org/wiki/Dry_valley An environmental material which is 1) composed primarily of soil or rock and included ice or organic material and 2) at or below the freezing point of water for two or more years. LTER:408 https://en.wikipedia.org/wiki/Permafrost envoPolar Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material. permafrost An environmental material which is 1) composed primarily of soil or rock and included ice or organic material and 2) at or below the freezing point of water for two or more years. https://en.wikipedia.org/wiki/Permafrost The region occupied by any more or less continuous, directed movement of ocean water that flows in one of the Earth's oceans. Ocean Currents are rivers of hot or cold water within the ocean. The currents are generated from the forces acting upon the water like the earth's rotation, the wind, the temperature and salinity differences and the gravitation of the moon. The depth contours, the shoreline and other movements influence the direction and strength of the movements of water that forms a given current. current EcoLexicon:ocean_current FTT:597 FTT:598 Geonames:H.CRNT LTER:386 SWEETRealm:OceanCurrent TGN:21169 https://en.wikipedia.org/wiki/Ocean_current Subclasses of this class are to be populated by inference. Definition modified from http://en.wikipedia.org/wiki/Ocean_current. ocean current The region occupied by any more or less continuous, directed movement of ocean water that flows in one of the Earth's oceans. Ocean Currents are rivers of hot or cold water within the ocean. The currents are generated from the forces acting upon the water like the earth's rotation, the wind, the temperature and salinity differences and the gravitation of the moon. The depth contours, the shoreline and other movements influence the direction and strength of the movements of water that forms a given current. BS:bs current ADL:FTT current Geonames:feature current Getty:TGN A landform elevated above the surrounding area. elevation LTER:177 SWEETRealm:Elevation https://en.wikipedia.org/wiki/Elevation elevated landform A landform elevated above the surrounding area. MA:ma A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes. EcoLexicon:landform EcoLexicon:landforms FTT:754 FTT:96 SWEETRealm:Landform TGN:21400 TGN:21401 geological feature landform physiographic feature solid astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform geological feature ADL:FTT Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders. EcoLexicon:scree FTT:1078 FTT:96 Geonames:T.TAL SWEETRealm:Talus TGN:21508 https://en.wikipedia.org/wiki/Scree ENVO TALUS talus slope ENVO:00000194 scree Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders. https://en.wikipedia.org/wiki/Scree TALUS USGS:SDTS talus slope Geonames:feature talus slope Getty:TGN A wetland ecosystem in which land mass is permanently inundated by shallow bodies of water, generally with a substantial number of hummocks, or dry-land protrusions. wetland EcoLexicon:swamp FTT:1226 FTT:185 FTT:480 Geonames:H.SWMP SPIRE:Swamp SWEETRealm:Swamp TGN:21324 https://en.wikipedia.org/wiki/Swamp Swamp swamp cienaga swamp ecosystem A wetland ecosystem in which land mass is permanently inundated by shallow bodies of water, generally with a substantial number of hummocks, or dry-land protrusions. https://en.wikipedia.org/wiki/Swamp wetland ADL:FTT wetland USGS:SDTS Swamp NASA:earthrealm swamp Geonames:feature cienaga ADL:FTT A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section. https://en.wikipedia.org/wiki/Glacial_valley ENVO valley ENVO:00000248 envoPolar glacial valley A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section. MA:ma valley USGS:SDTS An open-pit mine from which rock or minerals are extracted. EcoLexicon:quarry FTT:14 FTT:974 Geonames:S.MNQR TGN:54217 https://en.wikipedia.org/wiki/Quarry ENVO ENVO:00000284 quarry An open-pit mine from which rock or minerals are extracted. https://en.wikipedia.org/wiki/Quarry A field of ice, formed in regions of perennial frost. FTT:758 FTT:835 FTT:836 FTT:837 FTT:838 FTT:839 FTT:840 FTT:841 FTT:842 SWEETRealm:IceField TGN:21147 ice patch iceberg icefall IceSheet ice field ice sheet icecap envoPolar Ice mass may need to be resolved from ice field, the former referring simply to an accumulation of ice. ice field A field of ice, formed in regions of perennial frost. ADL:FTT ice patch ADL:FTT iceberg ADL:FTT icefall ADL:FTT IceSheet NASA:earthrealm ice field ADL:FTT ice sheet ADL:FTT icecap ADL:FTT Area covered with low-growing or stunted perennial vegetation and usually not mixed with trees. FTT:1191 FTT:262 FTT:374 FTT:473 FTT:792 FTT:991 Geonames:V.SCRB SWEETRealm:Scrub TGN:21644 TGN:21652 https://en.wikipedia.org/wiki/Scrubland scrubland bush chaparal area heath scrub shrubland scrubland area Area covered with low-growing or stunted perennial vegetation and usually not mixed with trees. ADL:FTT scrubland Geonames:feature bush ADL:FTT bush Getty:TGN chaparal area ADL:FTT heath ADL:FTT scrub USGS:SDTS shrubland ADL:FTT shrubland USGS:SDTS A landform sunken or depressed below the surrounding area. Clarify that this pertains to the planetary crust and create superclass for general topological depressions. https://github.com/EnvironmentOntology/envo/issues/486 depression EcoLexicon:depression FTT:175 FTT:215 FTT:216 Geonames:T.DPR Geonames:T.PAN Geonames:T.PANS SWEETRealm:Depression TGN:21454 TGN:21497 TGN:21521 barrier basin depression non tidal basin pan pan (geologic) pans tidal basin depressed landform A landform sunken or depressed below the surrounding area. https://en.wikipedia.org/wiki/Depression_%28geology%29 barrier basin USGS:SDTS depression Geonames:feature non tidal basin USGS:SDTS pan Geonames:feature pan Getty:TGN pan (geologic) ADL:FTT pans Geonames:feature tidal basin USGS:SDTS A mass of solid material which is composed primarily of rock. FTT:1010 FTT:145 Geonames:T.RK Geonames:T.RKS TGN:21444 piece of rock A particle which 1) is composed primarily of and derived from rock or mineral sources and 2) is or was part of a portion of sand. grain of sand granule of sand sand granule In general, sand grains are larger than those of silt, but finer than those of gravel. particle of sand A particle which 1) is composed primarily of and derived from rock or mineral sources and 2) is or was part of a portion of sand. A particle which 1) is primarily composed of quartz or feldspar and 2) is or was part of a portion of silt. grain of silt granule of silt The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. particle of silt The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. grain of desert sand 2 A biome is an ecosystem to which resident ecological communities have evolved adaptations. LTER:809 EcoLexicon:biome major habitat type EcosytemType There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar. biome A biome is an ecosystem to which resident ecological communities have evolved adaptations. DOI:10.1186/2041-1480-4-43 https://en.wikipedia.org/wiki/Biome LTER:809 https://vocab.lternet.edu/vocab/vocab/index.php?tema=809&/biomes major habitat type WWF:Biome EcosytemType NASA:earthrealm A biome which is primarily or completely situated on a landmass. LTER:798 SPIRE:Terrestrial terrestrial realm terrestrial biome A biome which is primarily or completely situated on a landmass. https://en.wikipedia.org/wiki/Biome#Terrestrial_biomes An aquatic biome which is determined by a marine water body. SPIRE:Marine marine realm envoPolar This biome includes open-ocean and unprotected coastal ecosystems, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt. marine biome An aquatic biome which is determined by a marine water body. ISBN:978-0-618-45504-1 MA:ma https://en.wikipedia.org/wiki/Ocean A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken. research facility A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken. MA:ma The portion of the ground surface which lies below water. BOTTOM EcoLexicon:bed FTT:804 SWEETRealm:Bottom https://en.wikipedia.org/wiki/Stream_bed submerged bed The portion of the ground surface which lies below water. USGS:SDTS BOTTOM USGS:SDTS A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. EcoLexicon:rock FTT:1010 FTT:145 Geonames:T.RK Geonames:T.RKS SWEETRealm:Rock TGN:21444 https://en.wikipedia.org/wiki/Rock From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure. rock A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. MA:ma https://en.wikipedia.org/wiki/Rock_(geology) An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms. The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg] regolith LTER:535 SPIRE:Soil SWEETRealm:Soil https://en.wikipedia.org/wiki/Soil 'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil " The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants. The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280 soil An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms. https://en.wikipedia.org/wiki/Soil A significant accumulation of water which is part of a marine biome. body of marine water marine waterbody Ideas like "significant" are fuzzy and need to be modelled more accurately. The definition is a candidate for review. marine water body A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land. EcoLexicon:slope SWEETRealm:Slope https://en.wikipedia.org/wiki/Slope flank side slope A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land. MA:ma The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. EcoLexicon:air LTER:18 SWEETRealm:Air https://en.wikipedia.org/wiki/Air envoPolar air The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. https://en.wikipedia.org/wiki/Air An environmental material primarily composed of dihydrogen oxide in its liquid form. water EcoLexicon:water LTER:617 https://en.wikipedia.org/wiki/Water liquid water An environmental material primarily composed of dihydrogen oxide in its liquid form. MA:ma Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. EcoLexicon:sediment EcoLexicon:sedimentation LTER:492 LTER:493 SWEETRealm:Sediment https://en.wikipedia.org/wiki/Sediment envoPolar It is recommended to use a combination of sediment terms to describe a more specific sediment type. sediment Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. https://en.wikipedia.org/wiki/Sediment Particulate environmental material with diameters less than 500 micrometers. Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible. EcoLexicon:dust SWEETRealm:Dust https://en.wikipedia.org/wiki/Dust envoPolar Dust occurs in and may be deposited from the atmosphere. dust Particulate environmental material with diameters less than 500 micrometers. https://en.wikipedia.org/wiki/Dust Water which contains a significant concentration of dissolved salts. EcoLexicon:saltwater SWEETRealm:SalineWater SWEETRealm:SaltWater https://en.wikipedia.org/wiki/Saline_water salt water The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight. saline water A rock formed by deposition of either clastic sediments, organic matter, or chemical precipitates (evaporites), followed by compaction of the particulate matter and cementation during diagenesis. EcoLexicon:sedimentary_rock SWEETRealm:SedimentaryRock https://en.wikipedia.org/wiki/Sedimentary_rock ENVO ENVO:00002016 sedimentary rock A rock formed by deposition of either clastic sediments, organic matter, or chemical precipitates (evaporites), followed by compaction of the particulate matter and cementation during diagenesis. https://en.wikipedia.org/wiki/Rock_%28geology%29 A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water. LTER:41 aquatic biome EcoLexicon:wood LTER:637 SWEETRealm:Wood https://en.wikipedia.org/wiki/Wood ENVO ENVO:00002040 wood Sediment which has increased levels of one or more chemical compounds. chemically enriched sediment A portion of contaminated soil is a portion of soil with elevated levels of some contaminant. ENVO ENVO:00002116 "contaminant" is more of a disposition - any material entity can be a contaminant in particular circumstances. contaminated soil Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean. When we have more classes representing the various processes which make seawater seawater, we can further axiomatise this class. EcoLexicon:sea_water LTER:701 SWEETRealm:SeaWater https://en.wikipedia.org/wiki/Sea_water ocean water seawater This definition refers to water that is actually in a sea or ocean. This water may have a wide range of salinity levels. sea water ENVO ENVO:00002167 platinum mine https://en.wikipedia.org/wiki/Gold_mine ENVO ENVO:00002168 gold mine https://en.wikipedia.org/wiki/Coal_mine ENVO ENVO:00002169 coal mine A hospital is a building in which health care services are provided by specialized staff and equipment. https://en.wikipedia.org/wiki/Hospital hospital A hospital is a building in which health care services are provided by specialized staff and equipment. https://en.wikipedia.org/wiki/Hospital EcoLexicon:water_pollution https://en.wikipedia.org/wiki/Contaminated_water polluted water ENVO ENVO:00002186 contaminated water Chemically-enriched sediment which has increased levels of organic compounds. organically enriched sediment Chemically-enriched sediment which has increased levels of inorganic compounds. inorganically enriched sediment coal mine waste ENVO coal refuse ENVO:00002206 coal mine waste material A power plant is a building which contains one or more generators which convert mechanical energy into electrical energy through the relative motion between a magnetic field and a conductor. The energy source harnessed to turn the generator varies widely. SWEETRealm:PowerPlant https://en.wikipedia.org/wiki/Power_plant generating plant generating station power station powerhouse ENVO ENVO:00002214 power plant A power plant is a building which contains one or more generators which convert mechanical energy into electrical energy through the relative motion between a magnetic field and a conductor. The energy source harnessed to turn the generator varies widely. https://en.wikipedia.org/wiki/Power_station A geothermal power plant is a power plant which uses heat generated by the decay of radioactive isotopes in the Earth's mantle and crust as well as primordial heat left over from the formation of the Earth to drive its generators. SWEETRealm:GeothermalPowerPlant https://en.wikipedia.org/wiki/Geothermal_power_plant ENVO ENVO:00002215 geothermal power plant A geothermal power plant is a power plant which uses heat generated by the decay of radioactive isotopes in the Earth's mantle and crust as well as primordial heat left over from the formation of the Earth to drive its generators. https://en.wikipedia.org/wiki/Earth's_internal_heat_budget https://en.wikipedia.org/wiki/Geothermal_energy A portion of soil which is found in a forested area. forest soil A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process). This seems more like a role than a material. Anything can be waste. Thus, a "waste" role or disposition will be created and this class can then be populated by inference: any environmental material which has [role,disposition] waste will be considered a waste material. EcoLexicon:waste SWEETRealm:Waste https://en.wikipedia.org/wiki/Waste ENVO ENVO:00002264 waste material Industrial wastes are liquid, solid and gaseous wastes originating from the manufacture of specific products. This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with industrial entities. industrial waste ENVO ENVO:00002267 industrial waste material Industrial wastes are liquid, solid and gaseous wastes originating from the manufacture of specific products. ISBN:978-92-1-161386-5 http://stats.oecd.org/glossary/detail.asp?ID=1340 A nuclear power plant is a power plant which uses heat generated by a radioactive decay in a nuclear reactor to convert water into steam in order to drive turbines in electrical generators through pressure. https://en.wikipedia.org/wiki/Nuclear_power_plant ENVO ENVO:00002271 nuclear power plant A nuclear power plant is a power plant which uses heat generated by a radioactive decay in a nuclear reactor to convert water into steam in order to drive turbines in electrical generators through pressure. https://en.wikipedia.org/wiki/Nuclear_power_plant A manufactuered product which is capable of removing heat and controlling the humidity of the air within a site. A/C A/C unit air conditioner air conditioning unit A manufactuered product which is capable of removing heat and controlling the humidity of the air within a site. Particulate environmental material which 1) is composed primarily of clay particles, with only minor proportions of other materials, 2) demonstrates plasticity when wet, and 3) is capable of hardening when dried or fired. Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible. EcoLexicon:clay SWEETRealm:Clay This definition is intentionally ambiguous to support the multiple thresholds set by different authorities.The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. Similar mixtures with greater than 40% clay are often considered clay soils. clay Particulate environmental material which 1) is composed primarily of clay particles, with only minor proportions of other materials, 2) demonstrates plasticity when wet, and 3) is capable of hardening when dried or fired. https://en.wikipedia.org/wiki/Clay This definition is intentionally ambiguous to support the multiple thresholds set by different authorities.The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. Similar mixtures with greater than 40% clay are often considered clay soils. A house used for sheltering non-human animals. While humans are animals, this class does not refer to human houses. animal house A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. manufactured good manufactured product A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. https://en.wikipedia.org/wiki/Manufactured_product A portion of enriched soil is a portion of soil with elevated levels of some material entity. This could be demoted to an inferred class if issues with double inheritance arise. enriched soil An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered. It's possible that this will become an inferred class in the future. The United Nations' International Standard Industrial Classification should be referred to when expanding this branch. ISIC can also be used to identify processes. See http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=27&Lg=1. industrial building An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered. https://en.wikipedia.org/wiki/Industry A brewery is a building in which alcoholic beverages are produced by brewing, that is, steeping a starch source (commonly cereal grains) in water and fermenting the resulting sweet liquid with yeast. At times, the products are also sold from the brewery. ENVO ENVO:00003885 brewery A brewery is a building in which alcoholic beverages are produced by brewing, that is, steeping a starch source (commonly cereal grains) in water and fermenting the resulting sweet liquid with yeast. At times, the products are also sold from the brewery. https://en.wikipedia.org/wiki/Brewery https://en.wikipedia.org/wiki/Brewing A building or collection of co-located buildings constructed for the purpose of undertaking scientific research. research station A building or collection of co-located buildings constructed for the purpose of undertaking scientific research. MA:ma https://en.wikipedia.org/wiki/Research_station A warehouse is a building which is used for the storage of goods. warehouse A warehouse is a building which is used for the storage of goods. https://en.wikipedia.org/wiki/Warehouse An air filter is a device that removes some substance from air. https://en.wikipedia.org/wiki/Air_filter ENVO ENVO:00003968 This is a general definition derived from the definitions for particulate, chemical, and other air filters. Subclasses should be created if needed. air filter An air filter is a device that removes some substance from air. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Air_filter Soil which has little to no water content and in which minerals and other soluble chemical entities have either bonded or become adsorbed to sold particles due to insufficient water availability. dry soil A portion of soil which is found in a grassland. grassland soil Soil which is part of some elevated land. upland soil Soil which is part of some elevated land. Sand which is part of a desert. desert sand The dwelling of an animal or group of similar animals. den nest This class represents habitations of non-human animals. This distinction may be removed in future releases. animal habitation The dwelling of an animal or group of similar animals. MA:ma A bird nest is the spot in which a bird lays and incubates its eggs and raises its young. bird nest bird's nest eyrie ENVO ENVO:00005805 nest of bird A bird nest is the spot in which a bird lays and incubates its eggs and raises its young. https://en.wikipedia.org/wiki/Bird_nest A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. portion of environmental material Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental material A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. DOI:10.1186/2041-1480-4-43 MA:ma ORCID:0000-0002-4366-3088 URL:http://ontology.buffalo.edu/smith/articles/niches.html A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings. EcoLexicon:surface http://sweetontology.net/reprSpaceGeometry/Surface https://en.wikipedia.org/wiki/Surface This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here. surface layer A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings. URL:http://www.merriam-webster.com/dictionary/surface Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. EcoLexicon:aerosol SWEETRealm:Aerosol envoAtmo Should connect to PATO as "quality of an aerosol" aerosol Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. https://en.wikipedia.org/wiki/Aerosol Anthropogenic material in or on which organisms may live. ENVO ENVO:0010001 anthropogenic environmental material Anthropogenic material in or on which organisms may live. MA:ma MERGED DEFINITION: TARGET DEFINITION: An oceanographic feature that involves wind-driven motion of dense, cooler, and usually nutrient-rich water towards the ocean surface, replacing the warmer, usually nutrient-deplete surface water. -------------------- SOURCE DEFINITION: A marine upwelling is a net flow of marine water to the surface of the water column from deeper regions. This is often a result of surface water displacement off continental coasts by wind action. Localised upwellings may also occur along divergent fronts around eddies and along some of the major oceanographic features. Deeper waters often have higher nutrient content; consequently blooms of primary producers, such as planktonic algae, are generally observed around upwelling zones. ENVO:01000063 EcoLexicon:upwell EcoLexicon:upwelling SWEETRealm:Upwelling https://en.wikipedia.org/wiki/Upwelling marine upwelling This term is specific to marine upwellings. upwelling MERGED DEFINITION: TARGET DEFINITION: An oceanographic feature that involves wind-driven motion of dense, cooler, and usually nutrient-rich water towards the ocean surface, replacing the warmer, usually nutrient-deplete surface water. -------------------- SOURCE DEFINITION: A marine upwelling is a net flow of marine water to the surface of the water column from deeper regions. This is often a result of surface water displacement off continental coasts by wind action. Localised upwellings may also occur along divergent fronts around eddies and along some of the major oceanographic features. Deeper waters often have higher nutrient content; consequently blooms of primary producers, such as planktonic algae, are generally observed around upwelling zones. https://en.wikipedia.org/wiki/Upwelling Particulate environmental material which is primarily composed of silt particles. Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible. EcoLexicon:silt SWEETRealm:Silt https://en.wikipedia.org/wiki/Silt This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider this soil material that contains 80% or more silt and less than 12% clay. In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity. silt Particulate environmental material which is primarily composed of silt particles. This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider this soil material that contains 80% or more silt and less than 12% clay. In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity. Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances. Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible. EcoLexicon:sand LTER:484 SWEETRealm:Sand https://en.wikipedia.org/wiki/Sand This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand. sand Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances. https://en.wikipedia.org/wiki/Sand This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand. https://sis.agr.gc.ca/cansis/glossary/t/index.html Expressions of the estuarine biome occur at wide lower courses of a rivers where they flow into a sea. Estuaries experience tidal flows and their water is a changing mixture of fresh and salt. ORCID:0000-0002-4366-3088 2010-03-15T11:17:06Z SPIRE:Estuarine estuarine biome Expressions of the estuarine biome occur at wide lower courses of a rivers where they flow into a sea. Estuaries experience tidal flows and their water is a changing mixture of fresh and salt. ISBN:978-92-1-161386-5 ORCID:0000-0002-4366-3088 The marine salt marsh biome comprises marshes that are transitional intertidals between land and salty or brackish marine water (e.g.: sloughs, bays, estuaries). It is dominated by halophytic (salt tolerant) herbaceous plants. The daily tidal surges bring in nutrients, which tend to settle in roots of the plants within the salt marsh. The natural chemical activity of salty (or brackish) water and the tendency of algae to bloom in the shallow unshaded water also allow for great biodiversity. ORCID:0000-0002-4366-3088 2010-03-15T11:17:06Z ENVO ENVO:01000022 marine salt marsh biome The marine salt marsh biome comprises marshes that are transitional intertidals between land and salty or brackish marine water (e.g.: sloughs, bays, estuaries). It is dominated by halophytic (salt tolerant) herbaceous plants. The daily tidal surges bring in nutrients, which tend to settle in roots of the plants within the salt marsh. The natural chemical activity of salty (or brackish) water and the tendency of algae to bloom in the shallow unshaded water also allow for great biodiversity. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Salt_marsh The marginal sea biome comprises parts of an ocean partially enclosed by land such as islands, archipelagos, or peninsulas. Unlike mediterranean seas, marginal seas have ocean currents caused by ocean winds. Many marginal seas are enclosed by island arcs that were formed from the subduction of one oceanic plate beneath another. ORCID:0000-0002-4366-3088 2010-03-15T11:23:23Z marginal sea biome The marginal sea biome comprises parts of an ocean partially enclosed by land such as islands, archipelagos, or peninsulas. Unlike mediterranean seas, marginal seas have ocean currents caused by ocean winds. Many marginal seas are enclosed by island arcs that were formed from the subduction of one oceanic plate beneath another. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Marginal_sea A marine biome which is determined by an ocean. ORCID:0000-0002-4366-3088 2010-03-15T11:23:23Z envoPolar Ocean biomes are determined by major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt. ocean biome A marine biome which is determined by an ocean. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Ocean An environmental material which is composed primarily of particles. Do not oversimplify this branch with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible. particulate matter envoAtmo envoPolar particulate environmental material A portion of planktonic material is a portion of environmental material primarily composed of plankton. See Issue #251. Awaiting class creation in PCO to attempt logical definitions. envoPolar planktonic material A water current which is maintained by a continuous, directed movement of marine water, generated by forces caused by breaking waves, wind, Coriolis force, temperature and salinity differences, and tides caused by the gravitational pull of astronomical bodies. Depth contours, shoreline configurations and interaction with other currents influence a current's direction and strength. ORCID:0000-0002-4366-3088 2010-03-16T12:16:11Z EcoLexicon:marine_current envoPolar marine current A water current which is maintained by a continuous, directed movement of marine water, generated by forces caused by breaking waves, wind, Coriolis force, temperature and salinity differences, and tides caused by the gravitational pull of astronomical bodies. Depth contours, shoreline configurations and interaction with other currents influence a current's direction and strength. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Ocean_current Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. ORCID:0000-0002-4366-3088 2010-03-20T08:40:04Z EcoLexicon:organic_material biomass organic material Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. ISBN:978-0-618-45504-1 ORCID:0000-0002-4366-3088 A forest ecosystem in which dominant ecological communities have reached their climax successional state. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z LTER:212 SPIRE:Forest Preliminary definition. forest biome A woodland biome is a terrestrial biome which includes, across its entire spatial extent, woody plants spaced sufficiently far apart to allow light penetration to support communities of herbaceous plants or shrubs living closer to the woodland floor. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z Preliminary definition. woodland biome A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z Preliminary definition. shrubland biome A woodland biome which has seasonal water availability and includes trees spaced sufficiently far apart to allow an unbroken layer of grass, sedge (Cyperaceae) or rush (Juncaceae) communities to live. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z SPIRE:Savannah_or_grassland savanna biome A desert biome is a terrestrial biome which loses more liquid water by evapotranspiration than is supplied by precipitation and includes communities adapted to these conditions. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z SPIRE:Desert_or_dune wwfBiome Preliminary definition. desert biome A subtropical desert biome is a desert biome which has communities adapted to temperatures above a monthly average of 18 degrees Celsius, high daily temperature ranges of approximately 20 degrees Celsius, high insolation (but lower than that of a tropical desert biome), inhibited cloud formation, and very low precipitation. Subtropical desert biomes located near coasts with cold upwellings may have cooler temperatures and reduced insolution due to fog. ORCID:0000-0002-4366-3088 2013-04-07T14:28:08Z Preliminary definition. The semantics and definitions of "mediterranean", "subtropical", "tropical", "temperate", "polar", and similar climate types may be transferred to an "environmental condition" class once the semantics of this class have been established. subtropical desert biome A subtropical desert biome is a desert biome which has communities adapted to temperatures above a monthly average of 18 degrees Celsius, high daily temperature ranges of approximately 20 degrees Celsius, high insolation (but lower than that of a tropical desert biome), inhibited cloud formation, and very low precipitation. Subtropical desert biomes located near coasts with cold upwellings may have cooler temperatures and reduced insolution due to fog. WWW:http://www.earthonlinemedia.com/ebooks/tpe_3e/title_page.html https://en.wikipedia.org/wiki/Subtropical#Semi-desert.2Fdesert_climate A savanna biome which is subject to temperate climate patterns. ORCID:0000-0002-4366-3088 2013-04-07T14:28:51Z prairie biome Preliminary definition. The semantics and definitions of "mediterranean", "subtropical", "tropical", "temperate", "polar", and similar climate types may be transferred to an "environmental condition" class once the semantics of this class have been established. temperate savanna biome ORCID:0000-0002-4366-3088 2013-04-07T14:29:48Z prairie biome Preliminary definition. The semantics and definitions of "mediterranean", "subtropical", "tropical", "temperate", "polar", and similar climate types may be transferred to an "environmental condition" class once the semantics of this class have been established. temperate grassland biome A coniferous forest biome is a forest biome which contains densely packed populations or communities of coniferous trees, strongly limiting light penetration to the forest floor. ORCID:0000-0002-4366-3088 2013-04-07T14:31:01Z ENVO ENVO:01000196 Preliminary definition. coniferous forest biome A broadleaf forest which is subject to temperate climate patterns. ORCID:0000-0002-4366-3088 2013-04-07T14:32:28Z wwfBiome temperate broadleaf forest biome An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. ORCID:0000-0002-4366-3088 2013-04-07T14:35:18Z envoPolar A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. environmental condition An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. DOI:10.1186/2041-1480-4-43 A tropical condition is an environmental condition in which an environmental system receives high yearly solar irradiance per unit area and, on Earth, the Sun reaches a subsolar point at least once during the solar year. This results in a hot and moist year-round climate at low elevations, which have a monthly average temperature above 18 degrees Celsius. ORCID:0000-0002-4366-3088 2013-04-07T14:36:47Z EcoLexicon:the_tropics SPIRE:Tropical tropical A tropical condition is an environmental condition in which an environmental system receives high yearly solar irradiance per unit area and, on Earth, the Sun reaches a subsolar point at least once during the solar year. This results in a hot and moist year-round climate at low elevations, which have a monthly average temperature above 18 degrees Celsius. https://en.wikipedia.org/wiki/Tropical A subtropical condition is an environmental condition in which an envrionmental system receives more solar irradiance than those with temperate conditions, but less than those with tropical conditions. At low elevations, this typically results in eight months of the year having average temperatures greater than or equal to 10 degrees Celsius with the coldest monthly temperature averaging between 2 and 13 degrees Celsius. ORCID:0000-0002-4366-3088 2013-04-07T14:36:47Z As with most other climatic zones and conditions, multiple classification schemes have somehat different definitions and criteria. To quote from https://en.wikipedia.org/wiki/ "Several methods have been used to define the subtropical climate. In the Trewartha climate classification, a subtropical region should have at least eight months with a mean temperature of 10 °C (50.0 °F) or above. German climatologists Carl Troll and Karlheinz Paffen defined Warm temperate zones as plain and hilly lands having an average temperature of the coldest month between 2 °C (35.6 °F) and 13 °C (55.4 °F) in the Northern Hemisphere and between 6 °C (42.8 °F) and 13 °C (55.4 °F) in the Southern Hemisphere, excluding oceanic and continental climates. According to the Troll-Paffen climate classification, there generally exists one large subtropical zone named the warm-temperate subtropical zone,[4] which is subdivided into seven smaller areas.[5] According to the E. Neef climate classification, the subtropical zone is divided into two parts: Rainy winters of the west sides and Eastern subtropical climate.[6] According to the Wilhelm Lauer & Peter Frankenberg climate classification, the subtropical zone is divided into three parts: high-continental, continental, and maritime.[7] According to the Siegmund/Frankenberg climate classification, subtropical is one of six climate zones in the world.[8]" subtropical A temperate condition is an environmental condition in which an environmental system receives less solar irradiance than those with subpolar conditions, but greater than those with subtropical conditions. ORCID:0000-0002-4366-3088 2013-04-07T14:36:47Z SPIRE:Temperate tepid climate This class' definition is less satisfactory than the other latitudinal conditoins. temperate A temperate condition is an environmental condition in which an environmental system receives less solar irradiance than those with subpolar conditions, but greater than those with subtropical conditions. https://en.wikipedia.org/wiki/Temperate_climate tepid climate https://en.wikipedia.org/wiki/Temperate_climate A coniferous forest biome which is subject to temperate climate patterns. ORCID:0000-0002-4366-3088 2013-04-07T14:39:14Z wwfBiome Preliminary definition. The semantics and definitions of "mediterranean", "subtropical", "tropical", "temperate", "polar", and similar climate types may be transferred to an "environmental condition" class once the semantics of this class have been established. temperate coniferous forest biome A temperate mixed forest in which dominant ecological communities have reached their climax successional state. ORCID:0000-0002-4366-3088 2013-04-07T14:39:30Z wwfBiome temperate mixed forest biome A shrubland biome which is subject to temperate climate patterns. ORCID:0000-0002-4366-3088 2013-04-07T14:40:32Z prairie biome Preliminary definition. The semantics and definitions of "mediterranean", "subtropical", "tropical", "temperate", "polar", and similar climate types may be transferred to an "environmental condition" class once the semantics of this class have been established. temperate shrubland biome A montane shrubland biome is a shrubland biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions. ORCID:0000-0002-4366-3088 2013-04-07T14:40:32Z wwfBiome Preliminary definition. montane shrubland biome An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity. ORCID:0000-0002-4366-3088 2013-04-07T14:45:22Z anthrome human biome Preliminary definition. anthropogenic terrestrial biome An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity. http://www.eoearth.org/view/article/150128/ A woodland biome which is subject to temperate climate patterns. ORCID:0000-0002-4366-3088 2013-04-07T15:01:04Z Preliminary definition. The semantics and definitions of "mediterranean", "subtropical", "tropical", "temperate", "polar", and similar climate types may be transferred to an "environmental condition" class once the semantics of this class have been established. temperate woodland biome An environmental condition in which annual precipitation is less than half of annual potential evapotranspiration. ORCID:0000-0002-4366-3088 2013-04-24T13:28:18Z EcoLexicon:aridity envoPolar arid A polar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area, resulting in colder climatic conditions. ORCID:0000-0002-4366-3088 2013-05-08T07:49:36Z SPIRE:Polar SWEETRealm:Polarization frigid envoPolar On Earth, polar conditions are such that every month has average temperature lower than 10 degrees Celsius. Note that this class refers to a climatic rather than a positional condition. polar A polar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area, resulting in colder climatic conditions. https://en.wikipedia.org/wiki/Polar_climate frigid https://en.wikipedia.org/wiki/Polar_climate A scrubland which is located in a desert. 2013-06-06T15:02:30Z desert scrub desert scrubland A scrubland which is located in a desert. ORCID:0000-0001-8743-9574 desert scrub ORCID:0000-0001-8743-9574 A dense settlement biome is an anthropogenic terrestrial biome which is primarily used for human habitation, recreation, and industry within built structures with little other land use. ORCID:0000-0002-4366-3088 2013-06-14T11:45:47Z ENVO ENVO:01000248 dense settlement biome A dense settlement biome is an anthropogenic terrestrial biome which is primarily used for human habitation, recreation, and industry within built structures with little other land use. DOI:10.1111/j.1466-8238.2010.00540.x DOI:10.1890/070062 A coniferous forest biome which includes communities adapted to subpolar conditions. 2013-09-04T06:41:53Z EcoLexicon:taiga LTER:72 SPIRE:Taiga boreal forest taiga wwfBiome subpolar coniferous forest biome A subpolar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area and is surrounded by large land masses. This results in very cold winters with temperatures potentially falling to around -40 degrees Celsius and summers which last no more than 3 months of the year with a 24-hour average temperature of at least 10 degrees Celsius. ORCID:0000-0002-4366-3088 2013-09-04T07:08:34Z boreal subarctic envoPolar Note that this class refers to a climatic rather than a positional condition. subpolar A subpolar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area and is surrounded by large land masses. This results in very cold winters with temperatures potentially falling to around -40 degrees Celsius and summers which last no more than 3 months of the year with a 24-hour average temperature of at least 10 degrees Celsius. https://en.wikipedia.org/wiki/Subarctic_climate boreal https://en.wikipedia.org/wiki/Subarctic_climate subarctic https://en.wikipedia.org/wiki/Subarctic_climate A system which has the disposition to environ one or more material entities. 2013-09-23T16:04:08Z EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system A system which has the disposition to environ one or more material entities. DOI:10.1186/2041-1480-4-43 A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure. Look for "mineral" in a chemical or geochemical ontology to formalise the composed primarily of link. From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure. ORCID:0000-0002-4366-3088 2013-10-05T12:37:41Z LTER:341 mineral material A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure. https://en.wikipedia.org/wiki/Mineral Water vapour is a vapour which is the gas phase of water. ORCID:0000-0002-4366-3088 2013-10-10T07:58:18Z aqueous vapor aqueous vapour water vapor Perhaps a better relation between water vapour and water can be found in or added to RO? water vapour Water vapour is a vapour which is the gas phase of water. https://en.wikipedia.org/wiki/Water_vapor aqueous vapor https://en.wikipedia.org/wiki/Water_vapor aqueous vapour https://en.wikipedia.org/wiki/Water_vapor water vapor https://en.wikipedia.org/wiki/Water_vapor An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body. ORCID:0000-0002-4366-3088 2013-10-10T08:14:50Z LTER:48 atmosphere An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body. https://en.wikipedia.org/wiki/Atmosphere https://en.wikipedia.org/wiki/Physical_geography Atmospheric water vapour is water vapour that is part of an atmosphere. ORCID:0000-0002-4366-3088 2013-10-10T08:22:07Z atmospheric water vapor ENVO ENVO:01000268 envoPolar atmospheric water vapour Atmospheric water vapour is water vapour that is part of an atmosphere. https://en.wikipedia.org/wiki/Water_vapor atmospheric water vapor https://en.wikipedia.org/wiki/Water_vapor A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. ORCID:0000-0002-4366-3088 2013-10-12T17:21:09Z envoPolar Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO. ecoregion A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. DOI:10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2 URL:http://worldwildlife.org/biomes Ice which is formed from water. 2013-10-13T12:01:28Z LTER:262 ice envoPolar Water ice can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance. When speaking about ice on Earth, usually water ice is meant - the solid, crystalline form of water found in the atmosphere as snow crystals, hail, ice pellets, etc., and on the earth's surface in forms such as hoarfrost, rime, glaze, sea ice, glacier ice, ground ice, frazil, anchor ice, etc. This form of water is, strictly speaking, called ice Ih, the Roman numeral I distinguishing it from more than a dozen other phases and the letter h distinguishing it from the metastable cubic phase ice Ic. Ice Ih is the only one of the several known phases of water ice that is stable at commonly occurring temperatures and pressures. (Some of the other forms have very unusual properties, ice VII, for example, being stable only at pressures above 22 400 kg/cm^2, but then existing at temperatures up to about 100C.) It has an open structure with a specific gravity of 0.9166 which is slightly less than water; because the water molecules bond to their neighbors covalently only in four directions; it therefore floats on higher density water, where broken molecular bonds permit closer packing. All commonly occurring forms of ice are crystalline, although large single crystals are relatively rare except in glaciers. The ice crystal lattice possesses hexagonal symmetry that manifests itself in the gross forms of such single crystals as are sometimes found in snow. At an air pressure of one atmosphere, ice melts at 0 C by definition of the Celsius temperature scale. (Strictly speaking the equilibrium point among water, ice, and vapor occurs at +0.01C, the triple point.) On the other hand, ice does not invariably form in liquid water cooled below this temperature; it has a tendency to supercool, more so in the absence of ice nuclei. In permafrost regions, ice may occupy voids in soils and rocks and may develop in a variety of forms. Ice may be colourless to pale blue or greenish-blue. It may appear white due to included gas bubbles; in exposures, ground ice may also appear black. In nature ice is formed either by: (a) the freezing of water, (b) the condensation of atmospheric water vapour direct into ice crystals, (c) the compaction of snow with or without the motion of a glacier, or (d) the impregnation of porous snow masses with water which subsequently freeze. water ice Ice which is formed from water. https://en.wikipedia.org/wiki/Ice ice http://www.eionet.europa.eu/gemet/concept/4131 Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration. ORCID:0000-0002-4366-3088 2013-10-13T18:32:46Z envoPolar ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO. https://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories. ecozone Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration. https://en.wikipedia.org/wiki/ecozone A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. ORCID:0000-0002-4366-3088 2013-10-15T16:42:02Z envoPolar Preliminary definition. layer A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. Wiktionary:layer A layer which is part of a lake. ORCID:0000-0002-4366-3088 2013-10-15T16:57:43Z ENVO ENVO:01000283 envoPolar Note that this class does not contain metalimnion as a subclass. The metaliminon is classified as a thermocline. lake layer A mass of water ice. Class should be populated by inference and asserted subclasses redistributed. ORCID:0000-0002-4366-3088 2013-10-15T19:49:11Z accumulation of ice ice accumulation http://sweetontology.net/phenCryo/Accumulation envoPolar ice mass A layer that is part of a marine water body. ORCID:0000-0002-4366-3088 envoMarine envoPolar marine layer A layer that is part of a marine water body. ORCID:0000-0002-4366-3088 An endolithic environment is an environment that exists within solid rock. endolithic environment An environmental system which has its properties and dynamics determined by saline water. Water (saline) envoEmpo envoOmics envoPolar saline water environment Water (saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environment which has a lower temperature than some local or global average. envoPolar The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'. cold environment An anthropogenic environment is an environmental system which is the product of human activity. Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic. anthropogenic environment A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes. high osmolarity environment An acidic environment is an environment in which material entities are exposed to a low pH. acidic environment An environment whose dynamics are strongly influenced by water. aquatic environment A rocky slope is a slope which has a surface primarily composed of rock. rocky slope A marine environment and enviroment which is determined by a marine water body. envoPolar marine environment A marine environment and enviroment which is determined by a marine water body. NM:nm An environmental system determined by seawater. ocean water environment envoPolar sea water environment The atmospheric boundary layer is the lowest layer of an atmosphere which is strongly influenced by its contact with a planetary surface with strong vertical mixing and in which physical quantities such as flow velocity, temperature, and moisture display rapid fluctuations (turbulence). planetary boundary layer envoPolar atmospheric boundary layer A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space. a useful class: this can be used to define sub-terrestrial and sub-marine entities planetary surface A layer in a water mass, itself composed primarily of water. envoPolar This class will eventually be populated by inference, and its asserted subclasses removed. aquatic layer A dome swamp is a swamp which occurs in a depression where deeper waters at the centre of the swamp allow trees to grow taller relative to those in shallower regions of the depression. This creates a dome-like shape. The logical def should be improved with the idea of a vegetation unit growing in a depression expressed. dome swamp A talus slope is a slope which has a surface layer composed of scree. scree slope talus slope An understory is a layer of plant life which grows below the canopy without penetrating it. under story undergrowth understorey understory An understory is a layer of plant life which grows below the canopy without penetrating it. https://en.wikipedia.org/wiki/Understory A shrub layer is a layer of vegetation in a woodland or forest consisting of low, woody vegetation of frutescent form. shrub layer A shrub layer is a layer of vegetation in a woodland or forest consisting of low, woody vegetation of frutescent form. http://www.treeterms.co.uk/definitions/shrub-layer A herb and fern layer is a layer of a forest or woodland which is composed of all vascular plant life that are one metre or less in height. fern layer herb layer herb stratum herbaceous layer herbaceous stratum herbaceous understory ground cover ground vegetation regeneration layer This definition is inclusive of non-herbaceous plants that may be transiently present in the "herb layer". See Gilliam FS (2007) The Ecological Significance of the Herbaceous Layer in Temperate Forest Ecosystems. BioScience. 57(10):845-858. (http://dx.doi.org/10.1641/B571007) for rationale and a review of definitional and terminological variation. herb and fern layer A herb and fern layer is a layer of a forest or woodland which is composed of all vascular plant life that are one metre or less in height. http://dx.doi.org/10.1641/B571007 ground layer Refers to the ground layer of a forest or woodland where leaf litter or other plant matter accumulates litter layer A biome which is subject to polar climatic conditions. envoPolar This class is primarily for inference and, in general, should not be used directly by annotators. If you're an annotator, please consider using a more informative term such as 'tundra biome'. polar biome An altitudinal condition which inheres in a bearer by virtue of the bearer having a monthly mean temperature is less than 10 degrees Celsius and being located at altitudes above the tree line and below the snowline. ORCID:0000-0002-4366-3088 LTER:26 envoPolar Requested term with preliminary def. See Issue 29 on the envo tracker. alpine An altitudinal condition which inheres in a bearer by virtue of the bearer having a monthly mean temperature is less than 10 degrees Celsius and being located at altitudes above the tree line and below the snowline. https://en.wikipedia.org/wiki/Altitudinal_zonation An altitudinal condition which inheres in a bearer by virtue of the bearer being located at an altitude between mid-altitude forests and the tree line. ORCID:0000-0002-4366-3088 LTER:350 envoPolar The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate. montane An altitudinal condition which inheres in a bearer by virtue of the bearer being located at an altitude between mid-altitude forests and the tree line. https://en.wikipedia.org/wiki/Altitudinal_zonation The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate. https://en.wikipedia.org/wiki/Altitudinal_zonation An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude. ORCID:0000-0002-4366-3088 envoPolar Depending on the latitude (and, to a lesser extent, other factors), the actual location of the zones where these conditions are in effect will change. altitudinal condition An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude. https://en.wikipedia.org/wiki/Altitudinal_zonation An organic material primarily composed of a portion of plant root. Requested in Issue 115 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive. root matter An unbroken expanse (as of ice) ORCID:0000-0002-4366-3088 envoPolar This class was created to accommodate "fields" from agricultural fields to marine mesoscale eddy fields. Thus, it has a very broad definition which makes it less than informative when annotating. Please consider using or requesting an appropriate subclass. field An unbroken expanse (as of ice) http://www.merriam-webster.com/dictionary/field A layer which is determined by a form of vegetation. forest layer forest stratum woodland layer woodland stratum Usually found in woodlands and forests. vegetation layer A portion of acidic water is a portion of water with a pH less than 7. acidic water An evergreen needleleaf forest which is subject to temperate climate patterns. coniferous forest This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000). temperate evergreen needleleaf forest A deciduous broadleaf forest which is subject to temperate climate patterns. This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000). temperate deciduous broadleaf forest A deciduous needleleaf forest which is subject to temperate climate patterns. coniferous forest This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000). temperate deciduous needleleaf forest A temperate mixed forest which has communities of trees composed primarily of species with broad leaves. This class corresponds to the "Temperate Mixed broadleaf / needleleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "temperate mixed needleleaf forest" class can be made. temperate mixed broadleaf forest A temperate mixed forest which has communities of trees composed primarily of species with needle-like leaves (e.g. conifers). coniferous forest This class corresponds to the "Temperate Mixed broadleaf / needleleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "temperate mixed broadleaf forest" class can be made. temperate mixed needleleaf forest A sclerophyllous forest which is subject to temperate climate patterns. This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000). temperate sclerophyllous dry forest A broadleaf evergreen forest which is subject to temperate climate patterns. This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000). temperate broadleaf evergreen forest A freshwater swamp forest which is subject to temperate climate patterns. This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000). It is currently unclear how to relate forests and swamps. temperate freshwater swamp forest Snow is an environmental material which is primarily composed of flakes of crystalline water ice. envoPolar snow Snow is an environmental material which is primarily composed of flakes of crystalline water ice. http://www.eionet.europa.eu/gemet/concept/7769 https://en.wikipedia.org/wiki/Snow A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. environmental area envoPolar Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. environmental zone A whole plant which is relatively old old plant A whole plant which is relatively young. young plant A house is a building that provides a dwelling-place for a living entity. The provisioning of a dwelling-place can perhaps be modelled as a role. house A house is a building that provides a dwelling-place for a living entity. https://en.wikipedia.org/wiki/Home https://en.wikipedia.org/wiki/House A human house is a house which provides a dwelling-place for humans. human house A building part is a construction which is part of a building. Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat. building part A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls. ORCID:0000-0002-4366-3088 room A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls. https://en.wikipedia.org/wiki/Room A forest biome which contains densely packed populations or communities of broadleaf trees, strongly limiting light penetration to the forest floor. A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending. broadleaf forest A forest ecosystem which contains densely packed populations or communities of broadleaf and coniferous trees, strongly limiting light penetration to the forest floor. A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending. The subclasses of this class need to be checked: are they properly placed under other classes or is this corrected and the dominant form of mixed vegetation noted in the label? mixed forest A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending. swamp forest coniferous forest A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending. needleleaf forest A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending. sclerophyllous forest A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending. montane forest A concrete masonry unit is a large, rectangular masonry unit primarily composed of concrete. ORCID:0000-0002-4366-3088 concrete masonry unit A concrete masonry unit is a large, rectangular masonry unit primarily composed of concrete. https://en.wikipedia.org/wiki/Concrete_masonry_unit A masonry unit is a solid piece of material, usually with a regular shape, used as a component in the construction of buildings. Masonry units are usually composed of brick, stone, marble, granite, travertine, limestone, cast stone, concrete block, glass block, stucco, tile, or cob. ORCID:0000-0002-4366-3088 masonry unit A masonry unit is a solid piece of material, usually with a regular shape, used as a component in the construction of buildings. Masonry units are usually composed of brick, stone, marble, granite, travertine, limestone, cast stone, concrete block, glass block, stucco, tile, or cob. https://en.wikipedia.org/wiki/Masonry Concrete is a composite material composed of an aggregate bonded together with a fluid cement which hardens over time. ORCID:0000-0002-4366-3088 Missing the class for "aggregate" - tricky to define what it is, exactly. Again, seems more like some sort of material/disposition hybrid. concrete Concrete is a composite material composed of an aggregate bonded together with a fluid cement which hardens over time. https://en.wikipedia.org/wiki/Concrete Masonry cement is a substance used in construction that has the disposition to set and harden and thus may be used to bind materials together. ORCID:0000-0002-4366-3088 cement "Cement" refers more to a disposition than a specific material. masonry cement Masonry cement is a substance used in construction that has the disposition to set and harden and thus may be used to bind materials together. https://en.wikipedia.org/wiki/Cement Building walls are bulding parts which serve to support roofs, floors and ceilings; enclose a space as part of the building envelope; give buildings form; and to provide shelter and security. This is a building part and not the same as a standalone wall, which is a building in its own right. building wall Building walls are bulding parts which serve to support roofs, floors and ceilings; enclose a space as part of the building envelope; give buildings form; and to provide shelter and security. https://en.wikipedia.org/wiki/Wall An exterior wall is a building wall which separates the interior of a building from the buildings surrounding environment. ORCID:0000-0002-4366-3088 exterior wall A building envelope is a building part composed of those building parts which physically separate the interior of a building from its surrounding environment. The building envelope provides resistance to air, water, heat, light, and noise transfer. The three basic elements of a building envelope are a weather barrier, air barrier, and thermal barrier. ORCID:0000-0002-4366-3088 building enclosure building envelope A building envelope is a building part composed of those building parts which physically separate the interior of a building from its surrounding environment. The building envelope provides resistance to air, water, heat, light, and noise transfer. The three basic elements of a building envelope are a weather barrier, air barrier, and thermal barrier. https://en.wikipedia.org/wiki/Building_envelope ORCID:0000-0002-4366-3088 A ceiling is an overhead interior surface that covers the upper limit of a room. It is not generally considered a structural element, but a finished surface concealing the underside of the floor or roof structure above. ceiling A ceiling is an overhead interior surface that covers the upper limit of a room. It is not generally considered a structural element, but a finished surface concealing the underside of the floor or roof structure above. https://en.wikipedia.org/wiki/Ceiling A roof is the covering on the uppermost part of a building which provides protection from animals and weather, notably rain, but also heat, wind and sunlight. A roof is also the framing or structure which supports the covering ORCID:0000-0002-4366-3088 roof This class is meant to represent roofs which are parts of buildings, rather than a roofs of cave and other natural formations. building roof A roof is the covering on the uppermost part of a building which provides protection from animals and weather, notably rain, but also heat, wind and sunlight. A roof is also the framing or structure which supports the covering https://en.wikipedia.org/wiki/Roof A portion of brick material is a material derived from a brick which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete that has been fire-hardened or air-dried. ORCID:0000-0002-4366-3088 brick material A portion of brick material is a material derived from a brick which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete that has been fire-hardened or air-dried. https://en.wikipedia.org/wiki/Brick A brick is a masonry unit which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete material, fire-hardened or air-dried. ORCID:0000-0002-4366-3088 Generally used to refer to the masonry unit rather than a material. brick A brick is a masonry unit which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete material, fire-hardened or air-dried. https://en.wikipedia.org/wiki/Brick A brick exterior wall is an exterior wall that is built from bricks. ORCID:0000-0002-4366-3088 brick wall brick exterior wall A concrete exterior wall is an exterior wall that is composed primarily of concrete. ORCID:0000-0002-4366-3088 concrete wall concrete exterior wall An iron sheet is a mass of iron which has been forged into a roughly planar form of less than 6 millimetres in thickness. ORCID:0000-0002-4366-3088 iron sheet An iron sheet is a mass of iron which has been forged into a roughly planar form of less than 6 millimetres in thickness. https://en.wikipedia.org/wiki/Sheet_metal A sheet-iron building roof is a building roof that is built from sheets of iron. ORCID:0000-0002-4366-3088 sheet iron roof sheet-iron roof iron sheet building roof sheet-iron building roof An asbestos building roof is a building roof that is built from asbestos. ORCID:0000-0002-4366-3088 asbestos roof asbestos exists in CHEBI and will be imported to complete this class' logical def. asbestos building roof A tile is a manufactured piece of hard-wearing material such as ceramic, stone, metal, or even glass, generally used for covering roofs, floors, walls, showers, or other objects such as tabletops. Alternatively, tile can sometimes refer to similar units made from lightweight materials such as perlite, wood, and mineral wool, typically used for wall and ceiling applications. ORCID:0000-0002-4366-3088 tile A tile is a manufactured piece of hard-wearing material such as ceramic, stone, metal, or even glass, generally used for covering roofs, floors, walls, showers, or other objects such as tabletops. Alternatively, tile can sometimes refer to similar units made from lightweight materials such as perlite, wood, and mineral wool, typically used for wall and ceiling applications. https://en.wikipedia.org/wiki/Tile A tile building roof is a building roof that is built using tiles. ORCID:0000-0002-4366-3088 tile roof tiled roof tile building roof tiled building roof A fixture which is used primarily for the collection and, in some cases, disposal of human urine and feces. ORCID:0000-0002-4366-3088 toilet "disposal" may not be the most precise way to describe fill-in latrines. Note that no assertion is made on whether these fixtures are in- or outdoors. toilet fixture A fixture which is used primarily for the collection and, in some cases, disposal of human urine and feces. https://en.wikipedia.org/wiki/Toilet A factory (previously manufactory) or manufacturing plant is an industrial site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where workers manufacture goods or operate machines processing one product into another. ORCID:0000-0002-4366-3088 manufactory manufacturing plant factory A factory (previously manufactory) or manufacturing plant is an industrial site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where workers manufacture goods or operate machines processing one product into another. https://en.wikipedia.org/wiki/Factory The layer of the atmosphere which is sandwiched between the troposphere and mesosphere. Of the energy that reaches the Earth from the sun, only 3% is absorbed in the stratosphere, but that includes the vitally important process of absorption of ultraviolet radiation by the stratospheric ozone layer. The stratosphere is cloudless and dust free, and almost unaffected by the turbulent conditions of the underlying level of the atmosphere. (Source: WRIGHT) ORCID:0000-0002-4366-3088 Definition from GEMET - will be refined. stratosphere The layer of the atmosphere which is sandwiched between the troposphere and mesosphere. Of the energy that reaches the Earth from the sun, only 3% is absorbed in the stratosphere, but that includes the vitally important process of absorption of ultraviolet radiation by the stratospheric ozone layer. The stratosphere is cloudless and dust free, and almost unaffected by the turbulent conditions of the underlying level of the atmosphere. (Source: WRIGHT) GEMET:http://www.eionet.europa.eu/gemet/concept/8128 The mesosphere is part of the earth's atmosphere which is between the stratosphere and the thermosphere in which temperature decreases with altitude to the atmosphere's absolute minimum ORCID:0000-0002-4366-3088 mesosphere The mesosphere is part of the earth's atmosphere which is between the stratosphere and the thermosphere in which temperature decreases with altitude to the atmosphere's absolute minimum http://www.merriam-webster.com/dictionary/mesosphere The lowest of the concentric layers of the atmosphere, occurring between the Earth's surface and the tropopause. It is the zone where atmospheric turbulence is at its greatest and where the bulk of the Earth's weather is generated. It contains almost all the water vapour and aerosols and three-quarters of the total gaseous mass of the atmosphere. Throughout the troposphere temperature decreases with height at a mean rate of 6.5°C/km and the whole zone is capped by either an inversion of temperature or an isothermal layer at the tropopause. (Source: WHIT) ORCID:0000-0002-4366-3088 Definition from GEMET - will be refined. troposphere The lowest of the concentric layers of the atmosphere, occurring between the Earth's surface and the tropopause. It is the zone where atmospheric turbulence is at its greatest and where the bulk of the Earth's weather is generated. It contains almost all the water vapour and aerosols and three-quarters of the total gaseous mass of the atmosphere. Throughout the troposphere temperature decreases with height at a mean rate of 6.5°C/km and the whole zone is capped by either an inversion of temperature or an isothermal layer at the tropopause. (Source: WHIT) GEMET:http://www.eionet.europa.eu/gemet/concept/8695 The thermosphere is a part of the earth's atmosphere that begins at about 50 miles (80 kilometers) above the earth's surface, extends to outer space, and is characterized by steadily increasing temperature with height thermosphere The thermosphere is a part of the earth's atmosphere that begins at about 50 miles (80 kilometers) above the earth's surface, extends to outer space, and is characterized by steadily increasing temperature with height http://www.merriam-webster.com/dictionary/thermosphere A layer that is part of the atmosphere. ORCID:0000-0002-4366-3088 atmospheric layering envoPolar This could be made into an inferred class, rather than having asserted subclasses. atmospheric layer atmospheric layering GEMET:http://www.eionet.europa.eu/gemet/concept/627 A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow. ORCID:0000-0002-4366-3088 boundary layer boundary layer A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow. https://en.wikipedia.org/wiki/Boundary_layer boundary layer http://www.eionet.europa.eu/gemet/concept/976 A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails. Subclasses will be added by inference. motor vehicle A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails. https://en.wikipedia.org/wiki/Motor_vehicle A vehicle is a mobile machine which transports people or cargo. vehicle A vehicle is a mobile machine which transports people or cargo. https://en.wikipedia.org/wiki/Vehicle A motor is a machine designed to convert one or more forms of energy into mechanical energy. engine motor A motor is a machine designed to convert one or more forms of energy into mechanical energy. https://en.wikipedia.org/wiki/Motor A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow. lentic water body Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase. condensation envoAtmo envoPolar "process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog) hydrological condensation process Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase. https://en.wikipedia.org/wiki/Condensation Leaf litter is dead plant material, such as leaves, bark, needles, and twigs, that has fallen to the ground. duff leaf litter litterfall soil litter tree litter plant litter Leaf litter is dead plant material, such as leaves, bark, needles, and twigs, that has fallen to the ground. https://en.wikipedia.org/wiki/Plant_litter A landmass which is part of a planet. land ground planetary landmass A landmass which is part of a planet. Adpated from https://en.wikipedia.org/wiki/Planetary_surface Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. space envoAstro outer space Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. https://en.wikipedia.org/wiki/Outer_space A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle. crust This class is meant to be applicable accross planets. Earth's crust would be an instance. planetary crust A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle. https://en.wikipedia.org/wiki/Crust_(geology) A planetary structural layer is laminar part of a terrestrial planet or other rocky body large enough to have differentiation by density. Planetary layers have differing physicochemical properties and composition. Label should be improved to match definition. planetary structural layer A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density. mantle This class is meant to be applicable accross planets. Earth's mantle would be an instance. planetary mantle A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density. https://en.wikipedia.org/wiki/Mantle_(geology) A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties. Earth's lithosphere includes the crust and uppermost mantle. lithosphere A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties. https://en.wikipedia.org/wiki/Lithosphere A role that is realized in some process wherein the bearer is discarded or not utilized further. This definition is preliminary. waste role A geological fracture is any separation in a geologic formation, such as a joint or a fault that divides a mass of rock into two or more pieces. fracture SWEETRealm:Fissure fissure geological fracture A geological fracture is any separation in a geologic formation, such as a joint or a fault that divides a mass of rock into two or more pieces. https://en.wikipedia.org/wiki/Fracture_(geology) fissure Genomes:fissure A geological fault is a planar fracture or discontinuity in a volume of rock, across which there has been significant displacement as a result of rock mass movement. fault The relationship between faults and active plate boundaries must be further developed, as there is some overlap. geological fault An active fault is a fault that is likely to become the source of another earthquake sometime in the future. Geologists commonly consider faults to be active if there has been movement observed or evidence of seismic activity during the last 10,000 years. active fault environmental_hazards active geological fault Contaminated air is air which has sufficient concentrations of environmental pollutants such that it may adversely affect a given ecosystem. contaminated air An earthquake is a process during which energy is released in an astronomical body's crust, causing the displacement of crustal parts and the generation of seismic waves. quake temblor tremor environmental_hazards Elastic strain, gravity, chemical reactions, or even the motion of massive bodies can produce earthquakes. earthquake An earthquake is a process during which energy is released in an astronomical body's crust, causing the displacement of crustal parts and the generation of seismic waves. Adapted from URL:http://www.britannica.com/science/earthquake-geology https://en.wikipedia.org/wiki/Earthquake An earthquake caused by the sudden release of energy accumulated in an astronomical body's crust, as the elastic strain placed on constituent rock masses causes them to fracture. environmental_hazards tectonic earthquake An earthquake caused by the sudden release of energy accumulated in an astronomical body's crust, as the elastic strain placed on constituent rock masses causes them to fracture. URL:http://www.britannica.com/science/earthquake-geology A lake which has concentrations of environmental contaminants high enough to harm the ecosystems associated with it. environmental_hazards polluted lake A mass of water. water mass A coast is the area where land meets the sea, ocean, or lake. Used for both marine and lake coasts. The boundary of the coast is fuzzy and it overlaps both the water body and land in quesiton. Compared to 'shore' coast A coast is the area where land meets the sea, ocean, or lake. https://en.wikipedia.org/wiki/Coast A tsunami is a process during which a series of waves is generated in a water body, typically an ocean or large lake, by the displacement of a large volume of water. Earthquakes, volcanic eruptions and other underwater explosions (including detonations of underwater nuclear devices), landslides, glacier calvings, meteorite impacts and other disturbances above or below water all have the potential to generate a tsunami. seismic sea wave tidal wave environmental_hazards tsunami A tsunami is a process during which a series of waves is generated in a water body, typically an ocean or large lake, by the displacement of a large volume of water. Earthquakes, volcanic eruptions and other underwater explosions (including detonations of underwater nuclear devices), landslides, glacier calvings, meteorite impacts and other disturbances above or below water all have the potential to generate a tsunami. https://en.wikipedia.org/wiki/Tsunami A material transport process during which a geological surface shifts downward relative to a datum such as sea-level. subsidence environmental_hazards geological subsidence A material transport process during which a geological surface shifts downward relative to a datum such as sea-level. https://en.wikipedia.org/wiki/Subsidence Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. precipitation "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) hydrological precipitation process Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. https://en.wikipedia.org/wiki/Precipitation Condensation is a process during which a gas undergoes a phase transition into a liquid. condensation process Condensation is a process during which a gas undergoes a phase transition into a liquid. https://en.wikipedia.org/wiki/Condensation Desublimation is a process in which a portion of some gas undergoes a phase transition into a portion of some solid. deposition desublimation process Desublimation is a process in which a portion of some gas undergoes a phase transition into a portion of some solid. https://en.wikipedia.org/wiki/Deposition_(phase_transition) An environmental system which can sustain and allow the growth of an ecological population. EcoLexicon:habitat LTER:238 SWEETRealm:Habitat https://en.wikipedia.org/wiki/Habitat A habitat's specificity to an ecological population differentiates it from other environment classes. habitat An environmental system which can sustain and allow the growth of an ecological population. EnvO:EnvO A process in which natural ecosystems present over an expanse of land are removed and replaced with anthropogenic ecosystems. An SDGIO request. Likely to be refined and revised. This looks like an aggregate class, subsuming a range of processes which can lead to degradation. These anthropogenic ecosystems may include urban or other built-up settlements or anthropogenic ecosystems used for activities such as forestry or agriculture. land consumption process A process in which natural ecosystems present over an expanse of land are removed and replaced with anthropogenic ecosystems. Adapted from EEA (1997) The concept of environmental space, Copenhagen, URL: http://www.eea.europa.eu/publications/92-9167-078-2/at_download/file A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. human dwelling A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. The range of entities that are considered "barren land" are not exhaustive, making axiomatisation risky at this stage. Barren Land (Rock/Sand/Clay) NLCD:31 envoPolar nlcd2011 According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition. area of barren land An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. https://en.wikipedia.org/wiki/Exosphere https://en.wikipedia.org/wiki/Planetary_surface https://www.mrlc.gov/nlcd11_leg.php A part of an astronomical body which is primarily composed of a continuous volume of gaseous or aerosolised material held in shape by one or more environmental processes. This may not need to be in the atmosphere, also note that "meteor" will do much of the same work. envoAtmo Similar, in spirit, to landform. This class may need to be split into aerosols and 'pure' volumes of gas. aeroform The system of public works in a country, state or region, including roads, utility lines and public buildings. infrastructure We label this as 'public infrastructure', as the OECD definition refers specifically to public constructed features. The parts of public infrastructure are not exhaustive and should be extended as needed. public infrastructure The system of public works in a country, state or region, including roads, utility lines and public buildings. https://stats.oecd.org/glossary/detail.asp?ID=4511 A building which is publically accessible. Created for SDGIO, we treat "public" as "publically accessible" where the semantics of access are dealt with in SDGIO. public building A planned process during which a portion of environmental material is removed from a material entity. Created for SDGIO and intended to be a more general form of resource extraction process. material extraction process A process whereby a large volume of gas moves due to a disequilibrium of physical forces. wind envoAtmo envoPolar This class refers to all forms of "wind": from the familiar movement of air in the Earth's atmosphere to the solar wind. Use a subclass to be more precise. mass gaseous flow A process whereby a large volume of gas moves due to a disequilibrium of physical forces. https://en.wikipedia.org/wiki/Wind wind A mass gaseous flow which occurrs in a planet's atmosphere due to internal pressure disequilibria. envoAtmo envoPolar atmospheric wind A mass gaseous flow which occurrs in a planet's atmosphere due to internal pressure disequilibria. https://en.wikipedia.org/wiki/Wind A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. This class is to be populated by inference. gas gaseous environmental material A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. http://www.merriam-webster.com/dictionary/gas A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields. An NTR for `quality of a plasma` has been posted on the PATO tracker: https://github.com/pato-ontology/pato/issues/88 plasma A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields. http://www.merriam-webster.com/dictionary/plasma https://en.wikipedia.org/wiki/Plasma_%28physics%29 An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. celestial body envoAstro Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'. astronomical body An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. https://en.wikipedia.org/wiki/Astronomical_object A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals. envoAstro envoPolar Considerable debate on the definition of planet exists. planet A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals. http://solarsystem.nasa.gov/planets/whatisaplanet https://en.wikipedia.org/wiki/Planet An astronomical object which is composed primarily of luminous plasma held in a spherical form by gravitational forces. Add qualities such as spherical. Request NTRs if not available in PATO. envoAstro envoPolar star An astronomical object which is composed primarily of luminous plasma held in a spherical form by gravitational forces. https://en.wikipedia.org/wiki/Star An object which is composed of one or more gravitationally bound structures that are associated with a position in space. celestial object envoAstro If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far. astronomical object An object which is composed of one or more gravitationally bound structures that are associated with a position in space. https://en.wikipedia.org/wiki/Astronomical_object A material part of an astronomical body. envoAstro envoPolar astronomical body part An environmental material which is in a solid state. This is a defined class: its subclasses will not be asserted, but filled by inference. solid environmental material An environmental material which is in a liquid state. envoPolar This is a defined class: most of its subclasses will not be asserted, but filled by inference. liquid environmental material A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact. Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion. envoAstro envoPolar The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations. biosphere A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact. http://www.biology-online.org/dictionary/Biosphere https://en.wikipedia.org/wiki/Biosphere An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet. envoAstro envoPolar This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. hydrosphere An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet. https://en.wikipedia.org/wiki/Hydrosphere An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere. envoAstro This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. pedosphere An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere. https://en.wikipedia.org/wiki/Pedosphere Air which has increased levels of water vapour. humid air Air which has a partial pressure of water vapour equal or near equal to its equilibrium vapor pressure at a given temperature. water-vapour-saturated air wet air "Near equal" is meant to reflect that there will be fluctuations around the equilibrium point. water vapour saturated air A hydrological precipitation process in which atmospheric water vapour condenses to form droplets of liquid water massive enough to fall to a planetary surface due to the planet's gravity. rain fall rainfall rain envoPolar This is the process which typically happens on Earth. Other planets may have different liquids involved in the process. water-based rainfall A hydrological precipitation process in which atmospheric water vapour condenses to form droplets of liquid water massive enough to fall to a planetary surface due to the planet's gravity. https://en.wikipedia.org/wiki/Rain A droplet is a small column of liquid, bounded completely or almost completely by free surfaces which maintains its shape due to the surface tension of the liquid. drop No attempt is made to differentiate between drops and droplets. This may be added, if requested. droplet A droplet is a small column of liquid, bounded completely or almost completely by free surfaces which maintains its shape due to the surface tension of the liquid. A droplet formed by condensation of vapour in an atmosphere and which is sufficiently massive to overcome atmospheric resistance and fall to a planetary surface due to gravity. raindrop A droplet of water A defined class which should be filled by inference. water droplet raindrop This is the class intended for use when describing raindrops on Earth. These typically have a diamter of 0.1 to 9 millimetres. water raindrop A solid material whose constituents, such as atoms, molecules or ions, are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions. This class refers to a portion of crystal and not an individual crystal. crystal A solid material whose constituents, such as atoms, molecules or ions, are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions. https://en.wikipedia.org/wiki/Crystal A crystal which is primarily composed of water ice. ice crystal envoPolar Any one of a number of macroscopic, crystalline forms in which ice appears, including hexagonal columns, hexagonal platelets, dendritic crystals, ice needles, and combinations of these forms. The crystal lattice of ice is hexagonal in its symmetry under most atmospheric conditions. water ice crystal Any one of a number of macroscopic, crystalline forms in which ice appears, including hexagonal columns, hexagonal platelets, dendritic crystals, ice needles, and combinations of these forms. The crystal lattice of ice is hexagonal in its symmetry under most atmospheric conditions. A marginal sea biome which is located in a region with a temperate climate. A component of the WWF Temperate Shelf and seas ecoregions grouping wwfBiome temperate marginal sea biome A marine biome which contains communities adapted to living in an environment determined by an upwelling process. marine upwelling biome A marine upwelling biome which is located in a region subject to temperate climate patterns. wwfBiome temperate marine upwelling biome An area of a planet's surface which is primarily covered by a shrubs, young trees, or stunted trees.. The surfaces of this area are in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. As noted in Wikipedia: "Because the criteria are matters of degree rather than of kind, the definition of a subshrub is not sharply distinguishable from that of a shrub" shrub/scrub NLCD:52 area of shrub nlcd2011 According to the NLCD 2011, areas of scrub or shrub are dominated by shrubs; less than 5 meters tall with shrub canopy typically greater than 20% of total vegetation. This class includes true shrubs, young trees in an early successional stage or trees stunted from environmental conditions. Such thresholds - which are themselves fuzzy - are not asserted in this definition. area of scrub An area of a planet's surface which is primarily covered by a shrubs, young trees, or stunted trees.. The surfaces of this area are in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. http://dx.doi.org/10.1016/j.rse.2015.07.014 https://en.wikipedia.org/wiki/Exosphere https://en.wikipedia.org/wiki/Planetary_surface https://en.wikipedia.org/wiki/Subshrub https://www.mrlc.gov/nlcd11_leg.php As noted in Wikipedia: "Because the criteria are matters of degree rather than of kind, the definition of a subshrub is not sharply distinguishable from that of a shrub" https://en.wikipedia.org/wiki/Subshrub A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force. precipitation process A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force. https://en.wikipedia.org/wiki/Precipitation_%28chemistry%29 https://en.wikipedia.org/wiki/Precipitation An area of a planet's surface which is primarily covered by cultivated or anthropically maintained vegetation planted for recreation, erosion control, or aesthetic purposes interspersed by constructed or manufactured objects and materials. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. This class is in need of refinement, particularly in linking to other entities in the ontology. This would be helped by more clear listings of entities included in this classification. However, the class is suitable for use in annotating remotely sensed land types. developed, open space NLCD:21 nlcd2011 According to the NLCD 2011, areas of developed open space are dominated by vegetation such as lawn grasses and include large-lot single-family housing units, parks, golf courses. Further, it is asserted that "impervious surfaces", most likely referring to concrete and related substances, cover less than 20% of the area. Such thresholds - which are themselves fuzzy - are not asserted in this definition. area of developed open space An area of a planet's surface which is primarily covered by cultivated or anthropically maintained vegetation planted for recreation, erosion control, or aesthetic purposes interspersed by constructed or manufactured objects and materials. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. https://en.wikipedia.org/wiki/Exosphere https://en.wikipedia.org/wiki/Planetary_surface https://www.mrlc.gov/nlcd11_leg.php An area of a planet's surface which is primarily covered by sedges or forbs, possibly interpersed with grasses or grass-like plants. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. This class is in need of refinement, particularly in linking to other entities in the ontology. However, it is suitable for use in annotating remotely sensed land types. sedge/herbaceous NLCD:72 nlcd2011 According to the NLCD 2011, at least 80% of these areas are covered by sedge or forbs. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The NLCD description also notes that land covered by sedge tundra and sedge tussock tundra are subsumed in this category. The original definition notes that this is intended as an "Alaska only" category. area of sedge- and forb-dominated herbaceous vegetation An area of a planet's surface which is primarily covered by sedges or forbs, possibly interpersed with grasses or grass-like plants. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. https://en.wikipedia.org/wiki/Exosphere https://en.wikipedia.org/wiki/Planetary_surface https://www.mrlc.gov/nlcd11_leg.php An area of a planet's surface which is primarily covered by gramanoid or herbaceous vegetation and which is not subject to intensive management by humans. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. This class is in need of refinement, particularly in linking to other entities in the ontology. However, it is suitable for use in annotating remotely sensed land types. grassland/herbaceous NLCD:71 nlcd2011 According to the NLCD 2011, at least 80% of these areas are covered by grasslands or non-woody, herbaceous plants. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The NLCD description also notes that, while no "intensive" management such as tilling is performed in these areas, they may be used for grazing. area of gramanoid or herbaceous vegetation An area of a planet's surface which is primarily covered by gramanoid or herbaceous vegetation and which is not subject to intensive management by humans. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. https://en.wikipedia.org/wiki/Exosphere https://en.wikipedia.org/wiki/Planetary_surface https://www.mrlc.gov/nlcd11_leg.php A hydrological process in which irregular aggregates of snow fall to the surface of an astronomical body. This is currently bound to water-based snow on Earth, may need revisions for interplanetary applications 2021-04-14T18:57:18.275Z snow fall environmental_hazards envoCryo envoPolar snowfall A human house which serves as a long-term shelter for its inhabitants and within which they store personal property. This is under "human house" due to the broad definition of "house". This term is not to be used for hotels, hostels, inns and the like, which provides shorter-term stays. residential building An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. non-anthropised environment non-anthropized environment In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised. natural environment An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. https://en.wikipedia.org/wiki/Anthropization https://en.wikipedia.org/wiki/Natural_environment A process during which a natural environmental system is altered by human action. anthropization An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action. anthropisation A process during which a natural environmental system is altered by human action. https://en.wikipedia.org/wiki/Anthropization An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action. https://en.wikipedia.org/wiki/Anthropization A planet that is composed primarily of silicate rocks or metals. rocky planet telluric planet Earth-like planet envoAstro terrestrial planet A planet that is composed primarily of silicate rocks or metals. https://en.wikipedia.org/wiki/Terrestrial_planet A manufactured product which is designed to catch and hold animals. envoCesab animal trap A manufactured product which is designed to catch and hold animals. http://www.thefreedictionary.com/trap A process whereby a volume of liquid moves due to a disequilibrium of physical forces. envoPolar This class can refer to the flow of any material in a liquid phase. mass liquid flow A process whereby a volume of liquid moves due to a disequilibrium of physical forces. https://en.wikipedia.org/wiki/Wind A material transport process during which a volume of liquid water is transported due to a disequilibria in physical forces. environmental_hazards water flow process A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body. envoAstro The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations. technosphere A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body. http://dx.doi.org/10.1177/2053019616677743 http://www.yourdictionary.com/technosphere https://www.sciencedaily.com/releases/2016/11/161130085021.htm An exchangeable device which can be connected to a plumbing system to deliver and drain water. plumbing fixture An exchangeable device which can be connected to a plumbing system to deliver and drain water. https://en.wikipedia.org/wiki/Plumbing_fixture A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale. manufacturing process A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. https://en.wikipedia.org/wiki/Manufacturing The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale. https://en.wikipedia.org/wiki/Manufacturing An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures. The nature of "structures" must be further specified. human-directed construction process An environmental system which is determined by materials bearing roughly homogeneous qualities. Organisational class. Not intended for annotation. environmental system determined by a quality An environmental system within which an environmental material strongly influences the system's composition and properties. Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump). environmental system determined by a material An environmental system which is determined by a living organism. host-associated environment envoEmpo envoOmics environmental system determined by an organism An environmental system determined by a green plant. Plant plant environment Viridiplantae-associated environment envoEmpo envoOmics plant-associated environment Plant http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system determined by an animal. Animal animal environment Metazoan-associated environment envoEmpo envoMeo envoOmics animal-associated environment Animal http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body. envoAtmo meteor A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body. https://cloudatlas.wmo.int/other-meteors.html A meteor which is primarily composed of water. envoAtmo hydrometeor A meteor which is primarily composed of water. https://cloudatlas.wmo.int/other-meteors.html A meteor which is primarily composed of rock. envoAtmo lithometeor A lake which has formed as the result of processes that are not or are only minimally driven by human activity. This class is to be filled by inference. natural lake A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium. Requires addition of waves for full axiomatisation. This should be linked to "subatomic particle" with an "or". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions). environmental_hazards envoAstro radiation A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium. https://en.wikipedia.org/wiki/Radiation A radiation process during which energy is transmitted or emitted by means of fast-moving subatomic particles. environmental_hazards envoAstro particle radiation A radiation process during which energy is transmitted or emitted by means of fast-moving subatomic particles. https://en.wikipedia.org/wiki/Particle_radiation A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy. EM radiation environmental_hazards envoAstro Note that this class is concerned only with active radiative processes: static electric and magnetic fields are not inlcuded. All electromagnetic radiation carries radiant energy. electromagnetic radiation A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy. https://en.wikipedia.org/wiki/Electromagnetic_radiation An environment which is determined by materials which bear significant concentrations of salts. Saline envoEmpo The thresholds for "significant" concentrations of salts vary widely and thus no committment is made in this class. Subclasses with more explicit thresholds can be made upon request. saline environment Saline http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system which has its properties and dynamics determined by soil. Soil (non-saline) envoEmpo envoOmics soil environment Soil (non-saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system which has its properties and dynamics determined by sediment. envoEmpo envoOmics sediment environment An environmental system which has its properties and dynamics determined by an aerosol. envoEmpo envoOmics aerosol environment An environmental system which has its properties and dynamics determined by a saline aerosol. Aerosol (saline) envoEmpo envoOmics saline aerosol environment Aerosol (saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ seaspray or other aerosolized saline material (>5 psu) An environmental system which has its properties and dynamics determined by an aerosol with a low concentration of dissolved solutes. Aerosol (non-saline) envoEmpo envoOmics non-saline aerosol environment Aerosol (non-saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ aerosolized dust or liquid An environmental system determined by part of a living or dead animal, or a whole small animal. Animal corpus envoEmpo envoMeo envoOmics environment associated with an animal part or small animal Animal corpus http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system determined by part of a living or dead plant, or a whole small plant. Plant corpus envoEmpo envoMeo envoOmics environment associated with a plant part or small plant Plant corpus http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids. envoAstro meteoroid An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids. https://en.wikipedia.org/wiki/Meteoroid A material which is composed primarily of one or more pure metals and which shows their properties. Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals. metal While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity. metallic material A material which is composed primarily of one or more pure metals and which shows their properties. https://en.wikipedia.org/wiki/Metal A process during which microscopic solid or liquid objects are formed. particle formation particulate matter formation process A process during which microscopic solid or liquid objects are formed. https://en.wikipedia.org/wiki/Particulates An aerosol formation process which occurs in an atmosphere. atmospheric aerosol formation envoAtmo atmospheric aerosol formation An aerosol formation process which occurs in an atmosphere. https://en.wikipedia.org/wiki/Particulates A process during which an aerosol, consisting of solid particulates suspended in a gas, is formed in an atmosphere. formation of solid particles in an atmosphere envoAtmo formation of a solid aerosol in an atmosphere A process during which an aerosol, consisting of solid particulates suspended in a gas, is formed in an atmosphere. https://en.wikipedia.org/wiki/Particulates A process during which an aerosol, consisting of droplets of liquid suspended in gas, is formed in an atmosphere. formation of liquid droplets in an atmosphere formation of liquid particles in an atmosphere envoAtmo formation of a liquid aerosol in an atmosphere A process during which an aerosol, consisting of droplets of liquid suspended in gas, is formed in an atmosphere. https://en.wikipedia.org/wiki/Particulates An aerosol which has non-gaseous parts that are primarily composed of liquid droplets. SWEETRealm:Aerosol liquid aerosol envoAtmo aerosolised liquids An aerosol which has non-gaseous parts that are primarily composed of liquid droplets. https://en.wikipedia.org/wiki/Aerosol An aerosol which has non-gaseous parts that are primarily composed of solid particles. SWEETRealm:Aerosol solid aerosol envoAtmo aerosolised solids An aerosol which has non-gaseous parts that are primarily composed of solid particles. https://en.wikipedia.org/wiki/Aerosol A process during which microscopic solid particulates are formed from gaseous materials in an atmosphere. atmospheric formation of a solid aerosol formation of a solid aerosol in an atmosphere formation of a solid aerosol in the atmosphere formation of solid particles from gaseous material in an atmosphere envoAtmo formation of a solid aerosol from gaseous material in an atmosphere A process during which microscopic solid particulates are formed from gaseous materials in an atmosphere. https://en.wikipedia.org/wiki/Particulates A process during which microscopic liquid droplets are formed from gaseous materials in an atmosphere. atmospheric formation of a liquid aerosol formation of a liquid aerosol in an atmosphere formation of a liquid aerosol in the atmosphere formation of liquid droplets from gaseous material in an atmosphere formation of liquid particles from gaseous material in an atmosphere envoAtmo formation of a liquid aerosol from gaseous material in an atmosphere A process during which microscopic liquid droplets are formed from gaseous materials in an atmosphere. https://en.wikipedia.org/wiki/Particulates A process during which pieces of a planetary crust and uppermost mantle move. tectonic movement A process during which pieces of a planetary crust and uppermost mantle move. https://en.wikipedia.org/wiki/Plate_tectonics https://en.wikipedia.org/wiki/List_of_tectonic_plates A part of a lithosphere which is separated by other such parts by geographic faults or similar geomorphological discontinuities. tectonic plate A part of a lithosphere which is separated by other such parts by geographic faults or similar geomorphological discontinuities. https://en.wikipedia.org/wiki/List_of_tectonic_plates 2 A geomorphological feature which is formed where two or more tectonic plates move towards, away from, or along one another, resulting in deformation of the lithosphere. tectonic plate boundary A geomorphological feature which is formed where two or more tectonic plates move towards, away from, or along one another, resulting in deformation of the lithosphere. https://en.wikipedia.org/wiki/Plate_tectonics An environmental system which includes both living and non-living components. LTER:173 This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem An environmental system which includes both living and non-living components. https://en.wikipedia.org/wiki/Ecosystem LTER:173 https://vocab.lternet.edu/vocab/vocab/index.php?tema=173&/ecosystems Organic material which is primarily composed of plant structures, living or dead. plant matter A planet which is primarily composed of hydrogen and helium. envoAstro Gas giants are composed of about 90% hydrogen and helium. Jupiter and Saturn are examples of gas giants. gas planet A planet which is primarily composed of hydrogen and helium. http://solarsystem.nasa.gov/planets/whatisaplanet https://en.wikipedia.org/wiki/List_of_planet_types https://en.wikipedia.org/wiki/Planet An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure. Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure. ice https://github.com/EnvironmentOntology/envo/issues/900 A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water. An axiom to express that the planet has a 'substantial' proportion of its mass in the form of water wound enhance this class. aquaplanet panthalassic planet water world envoAstro While this planetary form is still mostly theoretical, strong candidates exist such as the extrasolar planet GJ 1214 b and ocean planet candidate Kepler-22b. ocean planet A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water. https://en.wikipedia.org/wiki/Ocean_planet A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice. cryoplanet envoAstro While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane. ice planet A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice. https://en.wikipedia.org/wiki/Ice_planet While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane. https://en.wikipedia.org/wiki/Ice_planet Ice which is primarily composed of carbon dioxide. dry ice envoAstro carbon dioxide ice Ice which is primarily composed of carbon dioxide. https://en.wikipedia.org/wiki/Ice A gas planet which has an atmosphere composed primarily of helium. The placement of this class assumes that some traces of hydrogen are left in the atmosphere. If this is not the case, the axiom on gas planet must be updated. envoAstro A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet. helium planet A gas planet which has an atmosphere composed primarily of helium. https://en.wikipedia.org/wiki/Helium_planet A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet. https://en.wikipedia.org/wiki/Helium_planet A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet. Add and axiomatise with moon and lunar crust volatile envoAstro Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets. volatile astrogeological material A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet. https://en.wikipedia.org/wiki/Volatiles Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets. https://en.wikipedia.org/wiki/Volatiles An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium. gas envoAstro This is a term native to the fields of planetary science and astrophysics. Hydrogen has a boiling point of 20.271 Kelvin and a melting point of 13.99 Kelvin. Helium has a boiling point of 4.222 Kelvin and a melting point of 0.95 Kelvin. astrogeological gas An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium. https://en.wikipedia.org/wiki/Volatiles A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms. Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities. geodiversity A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms. https://en.wikipedia.org/wiki/Geodiversity Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities. An ecosystem which has been causally isolated from a larger ecosystem within which it was previously embedded, such that the direct exchange of materials, resources, and energy between these systems is severely or entirely curtailed. Often, ecosystem fragments are unable to sustain themselves without human intervention and management as they are not large enough to perform self-sustaining functions (e.g. nutrient recycling) or hold sufficient ecological resources such as genetic diversity of populations. ecosystem fragment A process during which one or more parts of an ecosystem become causally isolated such that the direct flow or exchange of materials, resources, and energy between a given fragment and the remainder of the original system is severely curtailed or entirely halted. ecosystem fragmentation process A process during which one or more parts of an ecosystem become causally isolated such that the direct flow or exchange of materials, resources, and energy between a given fragment and the remainder of the original system is severely curtailed or entirely halted. https://en.wikipedia.org/wiki/Ecosystem_decay https://en.wikipedia.org/wiki/Habitat_fragmentation https://en.wikipedia.org/wiki/Population_fragmentation A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective. ecosystem management Umweltmaßnahme environmental management active ecosystem management process A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective. https://www.iucn.org/theme/protected-areas/about/protected-areas-categories/category-iv-habitatspecies-management-area Umweltmaßnahme https://orcid.org/0000-0002-9620-2832 www.awi.de/internas An environment which has its properties and composition largely determined by the presence of a metazoan which lacks a vetebral column and which has a habitat that is found in an aquatic environmental system. http://purl.jp/bio/11/meo/MEO_0000871 envoMeo envoOmics environment associated with an aquatic invertebrate http://purl.jp/bio/11/meo/MEO_0000871 Not currently live, may need to be switched to alternative PURLs. Soil which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7. acidic soil Soil which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7. https://en.wikipedia.org/wiki/Acid This class will be axiomatised with "alga" once an approach to handle this term's ambiguous semantics has been agreed with PCO. An organic material which is primarily composed of living or dead algae, along with their exudates. algal material An organic material which is primarily composed of living or dead algae, along with their exudates. https://en.wikipedia.org/wiki/Algae The surface layer of a volume of water. EcoLexicon:surface_water SWEETRealm:SurfaceWater https://en.wikipedia.org/wiki/Surface_water surface of a body of water water body surface water surface The surface layer of a mass of sediment. surface of a sedimentary mass surface sediment sediment surface An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it. terrestrial environmental zone A terrestrial zone which is bounded by constructed, manufactured, or other anthropogenic material entities. anthropised terrestrial environmental zone An environmental zone which is bounded by material parts of a marine environment. This class will eventually be populated by inference alone, with its subclasses distributed in more process-linked hierarchies to improve semantic density. marine environmental zone A process during which sediments compact under pressure, expel connate fluids, and gradually become solid sedimentary rock. lithification A process during which sediments compact under pressure, expel connate fluids, and gradually become solid sedimentary rock. https://en.wikipedia.org/wiki/Lithification An ecosystem in which grasses (Graminae) are the dominant form of vegetation and determine the system's structure and dynamics. EcoLexicon:grassland FTT:259 FTT:760 FTT:766 Geonames:V.GRSLD LTER:232 TGN:21604 TGN:54052 GRASSLAND grassland Grassland down downland downs glade grazing area herbaceous area grassland ecosystem An ecosystem in which grasses (Graminae) are the dominant form of vegetation and determine the system's structure and dynamics. https://en.wikipedia.org/wiki/Grassland GRASSLAND USGS:SDTS grassland Geonames:feature Grassland NASA:earthrealm down USGS:SDTS downland USGS:SDTS downs USGS:SDTS glade ADL:FTT glade USGS:SDTS grazing area ADL:FTT grazing area Getty:TGN herbaceous area USGS:SDTS A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions. EcoLexicon:wetland FTT:1001 FTT:1060 FTT:1061 FTT:1118 FTT:1180 FTT:1190 FTT:1206 FTT:1207 FTT:1226 FTT:184 FTT:185 FTT:228 FTT:281 FTT:480 FTT:716 FTT:883 FTT:934 FTT:945 FTT:983 Geonames:H.WTLD LTER:630 SPIRE:Bog SWEETRealm:Wetland TGN:21301 TGN:21304 TGN:21305 https://en.wikipedia.org/wiki/Wetland WETLAND Wetland EstuarineWetland LacustrineWetland MarineWetland PalustrineWetland RiparianWetland TerrestialWetland back marsh backswamp backwater barrier flat blanket bog bog cienaga dismal everglade floating marsh forested wetland marsh mire mud flat peat cutting area peatland quagmire quaking bog riparian area slash slough slue swamp forest tulelands moor morass muskeg wetland ecosystem A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions. https://en.wikipedia.org/wiki/Wetland WETLAND USGS:SDTS Wetland NASA:earthrealm EstuarineWetland NASA:earthrealm LacustrineWetland NASA:earthrealm MarineWetland NASA:earthrealm PalustrineWetland NASA:earthrealm RiparianWetland NASA:earthrealm TerrestialWetland NASA:earthrealm back marsh USGS:SDTS backswamp USGS:SDTS backwater ADL:FTT barrier flat USGS:SDTS blanket bog USGS:SDTS bog ADL:FTT bog Getty:TGN cienaga ADL:FTT dismal USGS:SDTS everglade USGS:SDTS floating marsh USGS:SDTS forested wetland ADL:FTT marsh ADL:FTT mire ADL:FTT mire USGS:SDTS mud flat ADL:FTT peat cutting area ADL:FTT peatland ADL:FTT quagmire ADL:FTT quagmire USGS:SDTS quaking bog USGS:SDTS riparian area ADL:FTT slash USGS:SDTS slough ADL:FTT slough Getty:TGN slough USGS:SDTS slue ADL:FTT swamp forest USGS:SDTS tulelands USGS:SDTS moor USGS:SDTS morass USGS:SDTS muskeg USGS:SDTS A planned process during which an environmental system is modified to mitigate or nullify the impacts of flooding. defense against flooding defence against floods defense against floods flood defence flood defence intervention flood defense flood defense intervention defence against flooding An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a star. NCIT:C44445 solar radiation environmental_hazards envoAstro stellar radiation An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a star. https://en.wikipedia.org/wiki/Electromagnetic_radiation https://en.wikipedia.org/wiki/Solar_irradiance solar radiation NCIT:C44445 A commercial building which contains parts used as workplaces primarily for administrative and managerial workers. "An office building will be divided into sections for different companies or may be dedicated to one company. In either case, each company will typically have a reception area, one or several meeting rooms, singular or open-plan offices, as well as toilets." office building A commercial building which contains parts used as workplaces primarily for administrative and managerial workers. https://en.wikipedia.org/wiki/Office#Office_buildings "An office building will be divided into sections for different companies or may be dedicated to one company. In either case, each company will typically have a reception area, one or several meeting rooms, singular or open-plan offices, as well as toilets." https://en.wikipedia.org/wiki/Office#Office_buildings A building which is primarily used to facilitate the buying or selling of goods or services. "Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally." commercial building A building which is primarily used to facilitate the buying or selling of goods or services. https://en.wikipedia.org/wiki/Commercial_building "Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally." https://en.wikipedia.org/wiki/Commerce A building part within which administrative work is done by an organisations users in order to support and realise the objectives of that organization. office A building part within which administrative work is done by an organisations users in order to support and realise the objectives of that organization. https://en.wikipedia.org/wiki/Office#Office_buildings A natural environment which is located on a land mass. terrestrial natural environment A natural environment which is within a water body. aquatic natural environment EcoLexicon:canopy LTER:82 SWEETRealm:Canopy https://en.wikipedia.org/wiki/Canopy forest canopy A canopy which is part of a woodland ecosystem. EcoLexicon:canopy LTER:82 SWEETRealm:Canopy https://en.wikipedia.org/wiki/Canopy woodland canopy A canopy which is composed of the aboveground portion, or crowns, of a community of crop plants. EcoLexicon:canopy LTER:82 SWEETRealm:Canopy https://en.wikipedia.org/wiki/Canopy crop canopy A vegetation layer which is formed by a collection of individual plant crowns, themselves constituting part of the aboveground portion of a plant community. EcoLexicon:canopy LTER:82 SWEETRealm:Canopy false canopy A vegetation layer which is formed by a collection of individual plant crowns, themselves constituting part of the aboveground portion of a plant community. https://en.wikipedia.org/wiki/Canopy_%28biology%29 An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities form continuous or discontinuous regions of canopy cover. The correct usage of FLOPO terms in the axiomatisation needs to be confirmed. The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome. forest ecosystem An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities form continuous or discontinuous regions of canopy cover. http://www.fao.org/docrep/017/ap862e/ap862e00.pdf https://www1.usgs.gov/csas/nvcs/nvcsGetUnitDetails?elementGlobalId=860217 An ecosystem which 1) is determined by communities of annual crops, perennial woody crops, or by actively tilled land, 2) is primarily used for agricultural activity, and 3) contains no village or larger human settlement. cropland ecosystem An ecosystem which 1) is determined by communities of annual crops, perennial woody crops, or by actively tilled land, 2) is primarily used for agricultural activity, and 3) contains no village or larger human settlement. An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities are spaced sufficiently far apart to allow sunlight to illuminate the understory. The correct usage of FLOPO terms in the axiomatisation needs to be confirmed. Woodland understories are often populated with communities of shrubs and herbaceous plants including grasses. There are varying distinctions between woodland and forest, with a large degree of ambiguity. woodland ecosystem An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities are spaced sufficiently far apart to allow sunlight to illuminate the understory. https://en.wikipedia.org/wiki/Woodland A layer which is primarily composed of some liquid material. liquid layer A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid. solid layer A solid layer which is primarily composed of some water-based ice. water ice layer A vegetated area which has not been cleared or is sparsely settled, usually scrub-covered or forested the bush "Bush" is a rather loosely defined regional term, primarily used in Australia. bush area A vegetated area which has not been cleared or is sparsely settled, usually scrub-covered or forested https://www.merriam-webster.com/dictionary/bush#h1 An environmental zone which is part of an atmosphere. atmospheric area atmospheric zone A vegetated area is a geographic feature which has ground cover dominated by plant communities. ORCID:0000-0002-4366-3088 envoPolar vegetated area A liquid astronomical body part which is primarily composed of a continuous volume of liquid water and is held in shape or sustained by an environmental process. Should create links to envrionmental process with new relation like "sustained_by" Similar, in spirit, to landform. hydroform Should create links to envrionmental process with new relation like "sustained_by" ORCID:0000-0002-4366-3088 A liquid surface layer which is in contact with air. liquid air-water interface layer A surface layer which is composed primarily of some liquid. liquid surface layer A surface layer which is composed primarily of solid environmental material. solid surface layer A body of water which is primarily composed of saline water. saline body of water This class has its subclasses populated by inference. saline water body A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged. advective transport Advective processes are disjoint from diffusive processes. Typically, fluids are advected. advective transport process A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged. https://en.wikipedia.org/wiki/Advection https://en.wikipedia.org/wiki/Intensive_and_extensive_properties A water flow process during which movements of water masses caused by varying gravitational and rotational forces from astronomical bodies, combined with the rotation of the astronomical body containing the water mass, cause waters to undergo periodic depth oscillations (tides). tidal flow envoCmecs envoMarine tidal flow process An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited. erosion An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited. https://en.wikipedia.org/wiki/Erosion A landform which has been rendered barren or partially barren by environmental extremes, especially by low rainfall. desert A process during which particles suspended in a gaseous medium are formed. new particle formation process envoAtmo aerosolised particle formation process A process during which particles suspended in a gaseous medium are formed. https://en.wikipedia.org/wiki/Aerosol https://en.wikipedia.org/wiki/Particulates A material transport process during which solid or liquid particles are directly introduced into a volume of gas. primary aerosol formation primary aerosol formation process A material transport process during which solid or liquid particles are directly introduced into a volume of gas. https://en.wikipedia.org/wiki/Aerosol https://en.wikipedia.org/wiki/Particulates An organic environmental material which is primarily composed of gill tissue. gill tissue material An anthropogenic environment which is bounded by the building envelope of a laboratory and in which a system of manufactured products exert control on one or more of its environmental conditions. laboratory environment A research facility in which systems of manufactured products control internal conditions and in which scientific or technological research, experiments, and measurement may be performed. research laboratory laboratory facility A research facility in which systems of manufactured products control internal conditions and in which scientific or technological research, experiments, and measurement may be performed. https://en.wikipedia.org/wiki/Laboratory An anthropisation process during which terrestrial environments - natural or anthropised - or parts thereof are altered to facilitate human activities such as agriculture, settlement, or commerce. land conversion land development Further examples include subdividing real estate into lots, typically for the purpose of building homes and converting unused factories into condominia. land conversion process An anthropisation process during which terrestrial environments - natural or anthropised - or parts thereof are altered to facilitate human activities such as agriculture, settlement, or commerce. https://en.wikipedia.org/wiki/Land_development Further examples include subdividing real estate into lots, typically for the purpose of building homes and converting unused factories into condominia. https://en.wikipedia.org/wiki/Land_development An anthropogenic environmental process which includes all human activities undertaken in a natural, semi-natural, or anthropised environment. There are multiple systems of land use classification. This hierarchy aims to be generally applicable, but national systems can be added on request. land use process An anthropogenic environmental process which includes all human activities undertaken in a natural, semi-natural, or anthropised environment. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use A land use process during which materials of economic value are extracted from a planet, usually from an orebody, lode, vein, seam, reef or placer deposit. mining terrestrial mining A land use process during which materials of economic value are extracted from a planet, usually from an orebody, lode, vein, seam, reef or placer deposit. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://en.wikipedia.org/wiki/Mining https://www.eionet.europa.eu/gemet/en/concept/14837 A process during which an ecosystem - natural or anthropised - is changed by the actions of humans. anthropogenic ecosystem conversion process A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem. planned environmental usage process A planned environmental usage process during which a non-renewable resource such as petroleum, natural gas, or water is extracted from an ecosystem. mining A planned environmental usage process during which a non-renewable resource such as petroleum, natural gas, or water is extracted from an ecosystem. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://en.wikipedia.org/wiki/Mining https://www.eionet.europa.eu/gemet/en/concept/14837 A mining process which occurs in a marine ecosystem. marine mining A mining process during which coal is extracted from the rocky portion of an astronomical body. This may be either terrestrial or marine. coal mining A mining process during which coal is extracted from the rocky portion of an astronomical body. https://en.wikipedia.org/wiki/Mining https://www.eionet.europa.eu/gemet/en/concept/1507 A planned environmental usage process during which an environment facilitates the movement of materials and material objects (persons or goods) from place to place, typically with the assistance of a vehicle. transportation usage of an environment for transportation A planned environmental usage process during which an environment facilitates the movement of materials and material objects (persons or goods) from place to place, typically with the assistance of a vehicle. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://www.eionet.europa.eu/gemet/en/concept/8641 A planned environmental usage process during which an environment supports 1) enterprises concerned with the provision to the public of essentials, such as electricity or water or 2) the basic network or foundation of capital facilities or community investments which are necessary to support economic and community activities. transportation usage of an environment for infrastructure and utilities A planned environmental usage process during which an environment supports 1) enterprises concerned with the provision to the public of essentials, such as electricity or water or 2) the basic network or foundation of capital facilities or community investments which are necessary to support economic and community activities. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://www.eionet.europa.eu/gemet/en/concept/4321 https://www.eionet.europa.eu/gemet/en/concept/6822 A planned environmental usage process during which an environment supports the settlement and dwelling of a community of humans. residential This class does not include environments which are primarily used for commerce or industry. usage of an environment for residential activity A planned environmental usage process during which an environment supports the settlement and dwelling of a community of humans. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://www.eionet.europa.eu/gemet/en/concept/7143 A planned environmental usage process during which an environment supports manufacturing facilities producing commodities that are sold with the expectation of recovering the total cost of production. This class includes environments used to support the facilities engaged with a broad variety of manufacturing activities from food and tobacco, to textiles, metals, vehicles, and chemicals. usage of an environment for industry A planned environmental usage process during which an environment supports manufacturing facilities producing commodities that are sold with the expectation of recovering the total cost of production. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://www.eionet.europa.eu/gemet/en/concept/4279 A planned environmental usage process during which an environment supports facilities associated with commerce or the earning of a livelihood through means other than manufacturing or the provision of a public service. This class includes activities carried out in commercial offices, meeting centres, art studios, recording studios, film sets, warehouses, and distribution centres. usage of an environment for business A planned environmental usage process during which an environment supports facilities associated with commerce or the earning of a livelihood through means other than manufacturing or the provision of a public service. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/11493/144275.pdf https://en.wikipedia.org/wiki/Land_use https://www.eionet.europa.eu/gemet/en/concept/1084 A liquid astronomical body part which is continuous and is delimited by physical discontinuities or non-liquid boundaries. body of liquid A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. liquid astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform A part of an astronomical body which is primarily composed of a continuous volume of gaseous material, shaped by one or more environmental processes. gaseous astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of gaseous material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes. 2018-10-04T13:59:22Z fluid astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform A building which is primarily used for the long-term habitation of humans. 2018-10-04T14:04:49Z domestic building A building which is primarily used for the long-term habitation of humans. https://en.wikipedia.org/wiki/Commercial_building A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space. 2018-10-04T16:55:57Z land surface a useful class: this can be used to define sub-terrestrial and sub-marine entities surface of an astronomical body A vehicle which is able to travel through air in an atmosphere. 2018-10-04T19:28:01Z aircraft A vehicle which is able to travel through air in an atmosphere. https://en.wikipedia.org/wiki/Aircraft An elevation which is flattened across its highest surface. 2018-10-05T21:12:47Z flattened elevation A pollution process during which artificial light with wavelengths in the visible spectrum is released into the environment. 2019-01-09T09:05:35Z Lichtverschmutzung This form of pollution is typically the result of urbanisation or similar land use change. anthropogenic light pollution Lichtverschmutzung INTERNAS:WS2 http://www.awi.de/internas An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a manufactured product. 2019-01-09T09:07:24Z anthropogenic radiation artificial radiation environmental_hazards envoAstro radiation from a manufactured product An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a manufactured product. https://en.wikipedia.org/wiki/Electromagnetic_radiation https://en.wikipedia.org/wiki/Solar_irradiance Radiation from a manufactured product during which light between the wavelenghts of 380 nm and 760 nm is emitted. 2019-01-09T09:21:10Z optical radiation from a manufactured product visible spectrum radiation from a manufactured product Radiation from a manufactured product during which light between the wavelenghts of 380 nm and 760 nm is emitted. A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects. 2019-01-14T18:47:32Z congelation congelation process Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question. material congelation process A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects. https://en.wikipedia.org/wiki/Congelation Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question. https://en.wikipedia.org/wiki/Congelation Land which is below the freezing point of water. 2019-01-14T21:18:19Z http://sweetontology.net/realmCryo/FrozenGround frozen ground Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load. frozen land Land which is below the freezing point of water. https://orcid.org/0000-0003-4808-4736 Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load. https://orcid.org/0000-0003-4808-4736 Soil which is below the freezing point of water. 2019-01-14T21:26:59Z frozen soil A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point. 2019-01-31T21:13:16Z envoCryo envoPolar freezing A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point. https://en.wikipedia.org/wiki/Freezing A freezing process during which liquid water is transformed into water ice. 2019-01-31T21:16:46Z freezing of water into water ice A water surface that is part of a water body. 2019-02-27T21:22:13Z surface layer of a water body An aggregate of raindrops falling to a planetary surface during a precipitation process. 2019-03-02T13:50:58Z rain Rain which is composed of water droplets falling to a planetary surface during a rainfall process. 2019-03-02T13:52:48Z water-based rain An ecoregion which is located on a landmass. 2019-03-05T17:40:44Z https://www.worldwildlife.org/biome-categories/terrestrial-ecoregions terrestrial ecoregion A surface layer which is part of an ocean or sea. 2019-03-06T01:22:01Z envoMarine envoPlastics At this level, the depth of this layer is ambiguous. Some methods (telemetry) measure only the first few centimeters of the sea or ocean surface. In situ methods often sample the first few meters. Subclasses can be created for such cases. Sea surface layer is also used to refer to the surfaces of oceans. sea surface layer A hydroform which is maintained by a continuous, directed movement of water, generated by disequilibria in a water mass. 2019-03-19T16:31:41Z Depth contours, shoreline configurations and interaction with other currents influence a current's direction and strength. water current A layer which is part of a cryosphere. 2019-04-09T13:05:25Z envoPolar cryospheric layer Permafrost which contains inclusions of water-based ice. 2019-04-09T13:45:40Z ice-bearing permafrost A material accumulation process during which the mass of snow on a surface increases. 2019-04-24T18:29:18Z http://sweetontology.net/phenCryo/Accumulation This term is used both as a process and as an amount of mass added. Semantically speaking these are two distinct concepts (e.g., accumulation results in accumulation_amount of ice or snow gain), though accumulation_amount would more likely be an attribute. The scope of this term varies depending on the definition. Some definitions constrain themselves snow or ice added to glaciers; while others also include ice fields, snow cover, and/or floating ice. How to resolve this depends on the scope desired. Some definitions include additional discussion of the the physics involved which would be useful for connecting glacier ontologies to atmospheric, hydrologic, etc. ontologies. This information should be captured no matter how the inconsistencies above are resolved. snow accumulation process A material accumulation process during which the mass of snow on a surface increases. A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass. 2019-04-24T18:48:53Z http://sweetontology.net/phenCryo/Accumulation ice accumulation process A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass. A material accumulation process during which a accumulation of snow and ice forms or increases in mass. 2019-04-24T18:59:45Z http://sweetontology.net/phenCryo/Accumulation snow and ice accumulation process A material accumulation process during which a accumulation of snow and ice forms or increases in mass. A object which is composed primarily of water-based snow and ice. 2019-04-24T19:08:03Z http://sweetontology.net/phenCryo/Accumulation mass of ice and snow A process during which microscopic solid particulates are formed from liquid materials in an atmosphere. 2019-05-30T21:07:51Z atmospheric formation of a solid aerosol formation of a solid aerosol in an atmosphere formation of a solid aerosol in the atmosphere formation of solid particles from liquid material in an atmosphere envoAtmo formation of a solid aerosol from liquid material in an atmosphere A process during which microscopic solid particulates are formed from liquid materials in an atmosphere. https://en.wikipedia.org/wiki/Particulates That part of an atmosphere which is composed of gaseous material. 2019-06-02T07:52:47Z gaseous part of an atmosphere A solid material which does not have a regularly organised internal structure. 2019-06-02T11:07:47Z amorphous solid An aerosol that is suspended in an atmosphere. 2019-06-03T12:24:09Z atmospheric aerosol A material transformation process during which solid or liquid particles form and are suspended in a mass of air, thus creating an aerosol. 2019-06-24T13:43:29Z aerosol formation process A surface layer which is composed primarily of some liquid or gas. 2019-08-20T08:28:42Z fluid surface layer A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface. 2019-07-22T17:29:44Z fluid interface layer A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface. A layer which is composed primarily of some fluid. 2019-07-22T17:35:08Z fluid layer A fluid interface which separates two fluid masses with differing properties. 2019-07-22T17:43:32Z fluid front A fluid interface which separates two fluid masses with differing properties. A fluid front which is composed primarily of gaseous material and separates at least two gaseous masses. 2019-07-22T17:50:08Z gaseous front 2 A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena. 2019-07-22T17:57:21Z meteorological front envoAtmo This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms." weather front A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena. This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms." An object which is composed of a continuous mass of air. 2019-08-20T07:54:32Z envoAtmo air mass A fluid surface layer which is composed primarily of some gaseous material. 2019-08-20T08:30:01Z gaseous surface layer A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface. 2019-08-20T09:28:10Z interface layer An object which is composed primarily of an environmental material 2019-08-20T09:38:29Z This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of environmental material An mass of environmental material which is composed primarily of a solid environmental material 2019-08-20T09:41:27Z This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of solid material An object which is composed primarily of a fluid. 2019-08-20T09:42:35Z fluid mass This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of fluid An object which is composed primarily of a gas. 2019-08-20T09:44:01Z gaseous mass This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of gas An object which is composed primarily of a liquid. 2019-08-20T09:45:03Z liquid mass This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types. mass of liquid 2 An mass of environmental materials which has appreciable quantities of several individual materials, such that the removal of one would convert the mass into a different entity. 2019-08-20T09:47:10Z mass of compounded environmental materials A weather front which separates air masses of tropical and polar origin. 2019-08-20T13:46:42Z envoAtmo envoPolar polar front A weather front which separates air masses of tropical and polar origin. An environment which has a climate with continually high temperatures and with considerable precipitation, at least during part of the year. 2019-08-20T13:58:38Z tropical environment An environment which has a climate with continually high temperatures and with considerable precipitation, at least during part of the year. An environment which has a climate with warm temperatures and with meagre precipitation. 2019-08-20T14:50:35Z subtropical environment An environment which has a climate with warm temperatures and with meagre precipitation. An environment which is located in a part of an astronomical body subject to polar climatic conditions. 2019-08-20T14:53:26Z polar environment An environment which is located in a part of an astronomical body subject to polar climatic conditions. An environment which is located in a part of an astronomical body subject to subpolar climatic conditions. 2019-08-20T16:37:32Z subpolar environment An environment which is located in a part of an astronomical body subject to subpolar climatic conditions. An environment which is located in a part of an astronomical body subject to temperate climatic conditions. 2019-08-20T16:41:52Z temperate environment An environment which is located in a part of an astronomical body subject to temperate climatic conditions. An advective transport process during which a fluid moves. 2019-09-05T05:47:26Z mass fluid flow A wind storm during which strong gusts of wind occur, transporting atmospheric gas in a linear fashion. 2019-09-05T06:04:47Z hurricane of the prairie plough winds thundergust straight-line wind A wind storm during which strong gusts of wind occur, transporting atmospheric gas in a linear fashion. A process during which the ability of a material entity to maintain its internal organisation fails, resulting in deformation and a breakdown of that organisation. 2019-10-07T10:08:24Z This is a very general concept, and should likely be elevated to OBO Core rather than held in ENVO. structural collapse process A process during which the ability of a material entity to maintain its internal organisation fails, resulting in deformation and a breakdown of that organisation. An environmental zone which includes those regions of an astronomical body which are not exposed to its atmosphere or space. 2019-10-07T14:22:38Z subsurface zone of an astronomical body An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert. 2019-10-17T08:21:08Z desert ecosystem A solid astronomical body part which is part of the landmass of that body. 2019-10-17T08:27:17Z part of a landmass A large continuous area of land, either surrounded by sea or contiguous with another landmass. 2019-10-17T08:31:26Z landmass A large continuous area of land, either surrounded by sea or contiguous with another landmass. A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities. 2019-10-17T08:36:00Z compound astronomical body part A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities. https://en.wikipedia.org/wiki/Landform A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water. 2019-10-21T10:42:26Z land A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water. 2019-10-21T11:05:45Z aquatic ecosystem 2019-10-21T11:06:11Z marine ecosystem 2019-10-21T11:09:58Z terrestrial ecosystem A broadleaf forest which is subject to tropical climate conditions. 2019-10-21T11:38:45Z tropical broadleaf forest A broadleaf forest which is subject to temperate climate conditions. 2019-10-21T11:42:38Z temperate broadleaf forest An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem. 2019-10-21T11:52:55Z ecosystem process A mixed forest which is subject to temperate climatic conditions. 2019-10-27T15:52:50Z temperate mixed forest A mixed forest which is subject to tropical climatic conditions. 2019-10-27T16:02:01Z tropical mixed forest A forest ecosystem which is subject to tropical climate conditions. 2019-10-27T16:43:20Z This class is primarily to be populated by inference. tropical forest A forest ecosystem which is subject to subtropical climate conditions. 2019-10-27T16:45:16Z This class is primarily to be populated by inference. subtropical forest A forest ecosystem which is subject to temperate climate conditions. 2019-10-27T16:46:49Z This class is primarily to be populated by inference. temperate forest A grassland ecosystem which is subject to tropical climatic conditions. 2019-10-27T16:58:09Z tropical grassland A grassland which is subject to subtropical climatic conditions. 2019-10-27T17:00:35Z subtropical grassland 2019-10-27T17:00:35Z temperate grassland A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine. 2019-10-29T14:50:34Z construction An object which is formed as a result of one or more biological processes and is composed primarily of organic material. 2019-10-29T15:02:58Z organic object A biome which is subject to tropical climatic conditions. 2019-11-06T15:56:17Z tropical biome A biome which is subject to temperate climatic conditions. 2019-11-06T15:57:04Z temperate biome A biome which is subject to subtropical climatic conditions. 2019-11-06T15:57:36Z subtropical biome A biome which is subject to subpolar climatic conditions. 2019-11-06T15:58:56Z subpolar biome A biome which is subject to alpine altitudinal conditions. 2019-11-06T15:59:35Z alpine biome A biome which is subject to montane altitudinal conditions. 2019-11-06T16:00:33Z montane biome A biome which is subject to arid environmental conditions. 2019-11-06T16:06:47Z arid biome A process during which one entity loses energy to another entity. 2020-02-13T13:34:28Z energy transfer process A material accumulation process during which the volume of liquid entity increases. 2020-05-18T14:39:20Z liquid accumulation process An atmospheric wind which 1) has an increased rate relative to other winds in the same region and 2) is followed by a lull. 2020-05-19T21:47:51Z gust According to U.S. weather observing practice, gusts are reported when the peak wind speed reaches at least 16 knots and the variation in wind speed between the peaks and lulls is at least 9 knots. The duration of a gust is usually less than 20 seconds. wind gust An atmospheric wind which 1) has an increased rate relative to other winds in the same region and 2) is followed by a lull. According to U.S. weather observing practice, gusts are reported when the peak wind speed reaches at least 16 knots and the variation in wind speed between the peaks and lulls is at least 9 knots. The duration of a gust is usually less than 20 seconds. The concentration of carbon dioxide when measured in air that is part of an atmosphere. 2020-05-19T22:51:38Z envoAtmo envoNceas concentration of carbon dioxide in an atmosphere A landform which occurs on the surface of an astronomical body. 2021-05-15T09:16:23Z geographic feature The usage of "surface" here aligns with that of planetary surface: in contact with the atmosphere or space. The extent of the "surface" can vary. For rocky planets like Earth, astrogeologists consider the crust as the surface. surface landform A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body. 2021-05-15T09:40:37Z Landforms may be natural or anthropogenic. This term has often has loose usage when referencing entities which are either subterranean or submerged below water bodies. In some cases, oceans themselves are considered landforms. Here, we have provided subclasses to resolve this ambiguity, but place oceans and other water bodies elsewhere.In later revisions, this hiearchy is likely to be reordered based on the formation processes of the entities within it. landform A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body. A disposition of a material entity which is realised when it is saturated with liquid water. water-holding capacity A mass of solid material which is either 1) a minute fragment of a larger mass or 2) one of a collection of small masses composing an aggregate. grain particle A mass of solid material which is either 1) a minute fragment of a larger mass or 2) one of a collection of small masses composing an aggregate. A particle which 1) is composed primarily of hydrous aluminium phyllosilicate minerals, in turn composed of aluminium and silicon ions bonded into tiny, thin plates by interconnecting oxygen and hydroxide ions, and 2) is or was part of a portion of clay. clay particle The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. particle of clay A particle which 1) is composed primarily of hydrous aluminium phyllosilicate minerals, in turn composed of aluminium and silicon ions bonded into tiny, thin plates by interconnecting oxygen and hydroxide ions, and 2) is or was part of a portion of clay. The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. A material transport process which arises spontaneously due to physical heterogeneities in a portion of a material and forces which act throughout its volume. Most commonly, convective flows are generated by heterogeneities in density or the effects of gravity. When the cause of the convection is unspecified, convection due to the effects of thermal expansion and buoyancy can be assumed. Convection frequently occurs in fluids, but may also take place in soft solids or mixtures where particles can flow. convective transport process A material transport process which arises spontaneously due to physical heterogeneities in a portion of a material and forces which act throughout its volume. Most commonly, convective flows are generated by heterogeneities in density or the effects of gravity. When the cause of the convection is unspecified, convection due to the effects of thermal expansion and buoyancy can be assumed. Convection frequently occurs in fluids, but may also take place in soft solids or mixtures where particles can flow. A physical quality of a process which is characteristic of processes that transport material within a volume due to the combined effects of material property heterogeneity and body forces across that volume. convective A physical quality of a process which is characteristic of processes that transport material within a volume due to the combined effects of material property heterogeneity and body forces across that volume. A physical quality of a process which is characteristic of process that transport material without, themselves, changing the qualities of those materials or the processes that are unfolding within them. advective A physical quality of a process which is characteristic of process that transport material without, themselves, changing the qualities of those materials or the processes that are unfolding within them. A material transport process during which material moves from a region of higher concentration to a region of lower concentration. diffusion Diffusion is also applied to the movement of energy, thus the more specific label. This class will be repositioned (but with the core of its definition intact) if we include other forms of diffusion in ENVO. material diffusion process A material transport process during which material moves from a region of higher concentration to a region of lower concentration. A combustible black or brownish-black sedimentary rock usually occurring in rock strata in layers or veins called coal beds or coal seams. coal A combustible black or brownish-black sedimentary rock usually occurring in rock strata in layers or veins called coal beds or coal seams. iron mine uranium mine a type of rock that contains sufficient minerals with important elements including metals that can be economically extracted from the rock. ore Ore which contains uranium. The primary uranium ore mineral is uraninite uranium ore iron ore gold ore platinum ore Dust which is derived from coal. coal dust Dust which is derived from mineral material. mineral dust Dust which is composed primarily of some metallic material. metallic dust cement dust Dust which is derived from clay material. clay dust dust from plant parts A surface mine that utilizes a technique of extracting rock or minerals from the earth by their removal from an open pit or borrow. open-pit mine A surface mine that utilizes a technique of extracting rock or minerals from the earth by their removal from an open pit or borrow. A human construction which is used to initiate and control a fission nuclear chain reaction or nuclear fusion reactions. nuclear reactor A human construction which is used to initiate and control a fission nuclear chain reaction or nuclear fusion reactions. https://en.wikipedia.org/wiki/Nuclear_reactor A nuclear reactor which is used as a source of power. power reactor nuclear power reactor A nuclear reactor which is used as a source of power. https://en.wikipedia.org/wiki/Nuclear_reactor A liquid or a gas. fluid fluid environmental material A liquid or a gas. https://github.com/EnvironmentOntology/envo/issues/940 A process in which includes the components of an environmental system as participants. This is a convenience class for organisation and should not be used for annotation. environmental system process A type of land degradation in which terrestrial ecosystem becomes increasingly dry, typically losing its bodies of water as well as vegetation and wildlife. desertification A type of land degradation in which terrestrial ecosystem becomes increasingly dry, typically losing its bodies of water as well as vegetation and wildlife. A general and temporary condition of partial or complete inundation of normally dry land areas from the overflow of inland and/or tidal waters, and/or the unusual and rapid accumulation or runoff of surface waters from any source. A great flow along a watercourse or a flow causing inundation of lands not normally covered by water. environmental_hazards flooding A general and temporary condition of partial or complete inundation of normally dry land areas from the overflow of inland and/or tidal waters, and/or the unusual and rapid accumulation or runoff of surface waters from any source. A great flow along a watercourse or a flow causing inundation of lands not normally covered by water. GEMET: http://www.eionet.europa.eu/gemet/concept/3301 A process which occurs within an atmosphere. This class will be populated by inference and is primarily organisational. atmospheric process A process which diminishes the functioning of an ecosystem located on land. An SDGIO request. Likely to be refined and revised. This could include, for example, reducing soil health, pollinator activity, or an ecosystem's ability to sequester carbon. land degradation A process which diminishes the functioning of an ecosystem located on land. http://www.who.int/globalchange/ecosystems/desert/en/ https://en.wikipedia.org/wiki/Land_degradation Establishment of a new forest by seeding or planting of nonforested land. Prior to afforestation, the land cover of a region must not include forests. afforestation Establishment of a new forest by seeding or planting of nonforested land. GEMET:http://www.eionet.europa.eu/gemet/concept/167 An ecosystem process during which the flora and fauna belonging to a forest are removed or destroyed. clearance clearing deforestation An ecosystem process during which the flora and fauna belonging to a forest are removed or destroyed. http://www.eionet.europa.eu/gemet/en/concept/2036 To be populated through inference. Do not use for annotation. forest process forest area expansion A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process. Relabel the obo foundry unique label to be generic process anthropogenic modulatory intervention process An environmental process which is driven by the action of humans. anthropogenic environmental process An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited. envoPolar planetary erosion An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited. https://en.wikipedia.org/wiki/Erosion An environmental process which has water - in any of its states - as a participant. This classes asserted subclasses will be moved away as it should be an inferred class. hydrological process A planned process during which human agents establish plant communities in ecosystems which have previously been, partially or wholly, stripped of existing plant communities. planned revegetation An environmental system process that results in the introduction of contaminants into an environment. pollution environmental_hazards Pollutants may be material or immaterial (e.g. heat energy) environmental pollution An environmental system process that results in the introduction of contaminants into an environment. A pollution process during which particulates or other contaminants are released into a portion of air. environmental_hazards envoPolar air pollution A pollution process during which contaminants are released into soil. environmental_hazards envoPolar soil pollution A pollution process during which contaminants are released into soil. A pollution process during which contaminants are released into water. environmental_hazards envoPolar water pollution An process in which environmental parameters and variables are continually assayed. monitoring environmental monitoring A planned process during which the amount of pollutants released into an environmental system is regulated. pollution prevention pollution control A monitoring process that assays the level of environmental pollutants to determine the presence of effect of environmental pollution. envoPolar pollution monitoring A physical process during which atoms, molecules, or other consituents of a material entity are forced closer together. http://orcid.org/0000-0002-3410-4655 envoPolar compaction process A physical process during which atoms, molecules, or other consituents of a material entity are forced closer together. https://en.wikipedia.org/wiki/Compaction A process during which the mass of one or more materials, present within a given site, increases. http://orcid.org/0000-0002-3410-4655 envoPolar Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process. material accumulation process A process during which material is displaced from its original location and transported either to a new location or back to the original location. http://orcid.org/0000-0002-3410-4655 envoPolar Experimental class for structural purposes not recommended for annotation. material transport process A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed. The general semantics of depression and geographic basin are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486 http://orcid.org/0000-0002-3410-4655 envoPolar geographic basin A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed. https://en.wikipedia.org/wiki/Basin Particulate environmental material which is composed primarily of carbon particles formed through the incomplete combustion of hydrocarbons. Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible. http://orcid.org/0000-0002-3410-4655 envoPolar soot Particulate environmental material which is composed primarily of carbon particles formed through the incomplete combustion of hydrocarbons. https://en.wikipedia.org/wiki/Soot Sediment which has been transported through the marine water column, settling on the seafloor. http://orcid.org/0000-0002-3410-4655 marine sediments envoPolar Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input. marine sediment Sediment which has been transported through the marine water column, settling on the seafloor. https://en.wikipedia.org/wiki/Pelagic_sediment#_note-8 A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface. http://orcid.org/0000-0002-3410-4655 envoPolar sedimentation in a water body A process during which a portion of some environmental material is converted into a different material or a collection of materials. A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies. http://orcid.org/0000-0002-3410-4655 envoPolar Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another. material transformation process A desublimation process during which water vapour is frozen into water ice. http://orcid.org/0000-0002-3410-4655 envoPolar desublimation of water vapour into ice A solid astronomical body part which is primarily composed of a continuous mass of snow and/or ice. Place holder class. Also the axiom should be changed to something along the lines of 'primairly composed of’ some ‘environmental material’ and ‘has quality’ frozen once PATO:frozen is imported. http://orcid.org/0000-0002-3410-4655 envoPolar cryoform A mass of snow. http://orcid.org/0000-0002-3410-4655 accumulation of snow snow accumulation http://sweetontology.net/phenCryo/Accumulation envoPolar snow mass A water-based rainfall process during which water droplets with increased acidity fall towards a planetary surface. http://orcid.org/0000-0002-3410-4655 https://orcid.org/0000-0002-3884-3420 acid rain On Earth, the acidity of raindrops is typically increased through interactions of water molecules with sulfur dioxide or nitrogen oxide, released into the atmosphere by natural or anthropogenic processes. acid rainfall A water-based rainfall process during which water droplets with increased acidity fall towards a planetary surface. https://en.wikipedia.org/wiki/Acid_rain Water-based rain which has increased acidity. http://orcid.org/0000-0002-3410-4655 https://orcid.org/0000-0002-3884-3420 acid rain On Earth, the acidity of raindrops is typically increased through interactions of water molecules with sulfur dioxide or nitrogen oxide, released into the atmosphere by natural or anthropogenic processes. acidic water-based rain Water-based rain which has increased acidity. https://en.wikipedia.org/wiki/Acid_rain An astronomical body part which is composed primarily of environmental materials in their frozen form. For the moment the definition links to liquid water but in the future we might need to link to other materials for other planets, e.g., Mars. Need to make this planet agnostic. Might want to not have the definition link to years as some astronomical body parts might not be in systems with years. Note that in a strict sense, rocks are also frozen but in a practical sense we use terms like "solidified". This maybe something to revist if we add more astrogelogical content. 2021-04-14T18:57:18.275Z envoCryo envoPolar The term refers collectively to the portions of the earth (i.e., a planet) where water is in solid form, including snow cover, floating ice, glaciers, ice caps, ice sheets, seasonally frozen ground and perennially frozen ground (permafrost). The Cryosphere may be divided into the cryoatmosphere, the cryohydrosphere (snow cover, glaciers, and river, lake and sea Ice) and the cryolithosphere (perennially and seasonally cryotic ground, rock glacier). This is an Earth centric definition, other cryospheres will be considered later. Some definitions reffer to that which is sufficiently cold for pure water to freeze for at least a part of each year. It should be noted that "Some authorities exclude the earth's atmosphere from the Earth's Cryosphere; others restrict the term Cryosphere to the regions of the earth's crust where Permafrost exists." Definitions of Cryosphere come from several glossaries including: - PhysicalGeography.net http://physicalgeography.net/ - van Everdingen, Robert, ed., 2005 (1998 revised May 2005). Multi-language glossary of permafrost and related ground-ice terms. Boulder, CO: National Snow and Ice Data Center/World Data Center for Glaciology. [https://globalcryospherewatch.org/reference/glossary_docs/Glossary_of_Permafrost_and_Ground-Ice_IPA_2005.pdf] - American Meteorological Society, 2015. Glossary of Meteorology [online], Available at: http://glossary.ametsoc.org/wiki/Main_Page. [Accessed 27/01/2017]. - EU Climate-ADAPT (The European Climate Adaptation Platform), no date, Glossary, Available from: http://climate-adapt.eea.europa.eu/glossary - IPCC, 2014: Annex II: Glossary [Agard, J., Schipper, E. L. F., (ed.)]. In: Climate Change 2014: Impacts, Adaptation, and Vulnerability. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Birkmann, J., Campos, M., Dubeux, C., Nojiri, Y., Olsson, L., Osman-Elasha, B., Pelling, M., Prather, M. J., Rivera-Ferre M. G., Ruppel, O. C., Sallenger, A., Smith, K. R., St. Clair, A. L.,]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. [Link] - NSIDC, The National Snow and Ice Data Center glossary is available at https://nsidc.org/cryosphere/glossary, Last accessed [26/01/2016]. - Trombotto, D., P. Wainstein & L. Arenson, 2014, Guía Terminológica de la Geocriología Sudamericana” / “Terminological Guide of the South American Geocryology, 1a ed. 128 pp. [Link] - UNESCO-WMO, 2012, International Glossary of Hydrology, 3rd edition, WMO-No. 385. [Link] cryosphere An astronomical body part which is composed primarily of environmental materials in their frozen form. The term refers collectively to the portions of the earth (i.e., a planet) where water is in solid form, including snow cover, floating ice, glaciers, ice caps, ice sheets, seasonally frozen ground and perennially frozen ground (permafrost). The Cryosphere may be divided into the cryoatmosphere, the cryohydrosphere (snow cover, glaciers, and river, lake and sea Ice) and the cryolithosphere (perennially and seasonally cryotic ground, rock glacier). This is an Earth centric definition, other cryospheres will be considered later. Some definitions reffer to that which is sufficiently cold for pure water to freeze for at least a part of each year. It should be noted that "Some authorities exclude the earth's atmosphere from the Earth's Cryosphere; others restrict the term Cryosphere to the regions of the earth's crust where Permafrost exists." Definitions of Cryosphere come from several glossaries including: - PhysicalGeography.net http://physicalgeography.net/ - van Everdingen, Robert, ed., 2005 (1998 revised May 2005). Multi-language glossary of permafrost and related ground-ice terms. Boulder, CO: National Snow and Ice Data Center/World Data Center for Glaciology. [https://globalcryospherewatch.org/reference/glossary_docs/Glossary_of_Permafrost_and_Ground-Ice_IPA_2005.pdf] - American Meteorological Society, 2015. Glossary of Meteorology [online], Available at: http://glossary.ametsoc.org/wiki/Main_Page. [Accessed 27/01/2017]. - EU Climate-ADAPT (The European Climate Adaptation Platform), no date, Glossary, Available from: http://climate-adapt.eea.europa.eu/glossary - IPCC, 2014: Annex II: Glossary [Agard, J., Schipper, E. L. F., (ed.)]. In: Climate Change 2014: Impacts, Adaptation, and Vulnerability. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Birkmann, J., Campos, M., Dubeux, C., Nojiri, Y., Olsson, L., Osman-Elasha, B., Pelling, M., Prather, M. J., Rivera-Ferre M. G., Ruppel, O. C., Sallenger, A., Smith, K. R., St. Clair, A. L.,]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. [Link] - NSIDC, The National Snow and Ice Data Center glossary is available at https://nsidc.org/cryosphere/glossary, Last accessed [26/01/2016]. - Trombotto, D., P. Wainstein & L. Arenson, 2014, Guía Terminológica de la Geocriología Sudamericana” / “Terminological Guide of the South American Geocryology, 1a ed. 128 pp. [Link] - UNESCO-WMO, 2012, International Glossary of Hydrology, 3rd edition, WMO-No. 385. [Link] A human construction in which healthcare is provided. 2021-03-15T04:00:01.750Z health facility medical facility healthcare facility A human construction in which healthcare is provided. Any material containing unstable atoms that emit ionizing radiation as it decays. 2020-08-03T18:32:42Z radioactive material Any material containing unstable atoms that emit ionizing radiation as it decays. https://www.ehs.iastate.edu/research/radiation/radioactive-materials A water ice crystal which is constituted by water molecules aligned in a hexagonal array. snowflake snow crystal A water ice crystal which is constituted by water molecules aligned in a hexagonal array. snowflake Snow crystals and snowflakes are often noted as synonyms, however, the term "snowflake" is generally used more loosely. Some sites mention that snow crystals refer to individual crystals of ice, while the term "snowflake" can refer both to an individual crystal of ice and to a bundle of snow crystals. Please see here [https://github.com/EnvironmentOntology/envo/issues/998#issuecomment-685649444] Sediment which contains some chemical contaminant. See https://github.com/EnvironmentOntology/envo/issues/1102 for a possible design pattern. Uses undesirability standard, compared to polluted river's ecological impact standard. What is the relation to ENVO:00002114 'chemically enriched sediment'? Does 'element' in the definition refer to something found in the periosic table (like selenium) or the member of some set, aka an entity? 2021-04-05T16:38:47.162Z chemically contaminated sediment Sediment which contains some chemical contaminant. A human construction which is used to transport a material which is primarily composed of liquid or gas through a system of pipes. Getting an example of use could be helpful. Are some environmental samples collected from the outside of a pipe or its fittings? Or taken from inside the pipe? Removing "transport" from the label may make the labels of sublasses more readable. However, "pipeline" alone could mean several unrelated things, like software pipelines. https://www.eia.gov/energyexplained/natural-gas/natural-gas-pipelines.php uses the term "pipeline network". ALSO could this be a transport feature? Xref https://github.com/EnvironmentOntology/envo/issues/1111. 2021-04-05T16:38:47.162Z Pipeline networks typically materials either from 1) a production area to a market area for consumption, 2) a production area to an area for waste disposal. pipeline network A human construction which is used to transport a material which is primarily composed of liquid or gas through a system of pipes. A human construction which is used as a storage area for mining tailings. not placing under 'pond' class becasue contents may not be primarily be composed of water. consider revising 'pond' semantics 2021-04-05T16:38:47.162Z tailings pond A human construction which is used as a storage area for mining tailings. The concentration of carbon dioxide when measured in soil. 2019-03-14T21:13:30Z envoNceas concentration of carbon dioxide in soil The concentration of carbon dioxide when measured in air. 2019-03-14T21:24:04Z envoNceas concentration of carbon dioxide in air The concentration of carbon dioxide when measured in seawater. 2019-03-14T21:35:30Z envoNceas concentration of carbon dioxide in seawater Organic material in soil, which consists of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms. 2019-04-05T00:53:06Z envoNceas soil organic matter Organic material in soil, which consists of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms. https://en.wikipedia.org/wiki/Soil_organic_matter A surface layer which is composed primarily of soil. 2019-04-12T17:35:13Z envoNceas soil surface layer A layer that is composed primarily of soil. soil layer Texture which inheres in soil. 2021-12-26T21:49:12Z soil texture Water-holding capacity which inheres in some soil. soil water-holding capacity water-holding capacity of soil Water-holding capacity which inheres in some soil. The concentration of a clay when measured in soil. soil clay concentration concentration of clay in soil The concentration of a slit when measured in soil. soil slit concentration concentration of slit in soil The concentration of a sand when measured in soil. soil sand concentration concentration of sand in soil The concentration of a liquid water when measured in soil. soil liquid water concentration soil moisture content soil water content concentration of liquid water in soil The concentration of a salt when measured in soil. soil salt concentration concentration of salt in soil The concentration of a soil organic matter when measured in soil. soil soil organic matter concentration concentration of soil organic matter in soil The temperature of some environmental material. environmental material temperature temperature of environmental material The temperature of some air. air temperature temperature of air The quality of a environmental system process. quality of environmental system process environmental system process quality The porosity of some soil. soil porosity porosity of soil The composition of some soil. soil composition composition of soil The structure of some soil. soil structure structure of soil The acidity of some soil. soil acidity soil pH acidity of soil The temperature of some soil. soil temperature temperature of soil The wetness of some soil. soil wetness wetness of soil The temperature of some water. water temperature temperature of water The humidity of some soil. soil humidity humidity of soil The composition of some water. water composition composition of water The porosity of some snow. snow porosity porosity of snow The porosity of some water ice. water ice porosity porosity of water ice The generation of energy for use by humans 2018-11-03T20:02:04Z anthropogenic generation of energy 2018-11-03T20:04:34Z generation of energy from coal A disposition which is realized during the execution of work, the emission of heat, or the possession of mass. 2018-11-03T20:22:18Z Consider replacing with PATO class; note that PATO class is not a disposition. This should likely go into OBO Core and also have a physicist look at it. energy Energy possessed by an object because of its position relative to other objects, stresses within itself, its electric charge, or other factors. 2018-11-03T20:24:50Z potential energy Energy which is realised through motion. 2018-11-03T20:25:57Z kinetic energy Energy which is the sum of 1) kinetic energy and 2) potential energy. 2018-11-03T20:26:08Z mixed potential and kinetic energy potential energy that binds nucleons to form the atomic nucleus (and nuclear reactions). 2018-11-03T20:28:07Z nuclear energy Potential energy which is stored in the fields of propagated by electromagnetic radiation. 2018-11-03T20:29:21Z radiant energy Kinetic energy which is realised through the microscopic motion of particles. 2018-11-03T20:30:20Z A form of disordered mechanical energy. thermal energy Thermal energy which propagates through a solid (typically rocky) astronomical body. 2018-11-03T20:47:30Z Often, this term is used specifically for thermal energy spreading from heat sources (e.g. magma chambers, the planetary core) within the Earth. However, it is also used for extraterrestrial bodies. geothermal energy 2018-11-03T20:48:18Z stellar radiation energy A power station which burns a fossil fuel such as coal, natural gas, or petroleum to produce electricity. 2018-11-03T21:00:37Z fossil fuel power plant 2018-11-03T21:01:16Z coal power plant 2018-11-03T21:14:06Z solar power station 2018-11-03T21:15:52Z OTEC power plant OTEC power station ocean thermal power station 2018-11-03T21:21:48Z tidal power plant An environment which is determined by an anatomical entity. anatomical entity environment integumental system environment The concentration of dioxygen when measured in liquid water. liquid water dioxygen concentration concentration of dioxygen in liquid water The acidity of some water. water acidity acidity of water The concentration of dioxygen when measured in sea water. sea water dioxygen concentration concentration of dioxygen in sea water The concentration of oxygen when measured in soil. soil oxygen concentration concentration of oxygen in soil The concentration of iron molecular entity when measured in soil. soil iron molecular entity concentration concentration of iron molecular entity in soil The concentration of sodium molecular entity when measured in soil. soil sodium molecular entity concentration concentration of sodium molecular entity in soil The concentration of organic molecular entity when measured in soil. soil organic molecular entity concentration concentration of organic molecular entity in soil The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GOC:go_curators GOC:isa_complete GOC:jl ISBN:0198506732 The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton. biological_process GO:0000011 vacuole inheritance The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton. GOC:mcc PMID:10873824 PMID:14616069 The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. GO:0016359 mitotic chromosome segregation mitotic sister-chromatid adhesion release biological_process GO:0000070 mitotic sister chromatid segregation The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. GOC:ai GOC:jl The lipid bilayer surrounding any of the compartments of the Golgi apparatus. Golgi apparatus membrane cellular_component GO:0000139 Golgi membrane The lipid bilayer surrounding any of the compartments of the Golgi apparatus. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. https://github.com/geneontology/go-ontology/issues/23114 https://github.com/geneontology/go-ontology/issues/23195 microtubule cytoskeleton organisation biological_process microtubule cytoskeleton organization and biogenesis GO:0000226 microtubule cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah microtubule cytoskeleton organisation GOC:mah microtubule cytoskeleton organization and biogenesis GOC:mah A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. nuclear interphase chromosome cellular_component GO:0000228 nuclear chromosome A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. GOC:dph GOC:mah The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. glycan biosynthesis glycan biosynthetic process polysaccharide anabolism polysaccharide biosynthesis polysaccharide formation polysaccharide synthesis biological_process GO:0000271 polysaccharide biosynthetic process The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GO:0044244 polysaccharide breakdown polysaccharide catabolism polysaccharide degradation multicellular organismal polysaccharide catabolic process biological_process GO:0000272 polysaccharide catabolic process The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. PMID:33139480 Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 Wikipedia:Mitosis biological_process mitosis GO:0000278 Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis GO:0000280 nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah A ribosome contained within a subcellular membrane-bounded organelle. cellular_component GO:0000313 organellar ribosome A ribosome contained within a subcellular membrane-bounded organelle. GOC:mah GOC:mcc The joining of 2 or more lipid bilayer membranes that surround the nucleus. biological_process GO:0000740 nuclear membrane fusion The joining of 2 or more lipid bilayer membranes that surround the nucleus. GOC:elh The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. GO:0007335 Wikipedia:Karyogamy nuclear fusion nuclear fusion during karyogamy biological_process GO:0000741 karyogamy The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. GOC:elh The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. cell fusion biological_process GO:0000768 syncytium formation by plasma membrane fusion The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. GOC:mtg_muscle GOC:tb The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GO:0000789 GO:0000790 GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin cellular_component chromosome scaffold GO:0000785 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GOC:elh PMID:20404130 A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 GO:0005720 GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin transcriptionally silent chromatin nuclear heterochromatin cellular_component GO:0000792 heterochromatin A compact and highly condensed form of chromatin that is refractory to transcription. PMID:32017156 The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets. biological_process GO:0000819 sister chromatid segregation The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets. GOC:ai GOC:elh The developmental process in which the size or shape of a cell is generated and organized. GO:0007148 GO:0045790 GO:0045791 cellular morphogenesis biological_process GO:0000902 cell morphogenesis The developmental process in which the size or shape of a cell is generated and organized. GOC:clt GOC:dph GOC:go_curators GOC:tb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form. response to acid biological_process response to acid anion response to oxoanion GO:0001101 This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead. response to acid chemical Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form. GOC:go_curators GOC:rn The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). skeletal development biological_process GO:0001501 skeletal system development The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). GOC:dph GOC:jid GOC:tb The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. Wikipedia:Ossification bone biosynthesis bone formation osteogenesis biological_process GO:0001503 Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'. ossification The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:mtg_mpo PMID:17572649 A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. biological_process GO:0001508 Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. action potential A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. Wikipedia:Angiogenesis blood vessel formation from pre-existing blood vessels biological_process GO:0001525 angiogenesis Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. ISBN:0878932453 blood vessel formation from pre-existing blood vessels The developmental growth process in which an oocyte irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. biological_process GO:0001555 oocyte growth The developmental growth process in which an oocyte irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. https://www.ncbi.nlm.nih.gov/books/NBK279054/ A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization. Wikipedia:Oocyte_maturation biological_process GO:0001556 oocyte maturation A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization. GOC:devbiol https://www.ncbi.nlm.nih.gov/books/NBK279054/ Any process that modulates the frequency, rate, extent or direction of cell growth. biological_process GO:0001558 regulation of cell growth Any process that modulates the frequency, rate, extent or direction of cell growth. GOC:go_curators The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood. biological_process GO:0001568 blood vessel development The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood. GOC:hjd UBERON:0001981 The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system. patterning of blood vessels biological_process GO:0001569 branching involved in blood vessel morphogenesis The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system. GOC:dph patterning of blood vessels GOC:dph The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes. Wikipedia:Vasculogenesis vascular morphogenesis biological_process GO:0001570 vasculogenesis The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes. PMID:8999798 A process that results in a parallel arrangement of microtubules. microtubule bundling biological_process GO:0001578 microtubule bundle formation A process that results in a parallel arrangement of microtubules. GOC:dph The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight. GO:0042460 Wikipedia:Eye_development biological_process GO:0001654 eye development The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight. GOC:jid GOC:jl The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure. https://github.com/geneontology/go-ontology/issues/22178 biological_process GO:0001655 urogenital system development The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure. GOC:go_curators A homeostatic process in which an organism modulates its internal body temperature. Wikipedia:Thermoregulation thermoregulation biological_process GO:0001659 temperature homeostasis A homeostatic process in which an organism modulates its internal body temperature. GOC:jl thermoregulation GOC:dph GOC:tb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. response to hypoxic stress response to lowered oxygen tension response to intermittent hypoxia response to sustained hypoxia biological_process GO:0001666 Note that this term should not be confused with 'response to anoxia ; GO:0034059'. Note that in laboratory studies, hypoxia is typically studied at O2 concentrations ranging from 0.1 - 5%. response to hypoxia Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. GOC:hjd Cell migration that is accomplished by extension and retraction of a pseudopodium. ameboid cell migration amoeboid cell migration amoeboidal cell migration biological_process GO:0001667 Note that this term refers to a mode of migration rather than to any particular cell type. ameboidal-type cell migration Cell migration that is accomplished by extension and retraction of a pseudopodium. GOC:dph The nucleus of the female germ cell, a reproductive cell in females. GO:0043080 female germ-cell nucleus cellular_component GO:0001674 female germ cell nucleus The nucleus of the female germ cell, a reproductive cell in females. CL:0000021 GOC:hjd Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). translation initiation ternary complex assembly biological_process GO:0001677 formation of translation initiation ternary complex Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). GOC:hjd The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. hydrochloric acid secretion biological_process GO:0001696 gastric acid secretion The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. GOC:hjd The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster. biological_process GO:0001700 embryonic development via the syncytial blastoderm The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster. GOC:go_curators GOC:mtg_sensu The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. biological_process GO:0001701 in utero embryonic development The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. GOC:go_curators GOC:mtg_sensu The formation of the ectoderm, mesoderm and endoderm during gastrulation. biological_process GO:0001704 formation of primary germ layer The formation of the ectoderm, mesoderm and endoderm during gastrulation. GOC:go_curators The formation of ectoderm during gastrulation. biological_process GO:0001705 ectoderm formation The formation of ectoderm during gastrulation. GOC:go_curators The formation of the endoderm during gastrulation. endoblast formation biological_process GO:0001706 endoderm formation The formation of the endoderm during gastrulation. GOC:go_curators endoblast formation GOC:dph GOC:sdb_2009 GOC:tb The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts. biological_process GO:0001707 mesoderm formation The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts. GOC:go_curators The initial developmental process that will lead to the formation of an eye. biological_process optic placode formation GO:0001743 lens placode formation The initial developmental process that will lead to the formation of an eye. GOC:dph The morphogenetic process in which the anatomical structures of the compound eye are generated and organized. The adult compound eye is a precise assembly of 700-800 ommatidia. Each ommatidium is composed of 20 cells, identified by cell type and position. An example of compound eye morphogenesis is found in Drosophila melanogaster. insect-type retina morphogenesis biological_process GO:0001745 compound eye morphogenesis The morphogenetic process in which the anatomical structures of the compound eye are generated and organized. The adult compound eye is a precise assembly of 700-800 ommatidia. Each ommatidium is composed of 20 cells, identified by cell type and position. An example of compound eye morphogenesis is found in Drosophila melanogaster. GOC:dph GOC:mtg_sensu insect-type retina morphogenesis PMID:11735386 The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell. biological_process GO:0001751 compound eye photoreceptor cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell. GOC:go_curators The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms. biological_process GO:0001754 eye photoreceptor cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms. GOC:go_curators The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo. Wikipedia:Somitogenesis formation of mesodermal clusters biological_process GO:0001756 somitogenesis The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo. ISBN:0721662544 formation of mesodermal clusters The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes. branching morphogenesis biological_process GO:0001763 morphogenesis of a branching structure The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes. ISBN:0721662544 branching morphogenesis GOC:dph The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus. immune cell homeostasis leucocyte homeostasis biological_process GO:0001776 Note that this term represents the return of immune system cell levels to stable numbers following an immune response as well as the proliferation and elimination of cells of the immune system required to maintain stable numbers in the absence of an outside stimulus. leukocyte homeostasis The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus. GOC:add ISBN:0781735149 The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. 5-HT secretion 5-hydroxytryptamine secretion biological_process serotonin release GO:0001820 serotonin secretion The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. GOC:ef ISBN:0198506732 ISBN:0781735149 serotonin release GOC:tb The process whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm. biological_process GO:0001824 See also the Anatomical Dictionary for Mouse Development ontology terms 'TS5, embryo ; EMAP:23', 'TS5, inner cell mass ; EMAP:24' and 'TS5, trophectoderm; EMAP:28'. blastocyst development The process whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm. GOC:dph ISBN:0124020607 ISBN:0198542771 The initial formation of a blastocyst from a solid ball of cells known as a morula. biological_process GO:0001825 See also the Anatomical Dictionary for Mouse Development ontology term 'TS3, compacted morula ; EMAP:9'. blastocyst formation The initial formation of a blastocyst from a solid ball of cells known as a morula. GOC:dph ISBN:0124020607 ISBN:0198542771 The process in which a relatively unspecialized cell acquires specialized features of an inner cell mass cell. biological_process GO:0001826 See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, inner cell mass ; EMAP:14'. inner cell mass cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an inner cell mass cell. GOC:dph ISBN:0124020607 ISBN:0198542771 The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell. trophectoderm cell differentiation biological_process GO:0001829 See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19'. trophectodermal cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell. GOC:dph ISBN:0124020607 ISBN:0198542771 The morphogenesis of trophectoderm cells. trophectoderm cellular morphogenesis biological_process GO:0001831 See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19', 'TS5, trophectoderm ; EMAP:28' and 'TS6, trophectoderm ; EMAP:39'. trophectodermal cellular morphogenesis The morphogenesis of trophectoderm cells. GOC:dph ISBN:0124020607 ISBN:0198542771 An increase in size of a blastocyst due to expansion of the blastocoelic cavity cell shape changes and cell proliferation. biological_process GO:0001832 See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, blastocoelic cavity ; EMAP:17', 'TS5, blastocoelic cavity ; EMAP:27' and 'TS6, blastocoelic cavity ; EMAP:36'. blastocyst growth An increase in size of a blastocyst due to expansion of the blastocoelic cavity cell shape changes and cell proliferation. GOC:dph ISBN:0124020607 ISBN:0198542771 The proliferation of cells in the inner cell mass. biological_process GO:0001833 See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, inner cell mass ; EMAP:14' and 'TS5, inner cell mass ; EMAP:24'. inner cell mass cell proliferation The proliferation of cells in the inner cell mass. GOC:dph GOC:isa_complete ISBN:0124020607 ISBN:0198542771 The proliferation of cells in the trophectoderm. trophectoderm cell proliferation biological_process GO:0001834 See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19', 'TS5, trophectoderm ; EMAP:28' and 'TS6, trophectoderm ; EMAP:39'. trophectodermal cell proliferation The proliferation of cells in the trophectoderm. GOC:dph ISBN:0124020607 ISBN:0198542771 A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. EMT epithelial-mesenchymal transition mesenchymal cell differentiation from epithelial cell biological_process GO:0001837 epithelial to mesenchymal transition A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. GOC:dph PMID:14701881 mesenchymal cell differentiation from epithelial cell GOC:BHF GOC:dph GOC:rl The morphogenesis of an embryonic epithelium into a tube-shaped structure. biological_process GO:0001838 embryonic epithelial tube formation The morphogenesis of an embryonic epithelium into a tube-shaped structure. GOC:dph ISBN:0824072820 The process in which the anatomical structures of the neural plate are generated and organized. The neural plate is a specialized region of columnar epithelial cells in the dorsal ectoderm that will give rise to nervous system tissue. biological_process GO:0001839 neural plate morphogenesis The process in which the anatomical structures of the neural plate are generated and organized. The neural plate is a specialized region of columnar epithelial cells in the dorsal ectoderm that will give rise to nervous system tissue. GOC:dph ISBN:0878932437 The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system. biological_process GO:0001840 neural plate development The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system. GOC:dph GOC:ef ISBN:0878932437 ISBN:0878932585 The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation biological_process GO:0001841 neural tube formation The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GOC:dph ISBN:0878932437 neural tube morphogenesis GOC:dph The process in which the neural fold is formed. The edges of the neural plate thicken and move up to form a U-shaped structure called the neural groove. biological_process neural groove formation GO:0001842 neural fold formation The process in which the neural fold is formed. The edges of the neural plate thicken and move up to form a U-shaped structure called the neural groove. GOC:dph ISBN:0878932437 neural groove formation GOC:dph Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a yeast species. biological_process GO:0001878 defined as response to Saccharomycotina (true yeasts). This excludes fission yeast. response to yeast Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a yeast species. PMID:14707091 The progression of an endothelial cell over time, from its formation to the mature structure. biological_process GO:0001885 endothelial cell development The progression of an endothelial cell over time, from its formation to the mature structure. GOC:dph The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell. biological_process GO:0001886 endothelial cell morphogenesis The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell. GOC:ascb_2009 GOC:dph GOC:tb The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes. biological_process GO:0001889 liver development The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes. GOC:add ISBN:068340007X The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium. biological_process GO:0001935 endothelial cell proliferation The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium. GOC:add ISBN:0781735149 Any process that modulates the frequency, rate, or extent of endothelial cell proliferation. biological_process GO:0001936 regulation of endothelial cell proliferation Any process that modulates the frequency, rate, or extent of endothelial cell proliferation. GOC:add Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation. down regulation of endothelial cell proliferation down-regulation of endothelial cell proliferation downregulation of endothelial cell proliferation inhibition of endothelial cell proliferation biological_process GO:0001937 negative regulation of endothelial cell proliferation Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation. GOC:add Any process that activates or increases the rate or extent of endothelial cell proliferation. up regulation of endothelial cell proliferation up-regulation of endothelial cell proliferation upregulation of endothelial cell proliferation activation of endothelial cell proliferation stimulation of endothelial cell proliferation biological_process GO:0001938 positive regulation of endothelial cell proliferation Any process that activates or increases the rate or extent of endothelial cell proliferation. GOC:add The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism. biological_process vascular system development GO:0001944 vasculature development The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism. GOC:dph UBERON:0002409 A developmental process, independent of morphogenetic (shape) change, that is required for a blood vessel to attain its fully functional state. biological_process GO:0001955 blood vessel maturation A developmental process, independent of morphogenetic (shape) change, that is required for a blood vessel to attain its fully functional state. GOC:dph Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter. up regulation of neurotransmitter secretion up-regulation of neurotransmitter secretion upregulation of neurotransmitter secretion activation of neurotransmitter secretion stimulation of neurotransmitter secretion biological_process GO:0001956 positive regulation of neurotransmitter secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter. GOC:hjd Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells. Wikipedia:Intramembranous_ossification dermal ossification biological_process intramembranous bone ossification GO:0001957 An instance of intramembranous ossification may also be classified as metaplastic; the former classifies based on tissue type location, and the latter based on mechanism/cell division. intramembranous ossification Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells. ISBN:0878932437 dermal ossification GO_REF:0000034 intramembranous bone ossification GOC:cjm The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube. epithelium morphogenesis biological_process GO:0002009 morphogenesis of an epithelium The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube. GOC:dph GOC:jl GOC:tb ISBN:0198506732 The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells. biological_process GO:0002011 morphogenesis of an epithelial sheet The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells. GOC:jl Any process that modulates the frequency or rate of heart contraction. cardiac chronotropy regulation of heart contraction rate regulation of rate of heart contraction biological_process GO:0002027 regulation of heart rate Any process that modulates the frequency or rate of heart contraction. GOC:dph GOC:tb PMID:10358008 cardiac chronotropy GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. regulation of Na+ transport regulation of sodium transport biological_process GO:0002028 regulation of sodium ion transport Any process that modulates the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph Any process that activates or increases the rate of neuroblast proliferation. up regulation of neuroblast proliferation up-regulation of neuroblast proliferation upregulation of neuroblast proliferation activation of neuroblast proliferation stimulation of neuroblast proliferation biological_process GO:0002052 positive regulation of neuroblast proliferation Any process that activates or increases the rate of neuroblast proliferation. GOC:dph The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells. up regulation of mesenchymal cell proliferation up-regulation of mesenchymal cell proliferation upregulation of mesenchymal cell proliferation activation of mesenchymal cell proliferation stimulation of mesenchymal cell proliferation biological_process GO:0002053 positive regulation of mesenchymal cell proliferation The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells. GOC:dph The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage. biological_process GO:0002062 chondrocyte differentiation The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage. GOC:dph The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate. biological_process GO:0002063 chondrocyte development The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate. GOC:dph The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface. biological_process GO:0002064 epithelial cell development The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. biological_process GO:0002065 columnar/cuboidal epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. GOC:dph The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell over time, from its formation to the mature structure. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. biological_process GO:0002066 columnar/cuboidal epithelial cell development The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell over time, from its formation to the mature structure. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland. biological_process GO:0002067 glandular epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland. GOC:dph The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland. biological_process GO:0002068 glandular epithelial cell development The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland. GOC:dph The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell to attain its fully functional state. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. biological_process GO:0002069 columnar/cuboidal epithelial cell maturation The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell to attain its fully functional state. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. GOC:dph The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface. biological_process GO:0002070 epithelial cell maturation The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface. GOC:dph The developmental process, independent of morphogenetic (shape) change, that is required for a glandular epithelial cell to attain its fully functional state. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland. biological_process GO:0002071 glandular epithelial cell maturation The developmental process, independent of morphogenetic (shape) change, that is required for a glandular epithelial cell to attain its fully functional state. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland. GOC:dph The invagination of the optic vesicle to form two-walled indentations, the optic cups, that will go on to form the retina. This process begins with the optic vesicle becoming a two-walled structure and its subsequent shape changes. It does not include the fate commitment of cells to become the pigmented retina and the neural retina. An example of this process is found in Mus musculus. optic cup morphogenesis involved in camera-style eye development biological_process GO:0002072 optic cup morphogenesis involved in camera-type eye development The invagination of the optic vesicle to form two-walled indentations, the optic cups, that will go on to form the retina. This process begins with the optic vesicle becoming a two-walled structure and its subsequent shape changes. It does not include the fate commitment of cells to become the pigmented retina and the neural retina. An example of this process is found in Mus musculus. GOC:dph GOC:mtg_sensu GOC:sdb_2009 GOC:tb ISBN:0878932437 Any process that prevents the activation of neuroepithelial cell differentiation. Neuroepithelial cell differentiation is the process in which epiblast cells acquire specialized features of neuroepithelial cells. negative regulation of neural plate formation repression of premature neural plate formation biological_process GO:0002085 inhibition of neuroepithelial cell differentiation Any process that prevents the activation of neuroepithelial cell differentiation. Neuroepithelial cell differentiation is the process in which epiblast cells acquire specialized features of neuroepithelial cells. GOC:dph PMID:16678814 negative regulation of neural plate formation GOC:dph GOC:tb repression of premature neural plate formation GOC:dph GOC:tb A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates. neurological control of breathing regulation of respiratory gaseous exchange by neurological system process biological_process GO:0002087 regulation of respiratory gaseous exchange by nervous system process A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates. GOC:dph GOC:tb PMID:12458206 neurological control of breathing GOC:dph GOC:tb The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus. lens development lens development in camera-style eye biological_process GO:0002088 lens development in camera-type eye The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus. GOC:dph ISBN:0582064333 The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus. lens morphogenesis lens morphogenesis in camera-style eye biological_process GO:0002089 lens morphogenesis in camera-type eye The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus. GOC:dph GOC:mtg_sensu The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. biological_process GO:0002119 nematode larval development The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. GOC:ems GOC:kmv The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. The larva is the early, immature form of an that at birth or hatching is fundamentally unlike its parent and must metamorphose before assuming the adult characters. biological_process GO:0002164 larval development The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. The larva is the early, immature form of an that at birth or hatching is fundamentally unlike its parent and must metamorphose before assuming the adult characters. GOC:jid ISBN:0877795088 The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. haematopoietic progenitor cell differentiation haemopoietic progenitor cell differentiation hemopoietic progenitor cell differentiation biological_process GO:0002244 hematopoietic progenitor cell differentiation The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. GOC:add GOC:rl ISBN:0781735149 PMID:16551251 An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues. immune response in organ or tissue biological_process GO:0002251 organ or tissue specific immune response An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues. GOC:jal GO_REF:0000022 Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation. https://github.com/geneontology/go-ontology/issues/18737 biological_process GO:0002252 immune effector process Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation. GOC:add GO_REF:0000022 ISBN:0781735149 The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. biological_process GO:0002262 myeloid cell homeostasis The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. CL:0000763 GOC:add The process in which a precursor cell type acquires the specialized features of a myeloid progenitor cell. Myeloid progenitor cells include progenitor cells for any of the myeloid lineages. biological_process GO:0002318 myeloid progenitor cell differentiation The process in which a precursor cell type acquires the specialized features of a myeloid progenitor cell. Myeloid progenitor cells include progenitor cells for any of the myeloid lineages. GOC:add PMID:16551264 Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. Wikipedia:Immune_system biological_process GO:0002376 Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. GOC:add GO_REF:0000022 An immune response taking place in the liver. biological_process GO:0002384 hepatic immune response An immune response taking place in the liver. GOC:jal GO_REF:0000022 ISBN:0781735149 Any process involved in the carrying out of an immune response by a leukocyte. GO:0019723 GO:0042087 immune cell effector process immune cell mediated immunity leucocyte immune effector process leucocyte mediated immunity leukocyte immune effector process biological_process cell-mediated immune response cellular immune response GO:0002443 leukocyte mediated immunity Any process involved in the carrying out of an immune response by a leukocyte. GOC:add GO_REF:0000022 ISBN:0781735149 Any process involved in the carrying out of an immune response by a myeloid leukocyte. myeloid leucocyte immune effector process myeloid leucocyte mediated immunity myeloid leukocyte immune effector process biological_process GO:0002444 myeloid leukocyte mediated immunity Any process involved in the carrying out of an immune response by a myeloid leukocyte. GOC:add GO_REF:0000022 ISBN:0781735149 The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. biological_process GO:0002520 immune system development The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. GOC:add GOC:dph The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. immune cell differentiation leucocyte differentiation biological_process GO:0002521 leukocyte differentiation The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. CL:0000738 GOC:add PMID:16551264 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. myeloid leucocyte differentiation biological_process GO:0002573 myeloid leukocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. GOC:add PMID:16551251 Any process that modulates the frequency, rate, or extent of an immune system process. biological_process GO:0002682 regulation of immune system process Any process that modulates the frequency, rate, or extent of an immune system process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. down regulation of immune system process down-regulation of immune system process downregulation of immune system process inhibition of immune system process biological_process GO:0002683 negative regulation of immune system process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune system process. up regulation of immune system process up-regulation of immune system process upregulation of immune system process activation of immune system process stimulation of immune system process biological_process GO:0002684 positive regulation of immune system process Any process that activates or increases the frequency, rate, or extent of an immune system process. GOC:add Any process that modulates the frequency, rate, or extent of an immune effector process. biological_process GO:0002697 regulation of immune effector process Any process that modulates the frequency, rate, or extent of an immune effector process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process. down regulation of immune effector process down-regulation of immune effector process downregulation of immune effector process inhibition of immune effector process biological_process GO:0002698 negative regulation of immune effector process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune effector process. up regulation of immune effector process up-regulation of immune effector process upregulation of immune effector process activation of immune effector process stimulation of immune effector process biological_process GO:0002699 positive regulation of immune effector process Any process that activates or increases the frequency, rate, or extent of an immune effector process. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity. regulation of immune cell mediated immunity regulation of leucocyte mediated immunity biological_process GO:0002703 regulation of leukocyte mediated immunity Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity. down regulation of leukocyte mediated immunity down-regulation of leukocyte mediated immunity downregulation of leukocyte mediated immunity negative regulation of immune cell mediated immunity negative regulation of leucocyte mediated immunity inhibition of leukocyte mediated immunity biological_process GO:0002704 negative regulation of leukocyte mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity. positive regulation of immune cell mediated immunity positive regulation of leucocyte mediated immunity up regulation of leukocyte mediated immunity up-regulation of leukocyte mediated immunity upregulation of leukocyte mediated immunity activation of leukocyte mediated immunity stimulation of leukocyte mediated immunity biological_process GO:0002705 positive regulation of leukocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation. biological_process GO:0002761 regulation of myeloid leukocyte differentiation Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation. down regulation of myeloid leukocyte differentiation down-regulation of myeloid leukocyte differentiation downregulation of myeloid leukocyte differentiation inhibition of myeloid leukocyte differentiation biological_process GO:0002762 negative regulation of myeloid leukocyte differentiation Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation. up regulation of myeloid leukocyte differentiation up-regulation of myeloid leukocyte differentiation upregulation of myeloid leukocyte differentiation activation of myeloid leukocyte differentiation stimulation of myeloid leukocyte differentiation biological_process GO:0002763 positive regulation of myeloid leukocyte differentiation Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add The controlled release of a peptide from a cell or a tissue. biological_process GO:0002790 peptide secretion The controlled release of a peptide from a cell or a tissue. GOC:add Any process that modulates the frequency, rate, or extent of peptide secretion. biological_process GO:0002791 regulation of peptide secretion Any process that modulates the frequency, rate, or extent of peptide secretion. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. down regulation of peptide secretion down-regulation of peptide secretion downregulation of peptide secretion inhibition of peptide secretion biological_process GO:0002792 negative regulation of peptide secretion Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. GOC:add Any process that activates or increases the frequency, rate, or extent of peptide secretion. up regulation of peptide secretion up-regulation of peptide secretion upregulation of peptide secretion activation of peptide secretion stimulation of peptide secretion biological_process GO:0002793 positive regulation of peptide secretion Any process that activates or increases the frequency, rate, or extent of peptide secretion. GOC:add Any process that modulates the frequency, rate, or extent of a response to biotic stimulus. biological_process GO:0002831 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to biotic stimulus Any process that modulates the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus. down regulation of response to biotic stimulus down-regulation of response to biotic stimulus downregulation of response to biotic stimulus inhibition of response to biotic stimulus biological_process GO:0002832 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to biotic stimulus Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus. up regulation of response to biotic stimulus up-regulation of response to biotic stimulus upregulation of response to biotic stimulus activation of response to biotic stimulus stimulation of response to biotic stimulus biological_process GO:0002833 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to biotic stimulus Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that modulates the frequency, rate, or extent of myeloid leukocyte mediated immunity. biological_process GO:0002886 regulation of myeloid leukocyte mediated immunity Any process that modulates the frequency, rate, or extent of myeloid leukocyte mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte mediated immunity. down regulation of myeloid leukocyte mediated immunity down-regulation of myeloid leukocyte mediated immunity downregulation of myeloid leukocyte mediated immunity inhibition of myeloid leukocyte mediated immunity biological_process GO:0002887 negative regulation of myeloid leukocyte mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte mediated immunity. up regulation of myeloid leukocyte mediated immunity up-regulation of myeloid leukocyte mediated immunity upregulation of myeloid leukocyte mediated immunity activation of myeloid leukocyte mediated immunity stimulation of myeloid leukocyte mediated immunity biological_process GO:0002888 positive regulation of myeloid leukocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte mediated immunity. GOC:add The process whose specific outcome is the progression of a tendon sheath over time, from its formation to the mature structure. A tendon sheath is a layer of membrane around a tendon. It permits the tendon to move. hjd 2012-04-23T02:11:22Z biological_process GO:0002932 tendon sheath development The process whose specific outcome is the progression of a tendon sheath over time, from its formation to the mature structure. A tendon sheath is a layer of membrane around a tendon. It permits the tendon to move. PMID:20696843 The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment. biological_process pattern formation GO:0003002 regionalization The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment. GOC:dph GOC:isa_complete pattern formation GOC:dph A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process GO:0003006 developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. GOC:dph GOC:isa_complete puberty GOC:dph reproductive developmental process GOC:dph GOC:tb The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. biological_process cardiac morphogenesis GO:0003007 heart morphogenesis The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GOC:dph GOC:isa_complete A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. organ system process biological_process GO:0003008 system process A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. GOC:mtg_cardio A process in which force is generated within skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control. biological_process GO:0003009 skeletal muscle contraction A process in which force is generated within skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control. GOC:mtg_cardio GOC:mtg_muscle A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers. biological_process muscle physiological process GO:0003012 muscle system process A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers. GOC:mtg_cardio A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. Wikipedia:Circulatory_system biological_process GO:0003013 circulatory system process A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. GOC:mtg_cardio A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). excretory system process biological_process kidney system process GO:0003014 renal system process A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). GOC:cjm GOC:mtg_cardio GOC:mtg_kidney_jan10 A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. biological_process cardiac process GO:0003015 heart process A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GOC:mtg_cardio A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange. GO:0010802 respiratory gaseous exchange biological_process GO:0003016 respiratory system process A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange. GOC:dph GOC:mtg_cardio GOC:tb The series of events in which an oxygen stimulus is received by a cell and converted into a molecular signal. biological_process GO:0003032 detection of oxygen The series of events in which an oxygen stimulus is received by a cell and converted into a molecular signal. GOC:mtg_cardio The directed movement of sodium ions (Na+) by the renal system. biological_process GO:0003096 renal sodium ion transport The directed movement of sodium ions (Na+) by the renal system. GOC:mtg_cardio Any process that mediates the transfer of information from mesodermal cells to endodermal cells. tb 2009-09-22T03:07:34Z mesodermal-endodermal cell signalling biological_process GO:0003131 mesodermal-endodermal cell signaling Any process that mediates the transfer of information from mesodermal cells to endodermal cells. GOC:mtg_heart mesodermal-endodermal cell signalling GOC:mah Any process that mediates the transfer of information from endodermal cells to mesodermal cells. tb 2009-09-22T03:10:29Z endodermal-mesodermal cell signalling biological_process GO:0003133 endodermal-mesodermal cell signaling Any process that mediates the transfer of information from endodermal cells to mesodermal cells. GOC:mtg_heart endodermal-mesodermal cell signalling GOC:mah The process in which the anatomical structures of the cardiogenic plate are generated and organized. The cardiogenic plate is the first recognizable structure derived from the heart field. tb 2009-09-22T04:12:18Z cardiac crescent morphogenesis biological_process GO:0003142 cardiogenic plate morphogenesis The process in which the anatomical structures of the cardiogenic plate are generated and organized. The cardiogenic plate is the first recognizable structure derived from the heart field. GOC:mtg_heart cardiac crescent morphogenesis GOC:mtg_heart The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart. tb 2009-09-22T04:21:17Z biological_process GO:0003143 embryonic heart tube morphogenesis The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart. GOC:mtg_heart The process that gives rise to the embryonic heart tube. This process pertains to the initial formation of a structure from unspecified parts. The embryonic heart tube is an epithelial tube that will give rise to the mature heart. tb 2009-09-22T04:22:34Z biological_process GO:0003144 embryonic heart tube formation The process that gives rise to the embryonic heart tube. This process pertains to the initial formation of a structure from unspecified parts. The embryonic heart tube is an epithelial tube that will give rise to the mature heart. GOC:mtg_heart The process that gives rise to the embryonic heart tube by the cells of the heart field along a linear axis. tb 2009-09-22T04:26:03Z biological_process GO:0003145 embryonic heart tube formation via epithelial folding The process that gives rise to the embryonic heart tube by the cells of the heart field along a linear axis. GOC:mtg_heart The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract. tb 2009-09-22T07:51:01Z biological_process GO:0003148 outflow tract septum morphogenesis The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract. GOC:mtg_heart The process in which the membranous septum is generated and organized. The membranous septum is the upper part of ventricular septum. tb 2009-09-22T07:51:41Z biological_process GO:0003149 membranous septum morphogenesis The process in which the membranous septum is generated and organized. The membranous septum is the upper part of ventricular septum. GOC:mtg_heart The process in which the muscular septum is generated and organized. The muscular septum is the lower part of the ventricular septum. tb 2009-09-22T07:53:28Z biological_process GO:0003150 muscular septum morphogenesis The process in which the muscular septum is generated and organized. The muscular septum is the lower part of the ventricular septum. GOC:mtg_heart The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries. tb 2009-09-22T07:59:24Z biological_process GO:0003151 outflow tract morphogenesis The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries. GOC:mtg_heart UBERON:0004145 The morphogenetic process in which an epithelial sheet bends along a linear axis, contributing to embryonic heart tube formation. tb 2009-09-23T10:10:24Z biological_process GO:0003152 morphogenesis of an epithelial fold involved in embryonic heart tube formation The morphogenetic process in which an epithelial sheet bends along a linear axis, contributing to embryonic heart tube formation. GOC:mtg_heart Any process that modulates the rate, frequency or extent of animal organ formation. Organ formation is the process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. tb 2009-09-30T11:21:09Z biological_process GO:0003156 regulation of animal organ formation Any process that modulates the rate, frequency or extent of animal organ formation. Organ formation is the process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. GOC:dph GOC:mtg_heart GOC:tb The process whose specific outcome is the progression of the endocardium over time, from its formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. dph 2009-10-01T12:42:27Z biological_process GO:0003157 endocardium development The process whose specific outcome is the progression of the endocardium over time, from its formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. GOC:mtg_heart The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells. dph 2009-10-01T12:50:57Z biological_process GO:0003158 endothelium development The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells. GOC:mtg_heart The process in which the anatomical structure of an endothelium is generated and organized. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells. dph 2009-10-01T01:34:06Z biological_process GO:0003159 morphogenesis of an endothelium The process in which the anatomical structure of an endothelium is generated and organized. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells. GOC:mtg_heart The process in which the anatomical structure of the endocardium is generated and organized. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. dph 2009-10-01T01:37:26Z biological_process GO:0003160 endocardium morphogenesis The process in which the anatomical structure of the endocardium is generated and organized. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. GOC:mtg_heart The process whose specific outcome is the progression of the cardiac conduction system over time, from its formation to the mature structure. The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat. dph 2009-10-01T01:57:16Z cardiac impulse conducting system development heart conduction system development biological_process GO:0003161 cardiac conduction system development The process whose specific outcome is the progression of the cardiac conduction system over time, from its formation to the mature structure. The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat. GOC:mtg_heart cardiac impulse conducting system development GOC:mtg_heart heart conduction system development GOC:mtg_heart The process whose specific outcome is the progression of the atrioventricular (AV) node over time, from its formation to the mature structure. The AV node is part of the cardiac conduction system that controls the timing of ventricle contraction by receiving electrical signals from the sinoatrial (SA) node and relaying them to the His-Purkinje system. dph 2009-10-01T02:05:13Z AV node development biological_process GO:0003162 atrioventricular node development The process whose specific outcome is the progression of the atrioventricular (AV) node over time, from its formation to the mature structure. The AV node is part of the cardiac conduction system that controls the timing of ventricle contraction by receiving electrical signals from the sinoatrial (SA) node and relaying them to the His-Purkinje system. GOC:mtg_heart AV node development GOC:mtg_heart The process whose specific outcome is the progression of the sinoatrial (SA) node over time, from its formation to the mature structure. The SA node is part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node. dph 2009-10-01T02:06:09Z SA node development SAN development sinus node development biological_process GO:0003163 sinoatrial node development The process whose specific outcome is the progression of the sinoatrial (SA) node over time, from its formation to the mature structure. The SA node is part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node. GOC:mtg_heart SA node development GOC:mtg_heart SAN development GOC:BHF GOC:mtg_cardiac_conduct_nov11 sinus node development GOC:BHF GOC:mtg_cardiac_conduct_nov11 The process whose specific outcome is the progression of the His-Purkinje system over time, from its formation to the mature structure. The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles. dph 2009-10-01T02:07:12Z biological_process GO:0003164 His-Purkinje system development The process whose specific outcome is the progression of the His-Purkinje system over time, from its formation to the mature structure. The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles. GOC:mtg_heart The process whose specific outcome is the progression of a Purkinje myocyte over time, from its formation to the mature structure. The Purkinje myocyte (also known as cardiac Purkinje fiber) is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle. dph 2009-10-01T02:07:50Z cardiac Purkinje fiber development biological_process GO:0003165 Purkinje myocyte development The process whose specific outcome is the progression of a Purkinje myocyte over time, from its formation to the mature structure. The Purkinje myocyte (also known as cardiac Purkinje fiber) is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle. GOC:mtg_cardiac_conduct_nov11 GOC:mtg_heart The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a Purkinje myocyte (also known as cardiac Purkinje fiber cell). These cells are specialized cardiomyocytes that receive signals from the bundle of His and innervate the ventricular cardiac muscle. dph 2009-10-01T02:49:54Z cardiac Purkinje fiber cell differentiation biological_process GO:0003168 Purkinje myocyte differentiation The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a Purkinje myocyte (also known as cardiac Purkinje fiber cell). These cells are specialized cardiomyocytes that receive signals from the bundle of His and innervate the ventricular cardiac muscle. GOC:mtg_cardiac_conduct_nov11 GOC:mtg_heart The process in which the anatomical structures of veins of the heart are generated and organized. dph 2009-10-08T10:45:41Z biological_process GO:0003169 coronary vein morphogenesis The process in which the anatomical structures of veins of the heart are generated and organized. GOC:mtg_heart The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. dph 2009-10-08T01:17:43Z biological_process GO:0003197 endocardial cushion development The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. GOC:mtg_heart The process in which the anatomical structure of the endocardial cushion is generated and organized. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. dph 2009-10-08T01:43:22Z biological_process GO:0003203 endocardial cushion morphogenesis The process in which the anatomical structure of the endocardial cushion is generated and organized. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. GOC:mtg_heart The progression of the cardiac skeleton over time, from its formation to the mature structure. The cardiac skeleton is a specialized extracellular matrix that separates the atria from the ventricles and provides physical support for the heart. dph 2009-10-13T09:05:04Z heart fibrous skeleton development biological_process GO:0003204 cardiac skeleton development The progression of the cardiac skeleton over time, from its formation to the mature structure. The cardiac skeleton is a specialized extracellular matrix that separates the atria from the ventricles and provides physical support for the heart. GOC:mtg_heart heart fibrous skeleton development GOC:mtg_heart The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart. dph 2009-10-13T09:11:18Z biological_process GO:0003205 cardiac chamber development The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart. GOC:mtg_heart The process in which a cardiac chamber is generated and organized. A cardiac chamber is an enclosed cavity within the heart. dph 2009-10-13T09:14:51Z heart chamber morphogenesis biological_process GO:0003206 cardiac chamber morphogenesis The process in which a cardiac chamber is generated and organized. A cardiac chamber is an enclosed cavity within the heart. GOC:mtg_heart heart chamber morphogenesis GOC:mtg_heart The developmental process pertaining to the initial formation of a cardiac chamber from unspecified parts. A cardiac chamber is an enclosed cavity within the heart. dph 2009-10-13T09:29:13Z heart chamber formation biological_process GO:0003207 cardiac chamber formation The developmental process pertaining to the initial formation of a cardiac chamber from unspecified parts. A cardiac chamber is an enclosed cavity within the heart. GOC:mtg_heart heart chamber formation GOC:mtg_heart The process in which the cardiac ventricle is generated and organized. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart. dph 2009-10-13T09:38:44Z biological_process GO:0003208 cardiac ventricle morphogenesis The process in which the cardiac ventricle is generated and organized. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart. GOC:mtg_heart The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle. dph 2009-10-13T09:39:44Z biological_process GO:0003209 cardiac atrium morphogenesis The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle. GOC:mtg_heart The developmental process pertaining to the initial formation of a cardiac atrium from unspecified parts. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle. dph 2009-10-13T09:44:25Z biological_process GO:0003210 cardiac atrium formation The developmental process pertaining to the initial formation of a cardiac atrium from unspecified parts. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle. GOC:mtg_heart The developmental process pertaining to the initial formation of a cardiac ventricle from unspecified parts. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart. dph 2009-10-13T09:46:27Z biological_process GO:0003211 cardiac ventricle formation The developmental process pertaining to the initial formation of a cardiac ventricle from unspecified parts. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart. GOC:mtg_heart The process in which the left cardiac atrium is generated and organized. dph 2009-10-13T09:48:16Z biological_process GO:0003212 cardiac left atrium morphogenesis The process in which the left cardiac atrium is generated and organized. GOC:mtg_heart The process in which the right cardiac atrium is generated and organized. dph 2009-10-13T09:49:03Z biological_process GO:0003213 cardiac right atrium morphogenesis The process in which the right cardiac atrium is generated and organized. GOC:mtg_heart The process in which the left cardiac ventricle is generated and organized. dph 2009-10-13T09:50:08Z biological_process GO:0003214 cardiac left ventricle morphogenesis The process in which the left cardiac ventricle is generated and organized. GOC:mtg_heart The process in which the right cardiac ventricle is generated and organized. dph 2009-10-13T09:50:57Z biological_process GO:0003215 cardiac right ventricle morphogenesis The process in which the right cardiac ventricle is generated and organized. GOC:mtg_heart The developmental process pertaining to the initial formation of a left cardiac atrium from unspecified parts. dph 2009-10-13T09:52:31Z biological_process GO:0003216 cardiac left atrium formation The developmental process pertaining to the initial formation of a left cardiac atrium from unspecified parts. GOC:mtg_heart The developmental process pertaining to the initial formation of a cardiac right atrium from unspecified parts. dph 2009-10-13T09:53:12Z biological_process GO:0003217 cardiac right atrium formation The developmental process pertaining to the initial formation of a cardiac right atrium from unspecified parts. GOC:mtg_heart The developmental process pertaining to the initial formation of a left cardiac ventricle from unspecified parts. dph 2009-10-13T09:54:33Z biological_process GO:0003218 cardiac left ventricle formation The developmental process pertaining to the initial formation of a left cardiac ventricle from unspecified parts. GOC:mtg_heart The developmental process pertaining to the initial formation of a right cardiac ventricle from unspecified parts. dph 2009-10-13T09:55:38Z biological_process GO:0003219 cardiac right ventricle formation The developmental process pertaining to the initial formation of a right cardiac ventricle from unspecified parts. GOC:mtg_heart The process in which the anatomical structures of left cardiac ventricle muscle are generated and organized. dph 2009-10-13T10:18:05Z left ventricular myocardium morphogenesis biological_process GO:0003220 left ventricular cardiac muscle tissue morphogenesis The process in which the anatomical structures of left cardiac ventricle muscle are generated and organized. GOC:mtg_heart left ventricular myocardium morphogenesis GOC:mtg_heart The process in which the anatomical structures of the right cardiac ventricle muscle are generated and organized. dph 2009-10-13T10:26:33Z right ventricle myocardium morphogenesis biological_process GO:0003221 right ventricular cardiac muscle tissue morphogenesis The process in which the anatomical structures of the right cardiac ventricle muscle are generated and organized. GOC:mtg_heart right ventricle myocardium morphogenesis GOC:mtg_heart The process in which the anatomical structures of the trabecular cardiac ventricle muscle are generated and organized. dph 2009-10-13T10:33:00Z biological_process trabecula carnea morphogenesis GO:0003222 ventricular trabecula myocardium morphogenesis The process in which the anatomical structures of the trabecular cardiac ventricle muscle are generated and organized. GOC:mtg_heart trabecula carnea morphogenesis GOC:dph The process in which the anatomical structures of cardiac left ventricular trabecular myocardium are generated and organized. dph 2009-10-13T10:45:09Z biological_process GO:0003225 left ventricular trabecular myocardium morphogenesis The process in which the anatomical structures of cardiac left ventricular trabecular myocardium are generated and organized. GOC:mtg_heart The process in which the anatomical structures of the right ventricular myocardium are generated and organized. dph 2009-10-13T10:50:59Z biological_process GO:0003227 right ventricular trabecular myocardium morphogenesis The process in which the anatomical structures of the right ventricular myocardium are generated and organized. GOC:mtg_heart The process whose specific outcome is the progression of cardiac muscle of the atrium over time, from its formation to the mature structure. https://github.com/geneontology/go-ontology/issues/22614 dph 2009-10-13T10:53:18Z atrial myocardium development biological_process GO:0003228 atrial cardiac muscle tissue development The process whose specific outcome is the progression of cardiac muscle of the atrium over time, from its formation to the mature structure. GOC:mtg_heart atrial myocardium development GOC:mtg_heart The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure. dph 2009-10-13T10:56:01Z ventricular myocardium development biological_process GO:0003229 ventricular cardiac muscle tissue development The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure. GOC:mtg_heart ventricular myocardium development GOC:mtg_heart The process whose specific outcome is the progression of a cardiac atrium over time, from its formation to the mature structure. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle. dph 2009-10-13T11:02:07Z biological_process GO:0003230 cardiac atrium development The process whose specific outcome is the progression of a cardiac atrium over time, from its formation to the mature structure. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle. GOC:mtg_heart The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart. dph 2009-10-13T11:03:16Z biological_process GO:0003231 cardiac ventricle development The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart. GOC:mtg_heart The progression of the sinus venosus over time, from its formation to the mature structure. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart. dph 2009-10-13T11:12:34Z biological_process GO:0003235 sinus venosus development The progression of the sinus venosus over time, from its formation to the mature structure. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart. GOC:mtg_heart The process in which the sinus venosus is generated and organized. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart. dph 2009-10-13T11:16:52Z biological_process GO:0003236 sinus venosus morphogenesis The process in which the sinus venosus is generated and organized. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart. GOC:mtg_heart The developmental process pertaining to the initial formation of the sinus venosus from unspecified parts. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart. dph 2009-10-13T11:18:34Z biological_process GO:0003237 sinus venosus formation The developmental process pertaining to the initial formation of the sinus venosus from unspecified parts. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart. GOC:mtg_heart Developmental growth that contributes to the shaping of the heart. dph 2009-10-13T11:28:46Z biological_process GO:0003241 growth involved in heart morphogenesis Developmental growth that contributes to the shaping of the heart. GOC:mtg_heart The developmental growth of cardiac muscle tissue that contributes to the shaping of the heart. dph 2009-10-13T11:44:21Z biological_process GO:0003245 cardiac muscle tissue growth involved in heart morphogenesis The developmental growth of cardiac muscle tissue that contributes to the shaping of the heart. GOC:mtg_heart The increase in heart capillaries that accompanies physiological hypertrophy of cardiac muscle. dph 2009-10-13T11:53:12Z biological_process GO:0003248 heart capillary growth The increase in heart capillaries that accompanies physiological hypertrophy of cardiac muscle. GOC:mtg_heart The developmental process pertaining to the initial formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. dph 2009-10-20T08:53:19Z biological_process GO:0003272 endocardial cushion formation The developmental process pertaining to the initial formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. GOC:mtg_heart PMID:15797462 The orderly movement of a cell from one site to another that will contribute to the formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. dph 2009-10-20T09:08:44Z biological_process GO:0003273 cell migration involved in endocardial cushion formation The orderly movement of a cell from one site to another that will contribute to the formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. GOC:mtg_heart Any apoptotic process that contributes to the shaping of the outflow tract. The outflow tract is the portion of the heart through which blood flows into the arteries. dph 2009-10-20T09:30:01Z apoptosis involved in outflow tract morphogenesis biological_process GO:0003275 apoptotic process involved in outflow tract morphogenesis Any apoptotic process that contributes to the shaping of the outflow tract. The outflow tract is the portion of the heart through which blood flows into the arteries. GOC:mtg_apoptosis GOC:mtg_heart Any apoptotic process that contributes to the shaping of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. dph 2009-10-20T09:37:03Z apoptosis involved in endocardial cushion morphogenesis biological_process GO:0003277 apoptotic process involved in endocardial cushion morphogenesis Any apoptotic process that contributes to the shaping of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves. GOC:mtg_apoptosis GOC:mtg_heart Any apoptotic process that contributes to the shaping of the heart. dph 2009-10-20T09:40:22Z apoptosis involved in heart morphogenesis biological_process GO:0003278 apoptotic process involved in heart morphogenesis Any apoptotic process that contributes to the shaping of the heart. GOC:mtg_apoptosis GOC:mtg_heart The progression of a cardiac septum over time, from its initial formation to the mature structure. dph 2009-10-20T09:45:13Z heart septum development biological_process GO:0003279 cardiac septum development The progression of a cardiac septum over time, from its initial formation to the mature structure. GOC:mtg_heart heart septum development GOC:mtg_heart The progression of the ventricular septum over time from its formation to the mature structure. dph 2009-10-20T10:04:51Z interventricular septum development septum inferius development biological_process GO:0003281 ventricular septum development The progression of the ventricular septum over time from its formation to the mature structure. GOC:mtg_heart interventricular septum development GOC:mtg_heart septum inferius development GOC:mtg_heart The progression of the atrial septum over time, from its initial formation to the mature structure. dph 2009-10-20T10:10:38Z biological_process GO:0003283 atrial septum development The progression of the atrial septum over time, from its initial formation to the mature structure. GOC:mtg_heart The process in which an endocardial cushion cell becomes a cell of a cardiac septum. dph 2009-10-20T11:03:46Z biological_process GO:0003292 cardiac septum cell differentiation The process in which an endocardial cushion cell becomes a cell of a cardiac septum. GOC:mtg_heart The enlargement or overgrowth of all or part of a muscle organ or tissue due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development. dph 2009-10-22T09:24:51Z biological_process GO:0003298 physiological muscle hypertrophy The enlargement or overgrowth of all or part of a muscle organ or tissue due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development. GOC:mtg_heart The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division. dph 2009-10-22T10:33:56Z biological_process GO:0003300 cardiac muscle hypertrophy The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division. GOC:mtg_heart The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division. This process contributes to the developmental growth of the heart. dph 2009-10-22T10:38:10Z biological_process GO:0003301 physiological cardiac muscle hypertrophy The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division. This process contributes to the developmental growth of the heart. GOC:BHF GOC:mtg_cardiac_conduct_nov11 GOC:mtg_heart The process in which relatively unspecialized cells acquire specialized structural and/or functional features of a type B pancreatic cell. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin. dph 2009-10-26T09:27:23Z pancreatic B cell differentiation pancreatic beta cell differentiation biological_process GO:0003309 type B pancreatic cell differentiation The process in which relatively unspecialized cells acquire specialized structural and/or functional features of a type B pancreatic cell. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin. CL:0000169 GOC:dph PMID:11076772 pancreatic B cell differentiation GOC:mah pancreatic beta cell differentiation GOC:dph The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic A cell. A pancreatic A cell is a cell in the pancreas that secretes glucagon. dph 2009-10-26T09:28:05Z pancreatic alpha cell differentiation biological_process GO:0003310 pancreatic A cell differentiation The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic A cell. A pancreatic A cell is a cell in the pancreas that secretes glucagon. GOC:dph PMID:11076772 pancreatic alpha cell differentiation GOC:dph The process in which relatively unspecialized cells acquire specialized structural and functional features that characterize a pancreatic delta cell. A delta cell is a cell of the pancreas that produces somatostatin. dph 2009-10-26T09:30:27Z pancreatic delta cell differentiation biological_process GO:0003311 pancreatic D cell differentiation The process in which relatively unspecialized cells acquire specialized structural and functional features that characterize a pancreatic delta cell. A delta cell is a cell of the pancreas that produces somatostatin. GOC:dph PMID:11076772 pancreatic delta cell differentiation GOC:dph The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic polypeptide-producing cell. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide. dph 2009-10-26T09:32:32Z pancreatic polypeptide-producing cell differentiation biological_process GO:0003312 pancreatic PP cell differentiation The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic polypeptide-producing cell. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide. GOC:dph PMID:11076772 pancreatic polypeptide-producing cell differentiation GOC:dph The progression of the heart rudiment over time, from its initial formation to the mature structure. The heart rudiment is a cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. dph 2009-10-27T08:32:40Z heart cone development biological_process GO:0003313 heart rudiment development The progression of the heart rudiment over time, from its initial formation to the mature structure. The heart rudiment is a cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GOC:mtg_heart heart cone development GOC:mtg_heart The process in which the anatomical structures of the heart rudiment are generated and organized. dph 2009-10-27T08:38:04Z heart cone morphogenesis biological_process GO:0003314 heart rudiment morphogenesis The process in which the anatomical structures of the heart rudiment are generated and organized. GOC:mtg_heart heart cone morphogenesis GOC:mtg_heart The developmental process pertaining to the initial formation of the heart rudiment. dph 2009-10-27T08:43:37Z heart cone formation biological_process GO:0003315 heart rudiment formation The developmental process pertaining to the initial formation of the heart rudiment. GOC:mtg_heart heart cone formation GOC:mtg_heart The process whose specific outcome is the progression of a pancreatic A cell over time, from its formation to the mature structure. A pancreatic A cell is a cell in the pancreas that secretes glucagon. dph 2009-11-02T08:13:55Z pancreatic alpha cell development biological_process GO:0003322 pancreatic A cell development The process whose specific outcome is the progression of a pancreatic A cell over time, from its formation to the mature structure. A pancreatic A cell is a cell in the pancreas that secretes glucagon. GOC:dph pancreatic alpha cell development GOC:dph The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin. dph 2009-11-02T08:20:11Z pancreatic B cell development pancreatic beta cell development biological_process GO:0003323 type B pancreatic cell development The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin. CL:0000169 GOC:dph pancreatic B cell development GOC:mah pancreatic beta cell development GOC:dph The process whose specific outcome is the progression of a pancreatic delta cell over time, from its formation to the mature structure. A delta cell is a cell of the pancreas that produces somatostatin. dph 2009-11-02T08:23:26Z pancreatic delta cell development biological_process GO:0003324 pancreatic D cell development The process whose specific outcome is the progression of a pancreatic delta cell over time, from its formation to the mature structure. A delta cell is a cell of the pancreas that produces somatostatin. GOC:dph pancreatic delta cell development GOC:dph The process whose specific outcome is the progression of a pancreatic PP cell over time, from its formation to the mature structure. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide. dph 2009-11-02T08:25:03Z biological_process GO:0003325 pancreatic PP cell development The process whose specific outcome is the progression of a pancreatic PP cell over time, from its formation to the mature structure. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide. GOC:dph The process in which an amino acid is transported across a membrane. dph 2009-11-02T02:36:11Z amino acid membrane transport biological_process GO:0003333 Note that this term is not intended for use in annotating lateral movement within membranes. amino acid transmembrane transport The process in which an amino acid is transported across a membrane. GOC:dph GOC:tb The progression of the proepicardium from its formation to the mature structure. The proepicardium is an outpouching of the septum transversum. dph 2009-12-01T10:30:17Z biological_process GO:0003342 proepicardium development The progression of the proepicardium from its formation to the mature structure. The proepicardium is an outpouching of the septum transversum. GOC:dph PMID:18722343 The progression of the septum transversum from its initial formation to the mature structure. The septum transversum is a portion of the trunk mesenchyme. dph 2009-12-01T10:40:17Z biological_process GO:0003343 septum transversum development The progression of the septum transversum from its initial formation to the mature structure. The septum transversum is a portion of the trunk mesenchyme. GOC:dph PMID:18722343 The process in which the anatomical structure of the pericardium is generated and organized. dph 2009-12-01T10:46:34Z biological_process GO:0003344 pericardium morphogenesis The process in which the anatomical structure of the pericardium is generated and organized. GOC:dph PMID:18722343 The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac endothelial cell. dph 2009-12-01T11:12:05Z biological_process GO:0003348 cardiac endothelial cell differentiation The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac endothelial cell. GOC:dph PMID:18722343 The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron, a neuron that secretes noradrenaline. dph 2009-12-03T10:34:30Z norepinephrine secreting neuron differentiation biological_process GO:0003357 noradrenergic neuron differentiation The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron, a neuron that secretes noradrenaline. GOC:dph norepinephrine secreting neuron differentiation GOC:dph The process whose specific outcome is the progression of a noradrenergic neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. dph 2009-12-03T10:38:37Z norepinephrine secreting neuron development biological_process GO:0003358 noradrenergic neuron development The process whose specific outcome is the progression of a noradrenergic neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. GOC:dph norepinephrine secreting neuron development GOC:dph The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord. dph 2009-12-03T10:47:20Z biological_process GO:0003360 brainstem development The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron that is part of the brainstem. dph 2009-12-03T10:53:30Z biological_process GO:0003361 noradrenergic neuron differentiation involved in brainstem development The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron that is part of the brainstem. GOC:dph The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell. dph 2009-12-08T04:50:41Z biological_process GO:0003365 establishment of cell polarity involved in ameboidal cell migration The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell. GOC:ascb_2009 GOC:dph GOC:tb Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell. dph 2009-12-08T05:42:46Z biological_process GO:0003371 establishment or maintenance of cytoskeleton polarity involved in ameboidal cell migration Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell. GOC:ascb_2009 GOC:dph GOC:tb The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell taking part in gastrulation. dph 2009-12-09T06:54:44Z biological_process GO:0003379 establishment of cell polarity involved in gastrulation cell migration The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell taking part in gastrulation. GOC:ascb_2009 GOC:dph GOC:tb Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell taking part in gastrulation. dph 2009-12-09T07:10:57Z biological_process GO:0003380 establishment or maintenance of cytoskeleton polarity involved in gastrulation Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell taking part in gastrulation. GOC:ascb_2009 GOC:dph GOC:tb The change in form that occurs when an epithelial cell progresses from it initial formation to its mature state, contributing to the process of gastrulation. dph 2009-12-09T07:18:53Z biological_process GO:0003381 epithelial cell morphogenesis involved in gastrulation The change in form that occurs when an epithelial cell progresses from it initial formation to its mature state, contributing to the process of gastrulation. GOC:ascb_2009 GOC:dph GOC:tb The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state. dph 2009-12-09T07:21:06Z biological_process GO:0003382 epithelial cell morphogenesis The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state. GOC:ascb_2009 GOC:dph GOC:tb The developmental process pertaining to the initial formation of the optic vesicle from the lateral wall of the forebrain. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup. dph 2009-12-21T01:42:37Z biological_process GO:0003403 optic vesicle formation The developmental process pertaining to the initial formation of the optic vesicle from the lateral wall of the forebrain. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup. GOC:ascb_2009 GOC:dph GOC:tb The developmental process pertaining to the formation and shaping of the optic vesicle. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup. dph 2009-12-21T01:54:34Z biological_process GO:0003404 optic vesicle morphogenesis The developmental process pertaining to the formation and shaping of the optic vesicle. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup. GOC:ascb_2009 GOC:dph GOC:tb The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells. dph 2009-12-21T02:15:14Z biological_process GO:0003407 neural retina development The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells. GOC:ascb_2009 GOC:dph GOC:tb Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another and contributes to the physical shaping or formation of the camera-type eye. dph 2009-12-21T03:04:27Z biological_process GO:0003411 cell motility involved in camera-type eye morphogenesis Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another and contributes to the physical shaping or formation of the camera-type eye. GOC:ascb_2009 GOC:dph GOC:tb The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage. dph 2009-12-22T08:39:58Z biological_process GO:0003413 chondrocyte differentiation involved in endochondral bone morphogenesis The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage. GOC:ascb_2009 GOC:dph GOC:tb The process in which the structures of a chondrocyte that will contribute to bone development are generated and organized. dph 2009-12-22T08:42:55Z biological_process GO:0003414 chondrocyte morphogenesis involved in endochondral bone morphogenesis The process in which the structures of a chondrocyte that will contribute to bone development are generated and organized. GOC:ascb_2009 GOC:dph GOC:tb The increase in size or mass of an endochondral bone that contributes to the shaping of the bone. dph 2009-12-22T08:52:55Z biological_process GO:0003416 endochondral bone growth The increase in size or mass of an endochondral bone that contributes to the shaping of the bone. GOC:ascb_2009 GOC:dph GOC:tb The progression of a chondrocyte over time from after its commitment to its mature state where the chondrocyte will contribute to the shaping of an endochondral bone. dph 2009-12-22T12:42:44Z biological_process GO:0003433 chondrocyte development involved in endochondral bone morphogenesis The progression of a chondrocyte over time from after its commitment to its mature state where the chondrocyte will contribute to the shaping of an endochondral bone. GOC:ascb_2009 GOC:dph GOC:tb A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular process GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GOC:vw ISBN:0198506732 enzyme activity GOC:dph GOC:tb Catalysis of the hydrolysis of ester linkages within nucleic acids. molecular_function GO:0004518 Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', and 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906' do not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. nuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids. ISBN:0198547684 Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. GO:0004537 Reactome:R-HSA-211247 Reactome:R-HSA-5685994 Reactome:R-HSA-6785986 deoxyribonuclease activity caspase-activated deoxyribonuclease activity molecular_function GO:0004536 DNA nuclease activity Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah ISBN:0198547684 Reactome:R-HSA-211247 Cleavage of DNA by DFF40 Reactome:R-HSA-5685994 Long-range resection of DNA DSBs by EXO1 or DNA2 Reactome:R-HSA-6785986 DNA nucleases unhook the interstrand crosslink (ICL) Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GO:0005478 Reactome:R-HSA-168313 Reactome:R-HSA-178215 molecular_function carrier GO:0005215 Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. transporter activity Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GOC:ai GOC:dgf Reactome:R-HSA-168313 Virion-associated M2 protein mediated ion infusion Reactome:R-HSA-178215 SMAD7:SMURF1 complex is exported to the cytosol Enables the transfer of amines, including polyamines, from one side of a membrane to the other. Amines are organic compounds that are weakly basic in character and contain an amino (-NH2) or substituted amino group. GO:0005279 amine/amide/polyamine channel activity amine/polyamine transmembrane transporter activity amino acid-polyamine transmembrane transporter activity molecular_function GO:0005275 amine transmembrane transporter activity Enables the transfer of amines, including polyamines, from one side of a membrane to the other. Amines are organic compounds that are weakly basic in character and contain an amino (-NH2) or substituted amino group. GOC:mtg_transport ISBN:0198506732 ISBN:0815340729 Enables the transfer of acetylcholine from one side of a membrane to the other. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. Reactome:R-HSA-264615 molecular_function GO:0005277 acetylcholine transmembrane transporter activity Enables the transfer of acetylcholine from one side of a membrane to the other. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. GOC:ai Reactome:R-HSA-264615 Loading of acetylcholine in synaptic vesicles Enables the transfer of dicarboxylic acids from one side of a membrane to the other. A dicarboxylic acid is an organic acid with two COOH groups. GO:0005312 GO:0015365 Reactome:R-HSA-1614546 Reactome:R-HSA-372843 dicarboxylate carrier sodium:dicarboxylate/tricarboxylate symporter activity molecular_function dicarboxylate (succinate/fumarate/malate) antiporter activity dicarboxylic acid permease activity GO:0005310 dicarboxylic acid transmembrane transporter activity Enables the transfer of dicarboxylic acids from one side of a membrane to the other. A dicarboxylic acid is an organic acid with two COOH groups. GOC:ai Reactome:R-HSA-1614546 Sulfate is exported to the cytosol in exchange for dicarboxylate Reactome:R-HSA-372843 SLC25A10 mediates exchange of malate and phosphate Enables the directed movement of lipids into, out of or within a cell, or between cells. Reactome:R-HSA-1369028 Reactome:R-HSA-1369052 Reactome:R-HSA-174786 Reactome:R-HSA-5682285 Reactome:R-HSA-5682311 Reactome:R-HSA-5683672 Reactome:R-HSA-5683714 Reactome:R-HSA-5688397 Reactome:R-HSA-6801250 Reactome:R-HSA-8848053 Reactome:R-HSA-8866329 lipophorin molecular_function apolipoprotein GO:0005319 lipid transporter activity GO_REF:0000090 Enables the directed movement of lipids into, out of or within a cell, or between cells. GOC:ai Reactome:R-HSA-1369028 ABCAs mediate lipid efflux Reactome:R-HSA-1369052 ABCAs mediate lipid influx Reactome:R-HSA-174786 ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex Reactome:R-HSA-5682285 ABCA12 transports lipids from cytosol to extracellular region Reactome:R-HSA-5682311 Defective ABCA12 does not transport lipids from cytosol to extracellular region Reactome:R-HSA-5683672 Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body Reactome:R-HSA-5683714 ABCA3 transports PC, PG from ER membrane to lamellar body Reactome:R-HSA-5688397 Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body Reactome:R-HSA-6801250 TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane Reactome:R-HSA-8848053 ABCA5 transports CHOL from lysosomal lumen to cytosol Reactome:R-HSA-8866329 MTTP lipidates APOB-100, forming a pre-VLDL Enables the directed movement of a neurotransmitter into, out of or within a cell, or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. Reactome:R-HSA-374896 Reactome:R-HSA-374919 molecular_function neurotransmitter transporter activity GO:0005326 neurotransmitter transmembrane transporter activity GO_REF:0000090 Enables the directed movement of a neurotransmitter into, out of or within a cell, or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. GOC:ai ISBN:0198506732 Reactome:R-HSA-374896 Uptake of Noradrenaline Reactome:R-HSA-374919 Noradrenaline clearance from the synaptic cleft Enables the transfer of organic acids from one side of a membrane to the other. Organic acids are acidic compound containing carbon in covalent linkage. molecular_function GO:0005342 organic acid transmembrane transporter activity Enables the transfer of organic acids from one side of a membrane to the other. Organic acids are acidic compound containing carbon in covalent linkage. ISBN:0198506732 Enables the transfer of the hexose monosaccharide glucose from one side of a membrane to the other. GO:0015579 Reactome:R-HSA-499981 Reactome:R-HSA-5653873 glucose permease activity lactose/glucose efflux transporter activity molecular_function galactose/glucose (methylgalactoside) porter activity GO:0005355 glucose transmembrane transporter activity Enables the transfer of the hexose monosaccharide glucose from one side of a membrane to the other. GOC:ai GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-499981 Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2 Reactome:R-HSA-5653873 SLC2A1 tetramer transports Glc from cytosol to Golgi lumen cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GOC:pdt NIF_Subcellular:sao1337158144 A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). GOC:pdt A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). GOC:pdt subcellular entity NIF_Subcellular:nlx_subcell_100315 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. Wikipedia:Extracellular extracellular cellular_component GO:0005576 Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. extracellular region The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. GOC:go_curators A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds. fibrinogen fibrinogen alpha chain fibrinogen beta chain fibrinogen gamma chain cellular_component GO:0005577 fibrinogen complex A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds. ISBN:0198547684 A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer PMID:12382326 PMID:12382326 A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. GOC:dos GOC:mah ISBN:0721639976 PMID:19693541 PMID:21421911 Any triple helical collagen trimer that forms fibrils. cellular_component GO:0005583 fibrillar collagen trimer Any triple helical collagen trimer that forms fibrils. GOC:mah ISBN:0721639976 PMID:21421911 A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes. Wikipedia:Collagen_type_IV cellular_component GO:0005587 collagen type IV trimer A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes. ISBN:0721639976 PMID:19693541 PMID:21421911 A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. GO:0005605 GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina basement lamina lamina densa GO:0005604 Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. basement membrane A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. ISBN:0198547684 PMID:22505934 That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. NIF_Subcellular:sao1425028079 cellular_component intercellular space GO:0005615 Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. extracellular space That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. ISBN:0198547684 A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. https://github.com/geneontology/go-ontology/issues/17776 NCIt:C28217 SNOMEDCT:83167003 Wikipedia:Intracellular internal to cell intracellular protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular anatomical structure A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GOC:go_curators horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005636 Wikipedia:Nuclear_envelope cellular_component GO:0005635 nuclear envelope The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). ISBN:0198547684 The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes. NIF_Subcellular:sao1617136075 nucleus outer envelope perinuclear membrane cellular_component GO:0005640 nuclear outer membrane The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes. ISBN:0198547684 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid GO:0005694 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. ISBN:0198547684 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. NIF_Subcellular:sao1820400233 Wikipedia:Nucleolus cellular_component GO:0005730 nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. ISBN:0198506732 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. https://github.com/geneontology/go-ontology/issues/23023 MeSH:D003593 NCIt:C13226 Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. Wikipedia:Vacuole cellular_component vacuolar carboxypeptidase Y GO:0005773 vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GOC:mtg_sensu ISBN:0198506732 The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell. cellular_component GO:0005774 vacuolar membrane The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell. GOC:ai The volume enclosed within the vacuolar membrane. cellular_component GO:0005775 vacuolar lumen The volume enclosed within the vacuolar membrane. ISBN:0198506732 A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. Golgi NIF_Subcellular:sao451912436 Wikipedia:Golgi_apparatus Golgi complex Golgi ribbon cellular_component GO:0005794 Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. Golgi apparatus A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. ISBN:0198506732 Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. NIF_Subcellular:sao819927218 cellular_component Golgi vesicle vesicular component GO:0005798 Note that this definition includes vesicles that are transiently associated with the Golgi. Golgi-associated vesicle Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. GOC:mah vesicular component NIF_Subcellular:sao138219748 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome membrane bound ribosome cellular_component ribosomal RNA GO:0005840 ribosome An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. ISBN:0198506732 free ribosome NIF_Subcellular:sao1139385046 membrane bound ribosome NIF_Subcellular:sao1291545653 A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. Wikipedia:Cytoskeleton cellular_component GO:0005856 cytoskeleton A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. GOC:mah PMID:16959967 PMID:27419875 Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. NIF_Subcellular:sao1846835077 Wikipedia:Microtubule microtubuli microtubulus neurotubule cellular_component GO:0005874 microtubule Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. ISBN:0879693568 neurotubule NIF_Subcellular:sao248349196 A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules. cellular_component GO:0005879 axonemal microtubule A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules. GOC:cilia ISBN:0815316194 Any microtubule in the nucleus of a cell. cellular_component GO:0005880 nuclear microtubule Any microtubule in the nucleus of a cell. GOC:mah Any microtubule in the cytoplasm of a cell. non-spindle-associated astral microtubule cellular_component GO:0005881 cytoplasmic microtubule Any microtubule in the cytoplasm of a cell. GOC:mah A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. FMA:63850 NIF_Subcellular:sao1588493326 Wikipedia:Actin microfilament cellular_component GO:0005884 actin filament A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. GOC:mah ISBN:0198506732 PMID:10666339 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005887 GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane integral component of plasma membrane integral to plasma membrane plasma membrane lipid bilayer cellular_component GO:0005886 plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. ISBN:0716731363 cellular membrane NIF_Subcellular:sao6433132645 plasma membrane lipid bilayer GOC:mah Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. NIF_Subcellular:sao671419673 Wikipedia:Microvillus cellular_component microvilli GO:0005902 Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta. microvillus Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. ISBN:0815316194 microvilli NIF_Subcellular:sao671419673 A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects. https://github.com/geneontology/go-ontology/issues/22122 cell-cell contact region cell-cell contact zone NIF_Subcellular:sao1922892319 intercellular junction cellular_component GO:0005911 cell-cell junction A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects. GOC:aruk GOC:bc GOC:dgh GOC:hb GOC:mah PMID:21422226 PMID:28096264 intercellular junction NIF_Subcellular:sao1395777368 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO:0072372 FMA:67181 NIF_Subcellular:sao787716553 Wikipedia:Cilium eukaryotic flagellum microtubule-based flagellum primary cilium cellular_component flagellum GO:0005929 Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. cilium A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GOC:cilia GOC:curators GOC:kmv GOC:vw ISBN:0198547684 PMID:16824949 PMID:17009929 PMID:20144998 The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GO:0035085 GO:0035086 Wikipedia:Axoneme ciliary axoneme cilium axoneme flagellar axoneme flagellum axoneme cellular_component GO:0005930 Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane. axoneme The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GOC:bf GOC:cilia ISBN:0198547684 The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. https://github.com/geneontology/go-ontology/issues/26298 Wikipedia:Cell_cortex ectoplasm cellular_component cell periphery peripheral cytoplasm GO:0005938 cell cortex The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:mah ISBN:0815316194 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. https://github.com/geneontology/go-ontology/issues/22880 jl 2012-10-23T15:40:34Z GO:0044261 GO:0044723 Wikipedia:Carbohydrate_metabolism carbohydrate metabolism biological_process GO:0005975 carbohydrate metabolic process The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GOC:mah ISBN:0198506732 The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GO:0044263 polysaccharide metabolism glycan metabolic process glycan metabolism multicellular organismal polysaccharide metabolic process biological_process GO:0005976 polysaccharide metabolic process The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. ISBN:0198547684 The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages. glycogen metabolism biological_process GO:0005977 glycogen metabolic process The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. MetaCyc:GLYCOGENSYNTH-PWY glycogen anabolism glycogen biosynthesis glycogen formation glycogen synthesis biological_process GO:0005978 glycogen biosynthetic process The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. regulation of glycogen anabolism regulation of glycogen biosynthesis regulation of glycogen formation regulation of glycogen synthesis biological_process GO:0005979 regulation of glycogen biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. MetaCyc:GLYCOCAT-PWY glycogen breakdown glycogen catabolism glycogen degradation glycogenolysis biological_process GO:0005980 glycogen catabolic process The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. ISBN:0198506732 glycogenolysis GOC:sl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. regulation of glycogen breakdown regulation of glycogen catabolism regulation of glycogen degradation regulation of glycogenolysis biological_process GO:0005981 regulation of glycogen catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. GOC:go_curators regulation of glycogenolysis GOC:sl The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. monosaccharide metabolism biological_process GO:0005996 monosaccharide metabolic process The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. ISBN:0198506732 The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. cellular glucose metabolic process glucose metabolism biological_process GO:0006006 glucose metabolic process The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. ISBN:0198506732 cellular glucose metabolic process GOC:vw The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose. glucose breakdown glucose catabolism glucose degradation biological_process GO:0006007 glucose catabolic process The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose. GOC:ai The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. aminoglycan metabolism biological_process GO:0006022 aminoglycan metabolic process The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. GOC:ai ISBN:0198506732 The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. aminoglycan anabolism aminoglycan biosynthesis aminoglycan formation aminoglycan synthesis biological_process GO:0006023 aminoglycan biosynthetic process The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. GOC:ai ISBN:0198506732 The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. glycosaminoglycan anabolism glycosaminoglycan biosynthesis glycosaminoglycan formation glycosaminoglycan synthesis biological_process GO:0006024 glycosaminoglycan biosynthetic process The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. ISBN:0192800981 The chemical reactions and pathways resulting in the breakdown of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. aminoglycan breakdown aminoglycan catabolism aminoglycan degradation biological_process GO:0006026 aminoglycan catabolic process The chemical reactions and pathways resulting in the breakdown of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. GOC:ai ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. glycosaminoglycan breakdown glycosaminoglycan catabolism glycosaminoglycan degradation biological_process GO:0006027 glycosaminoglycan catabolic process The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. ISBN:0192800981 The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. organic acid metabolism biological_process GO:0006082 organic acid metabolic process The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 The chemical reactions and pathways involving acetate, the anion of acetic acid. acetate metabolism biological_process GO:0006083 acetate metabolic process The chemical reactions and pathways involving acetate, the anion of acetic acid. GOC:go_curators The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. energy pathways biological_process intermediary metabolism metabolic energy generation GO:0006091 generation of precursor metabolites and energy The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. GOC:jl intermediary metabolism GOC:mah The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol. MetaCyc:GLUCONEO-PWY Wikipedia:Gluconeogenesis glucose biosynthesis glucose biosynthetic process biological_process GO:0006094 gluconeogenesis The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol. MetaCyc:GLUCONEO-PWY Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates. regulation of carbohydrate metabolism biological_process GO:0006109 regulation of carbohydrate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates. GOC:go_curators Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol. tb 2013-01-18T12:47:43Z GO:0090526 regulation of glucose biosynthesis regulation of glucose biosynthetic process biological_process regulation of gluconeogenesis involved in cellular glucose homeostasis GO:0006111 regulation of gluconeogenesis Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol. GOC:go_curators The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen. energy reserve metabolism biological_process GO:0006112 energy reserve metabolic process The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen. GOC:mah Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006139 nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0055132 DNA metabolism cellular DNA metabolism biological_process GO:0006259 DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. ISBN:0198506732 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. Wikipedia:DNA_repair biological_process GO:0006281 DNA repair The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. PMID:11563486 Any process that modulates the frequency, rate or extent of DNA repair. biological_process GO:0006282 regulation of DNA repair Any process that modulates the frequency, rate or extent of DNA repair. GOC:go_curators The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. DNA breakdown DNA catabolism DNA degradation biological_process GO:0006308 DNA catabolic process The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. GOC:go_curators ISBN:0198506732 The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments. https://github.com/geneontology/go-ontology/issues/24396 GO:0008178 DNA fragmentation chromatinolysis DNA catabolic process during apoptosis DNA catabolism during apoptosis DNA fragmentation involved in apoptotic nuclear change endonucleolytic DNA catabolic process involved in apoptosis biological_process GO:0006309 DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341). apoptotic DNA fragmentation The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb ISBN:0721639976 PMID:15723341 PMID:23379520 chromatinolysis GOC:mtg_apoptosis DNA fragmentation involved in apoptotic nuclear change GOC:cjm GOC:dph GOC:tb The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA. https://github.com/geneontology/go-ontology/issues/22130 https://github.com/geneontology/go-ontology/issues/23549 GO:0006333 GO:0006336 GO:0016568 GO:0031497 GO:0034724 chromatin maintenance chromatin organisation establishment of chromatin architecture establishment or maintenance of chromatin architecture DNA replication-independent chromatin assembly DNA replication-independent chromatin organization DNA replication-independent nucleosome organisation DNA replication-independent nuclesome assembly chromatin assembly transcription-coupled nucleosome assembly biological_process chromatin assembly or disassembly chromatin assembly/disassembly chromatin modification GO:0006325 chromatin organization The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA. PMID:20404130 chromatin organisation GOC:mah establishment of chromatin architecture GOC:mah establishment or maintenance of chromatin architecture GOC:mah The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. RNA breakdown RNA catabolism RNA degradation biological_process GO:0006401 RNA catabolic process The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. ISBN:0198506732 A process in which RNA is transported to, or maintained in, a specific location. RNA localisation establishment and maintenance of RNA localization biological_process GO:0006403 RNA localization A process in which RNA is transported to, or maintained in, a specific location. GOC:ai RNA localisation GOC:mah The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0006416 GO:0006453 GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis protein biosynthetic process protein formation protein synthesis protein translation biological_process GO:0006412 translation The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GOC:go_curators The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. GO:0006440 GO:0006454 biopolymerisation biopolymerization protein synthesis initiation translation initiation biological_process GO:0006413 translational initiation The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. ISBN:019879276X The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GO:0006442 GO:0006455 protein synthesis elongation translation elongation biological_process GO:0006414 translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GOC:ems The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). GO:0006443 GO:0006456 protein synthesis termination translation termination translational complex disassembly biological_process GO:0006415 translational termination The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). GOC:hjd ISBN:019879276X Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0006445 regulation of protein anabolism regulation of protein biosynthesis regulation of protein formation regulation of protein synthesis biological_process GO:0006417 regulation of translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:isa_complete Any process that modulates the frequency, rate or extent of translational initiation. biological_process GO:0006446 regulation of translational initiation Any process that modulates the frequency, rate or extent of translational initiation. GOC:go_curators Any process that modulates the frequency, rate, extent or accuracy of translational elongation. biological_process GO:0006448 regulation of translational elongation Any process that modulates the frequency, rate, extent or accuracy of translational elongation. GOC:go_curators Any process that modulates the frequency, rate or extent of translational termination. biological_process GO:0006449 regulation of translational termination Any process that modulates the frequency, rate or extent of translational termination. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. glycoprotein breakdown glycoprotein catabolism glycoprotein degradation biological_process GO:0006516 glycoprotein catabolic process The chemical reactions and pathways resulting in the breakdown of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. peptide metabolism biological_process GO:0006518 peptide metabolic process The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. GOC:go_curators The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. https://github.com/geneontology/go-ontology/issues/17904 GO:0006519 cellular amino acid metabolic process cellular amino acid metabolism biological_process amino acid and derivative metabolism cellular amino acid and derivative metabolic process GO:0006520 amino acid metabolic process The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids. regulation of amino acid metabolism biological_process GO:0006521 regulation of cellular amino acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids. GOC:go_curators The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters. biogenic amine metabolism cellular biogenic amine metabolic process biological_process GO:0006576 biogenic amine metabolic process The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters. GOC:jl ISBN:0395825172 The chemical reactions and pathways resulting in the breakdown of acetylcholine, the acetic acid ester of the organic base choline. acetylcholine breakdown acetylcholine catabolism acetylcholine degradation biological_process GO:0006581 acetylcholine catabolic process The chemical reactions and pathways resulting in the breakdown of acetylcholine, the acetic acid ester of the organic base choline. GOC:jl ISBN:0192800752 The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. catecholamine metabolism biological_process GO:0006584 catecholamine metabolic process The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group. indolamine metabolic process indolamine metabolism indolalkylamine metabolism biological_process GO:0006586 indolalkylamine metabolic process The chemical reactions and pathways involving indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group. GOC:curators The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. Wikipedia:Lipid_metabolism lipid metabolism biological_process GO:0006629 lipid metabolic process The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. GOC:ma The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification. Wikipedia:Steroid_metabolisms#Steroid_biosynthesis steroid anabolism steroid biosynthesis steroid formation steroid synthesis steroidogenesis biological_process GO:0006694 steroid biosynthetic process The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification. GOC:go_curators The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile. bile acid anabolism bile acid biosynthesis bile acid formation bile acid synthesis biological_process GO:0006699 bile acid biosynthetic process The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. steroid breakdown steroid catabolism steroid degradation biological_process GO:0006706 steroid catabolic process The chemical reactions and pathways resulting in the breakdown of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:go_curators The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GO:0006725 cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GOC:ai ISBN:0198506732 The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. Wikipedia:Sulfur_metabolism sulfur metabolism sulphur metabolic process sulphur metabolism biological_process GO:0006790 sulfur compound metabolic process The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. GOC:ai The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). phosphorus metabolism biological_process GO:0006793 phosphorus metabolic process The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). GOC:ai The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. phosphate metabolism biological_process phosphate metabolic process GO:0006796 phosphate-containing compound metabolic process The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. GOC:ai The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. https://github.com/geneontology/go-ontology/issues/26424 nitrogen compound metabolism biological_process GO:0006807 nitrogen compound metabolic process The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GOC:jl ISBN:0198506732 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 jl 2012-12-13T16:25:32Z GO:0015457 GO:0015460 GO:0044765 biological_process single-organism transport GO:0006810 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. GOC:dos GOC:dph GOC:jl GOC:mah The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. ion transport biological_process GO:0006811 monoatomic ion transport The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GOC:ai The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom. GO:0006819 GO:0015674 GO:0072512 cation transport di-, tri-valent inorganic cation transport trivalent inorganic cation transport biological_process GO:0006812 monoatomic cation transport The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom. GOC:ai di-, tri-valent inorganic cation transport GOC:mah The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006834 GO:0016974 sodium/potassium transport sodium transport mitochondrial sodium/calcium ion exchange sodium:calcium exchange sodium:solute transport biological_process sodium channel auxiliary protein activity GO:0006814 sodium ion transport The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai sodium channel auxiliary protein activity GOC:mah The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process phosphate transport GO:0006817 phosphate ion transport The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006841 biological_process sodium:dicarboxylate transport GO:0006835 dicarboxylic acid transport The directed movement of dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. sodium:neurotransmitter transport biological_process GO:0006836 neurotransmitter transport The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. GOC:ai The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. biological_process GO:0006837 serotonin transport The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. GOC:ai The directed movement of acetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0006846 acetate transport The directed movement of acetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of acetate across a plasma membrane. biological_process GO:0006847 plasma membrane acetate transport The directed movement of acetate across a plasma membrane. GOC:ai The transport of substances that occurs outside cells. biological_process GO:0006858 extracellular transport The transport of substances that occurs outside cells. GOC:go_curators The directed extracellular movement of amino acids. biological_process GO:0006860 extracellular amino acid transport The directed extracellular movement of amino acids. GOC:ai The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006866 biological_process GO:0006865 amino acid transport The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. biological_process GO:0006869 lipid transport The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. ISBN:0198506732 The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GO:0032779 biological_process copper-induced intracellular protein transport GO:0006886 intracellular protein transport The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GOC:mah copper-induced intracellular protein transport GOC:al A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GO:0016194 GO:0016195 Wikipedia:Exocytosis vesicle exocytosis biological_process nonselective vesicle exocytosis GO:0006887 exocytosis A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GOC:mah ISBN:0716731363 PMID:22323285 The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles. post-Golgi transport biological_process GO:0006892 post-Golgi vesicle-mediated transport The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles. GOC:ai GOC:mah The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis. Golgi to plasma membrane vesicle-mediated transport biological_process GO:0006893 Golgi to plasma membrane transport The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis. ISBN:0716731363 The directed movement of substances from the Golgi to the vacuole. Golgi to vacuole vesicle-mediated transport biological_process GO:0006896 Golgi to vacuole transport The directed movement of substances from the Golgi to the vacuole. GOC:ai The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. biological_process GO:0006903 vesicle targeting The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. GOC:mah PMID:17335816 Fusion of the membrane of a transport vesicle with its target membrane. biological_process GO:0006906 vesicle fusion Fusion of the membrane of a transport vesicle with its target membrane. GOC:jid A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GO:0006917 GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis apoptotic cell death apoptotic programmed cell death programmed cell death by apoptosis activation of apoptosis apoptosis apoptosis signaling apoptotic program type I programmed cell death biological_process apoptosis activator activity caspase-dependent programmed cell death commitment to apoptosis induction of apoptosis induction of apoptosis by p53 signaling (initiator) caspase activity GO:0006915 apoptotic process A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:cjm GOC:dhl GOC:ecd GOC:go_curators GOC:mtg_apoptosis GOC:tb ISBN:0198506732 PMID:18846107 PMID:21494263 apoptotic cell death GOC:sl apoptotic program GOC:add The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. cellular component disassembly involved in apoptotic process disassembly of cell structures cellular component disassembly involved in apoptosis biological_process GO:0006921 cellular component disassembly involved in execution phase of apoptosis The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Wikipedia:Muscle_contraction biological_process GO:0006936 muscle contraction A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. GOC:ef GOC:mtg_muscle ISBN:0198506732 Any process that modulates the frequency, rate or extent of muscle contraction. biological_process GO:0006937 regulation of muscle contraction Any process that modulates the frequency, rate or extent of muscle contraction. GOC:go_curators A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length. visceral muscle contraction biological_process GO:0006939 smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length. GOC:ef GOC:jl GOC:mtg_muscle ISBN:0198506732 Any process that modulates the frequency, rate or extent of smooth muscle contraction. biological_process GO:0006940 regulation of smooth muscle contraction Any process that modulates the frequency, rate or extent of smooth muscle contraction. GOC:go_curators A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope. sarcomeric muscle contraction biological_process GO:0006941 striated muscle contraction A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope. GOC:jl GOC:mtg_muscle ISBN:0198506732 Any process that modulates the frequency, rate or extent of striated muscle contraction. biological_process GO:0006942 regulation of striated muscle contraction Any process that modulates the frequency, rate or extent of striated muscle contraction. GOC:go_curators The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. biological_process GO:0006949 syncytium formation The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. ISBN:0198506732 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process response to abiotic stress response to biotic stress GO:0006950 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. biological_process GO:0006955 immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. GOC:add GO_REF:0000022 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. https://github.com/geneontology/go-ontology/issues/24775 GO:0034984 response to DNA damage stimulus cellular DNA damage response cellular response to DNA damage stimulus response to genotoxic stress biological_process GO:0006974 DNA damage response Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. GOC:go_curators A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GO:0048287 nuclear organisation nuclear organization biological_process nuclear morphology nuclear organization and biogenesis nucleus organization and biogenesis GO:0006997 nucleus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GOC:dph GOC:ems GOC:jl GOC:mah nuclear organization and biogenesis GOC:mah nucleus organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope. nuclear envelope organisation biological_process nuclear envelope organization and biogenesis GO:0006998 nuclear envelope organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope. GOC:dph GOC:ems GOC:jl GOC:mah nuclear envelope organisation GOC:mah nuclear envelope organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus. nucleolus organisation biological_process nucleolus organization and biogenesis GO:0007000 nucleolus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus. GOC:dph GOC:jid GOC:jl GOC:mah nucleolus organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. plasma membrane organisation biological_process plasma membrane organization and biogenesis GO:0007009 plasma membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. GOC:dph GOC:jl GOC:mah plasma membrane organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. cytoskeleton organisation biological_process cytoskeletal organization and biogenesis cytoskeletal regulator activity cytoskeleton organization and biogenesis GO:0007010 cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:dph GOC:jl GOC:mah cytoskeletal organization and biogenesis GOC:mah cytoskeleton organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking. actin filament organisation regulation of actin filament localization biological_process GO:0007015 actin filament organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking. GOC:mah Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. https://github.com/geneontology/go-ontology/issues/19809 biological_process GO:0007017 microtubule-based process Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. GOC:mah A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. biological_process GO:0007018 microtubule-based movement A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. GOC:cjm ISBN:0815316194 The removal of tubulin heterodimers from one or both ends of a microtubule. microtubule disassembly microtubule shortening microtubule catastrophe microtubule depolymerization during nuclear congression biological_process GO:0007019 microtubule depolymerization The removal of tubulin heterodimers from one or both ends of a microtubule. ISBN:0815316194 microtubule catastrophe GOC:dph GOC:tb The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation). Wikipedia:Microtubule_nucleation biological_process GO:0007020 microtubule nucleation The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation). GOC:go_curators ISBN:0815316194 PMID:12517712 Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol. down regulation of microtubule depolymerization down-regulation of microtubule depolymerization downregulation of microtubule depolymerization microtubule stabilization negative regulation of microtubule disassembly inhibition of microtubule depolymerization microtubule rescue negative regulation of microtubule catastrophe biological_process GO:0007026 negative regulation of microtubule depolymerization Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol. GOC:mah ISBN:0815316194 microtubule rescue GOC:dph GOC:tb negative regulation of microtubule catastrophe GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the depolymerization of the specialized microtubules of the axoneme. axonemal microtubule stabilization biological_process negative regulation of microtubule depolymerization in axoneme GO:0007027 negative regulation of axonemal microtubule depolymerization Any process that stops, prevents, or reduces the frequency, rate or extent of the depolymerization of the specialized microtubules of the axoneme. GOC:dph GOC:mah negative regulation of microtubule depolymerization in axoneme GOC:dph A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. cytoplasm organisation biological_process cytoplasm organization and biogenesis GO:0007028 cytoplasm organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GOC:curators GOC:dph GOC:jl GOC:mah cytoplasm organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus. Golgi apparatus organization Golgi organisation biological_process Golgi organization and biogenesis GO:0007030 Golgi organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus. GOC:dph GOC:jl GOC:mah Golgi organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole. GO:0044086 vacuole organisation vacuolar assembly biological_process vacuole biogenesis vacuole organization and biogenesis GO:0007033 vacuole organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole. GOC:mah vacuolar assembly GOC:mah vacuole biogenesis GOC:mah vacuole organization and biogenesis GOC:mah The directed movement of substances into, out of or within a vacuole. biological_process GO:0007034 vacuolar transport The directed movement of substances into, out of or within a vacuole. GOC:ai The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases. biological_process vacuolar protein breakdown vacuolar protein catabolic process vacuolar protein catabolism vacuolar protein degradation GO:0007039 protein catabolic process in the vacuole The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases. GOC:mah GOC:vw The aggregation, arrangement and bonding together of a set of components to form a junction between cells. intercellular junction assembly biological_process GO:0007043 cell-cell junction assembly The aggregation, arrangement and bonding together of a set of components to form a junction between cells. GOC:ai The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. GOC:go_curators GOC:mtg_cell_cycle The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. Wikipedia:Chromosome_segregation chromosome division biological_process chromosome transmission GO:0007059 chromosome segregation The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:jl GOC:mah GOC:mtg_cell_cycle GOC:vw The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. biological_process GO:0007076 mitotic chromosome condensation The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. GOC:mah ISBN:0815316194 The mitotic cell cycle process in which the controlled partial or complete breakdown of the nuclear membranes during occurs during mitosis. NEB local NEB nuclear envelope breakdown mitotic nuclear envelope breakdown biological_process mitotic nuclear envelope catabolism mitotic nuclear envelope degradation mitotic nuclear envelope disassembly GO:0007077 mitotic nuclear membrane disassembly The mitotic cell cycle process in which the controlled partial or complete breakdown of the nuclear membranes during occurs during mitosis. GOC:bf PMID:32848252 Any process that modulates the frequency, rate or extent of mitosis. regulation of mitosis biological_process GO:0007088 regulation of mitotic nuclear division Any process that modulates the frequency, rate or extent of mitosis. GOC:go_curators The directed movement of the nucleus to a specific location within a cell. GO:0040023 establishment of position of nucleus nuclear movement nuclear positioning nucleus migration nucleus positioning positioning of nucleus biological_process establishment of cell nucleus localization establishment of localization of nucleus establishment of nucleus localisation establishment of nucleus localization GO:0007097 nuclear migration The directed movement of the nucleus to a specific location within a cell. GOC:ai establishment of nucleus localisation GOC:mah A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. Wikipedia:Mitosis#Endomitosis biological_process endomitosis GO:0007113 Note that this term should not be confused with 'abortive mitotic cell cycle ; GO:0033277'. Although abortive mitosis is sometimes called endomitosis, GO:0033277 refers to a process in which a mitotic spindle forms and chromosome separation begins. endomitotic cell cycle A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. GOC:curators GOC:dos GOC:expert_vm A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. female meiosis female meiotic division biological_process GO:0007143 Note that female germ lines can be found in female or hermaphroditic organisms, so this term can be used to annotate gene products from hermaphrodites such as those of C. elegans. See also the biological process term 'meiotic nuclear division; GO:0140013'. female meiotic nuclear division A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. GOC:dph GOC:ems GOC:mah GOC:vw Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. Wikipedia:Cell_signaling biological_process GO:0007154 cell communication Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:mah Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. GO:0030012 GO:0030467 biological_process cell polarity establishment and/or maintenance of cell polarity establishment and/or maintenance of cell polarization GO:0007163 establishment or maintenance of cell polarity Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. GOC:mah cell polarity GOC:mah GOC:vw The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0023014 GO:0023015 GO:0023016 GO:0023033 GO:0023045 Wikipedia:Signal_transduction signal transduction by cis-phosphorylation signal transduction by conformational transition signal transduction by protein phosphorylation signal transduction by trans-phosphorylation signaling cascade signalling cascade biological_process signaling pathway signalling pathway GO:0007165 Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GOC:go_curators GOC:mtg_signaling_feb11 signalling pathway GOC:mah Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. cell-cell signalling biological_process GO:0007267 cell-cell signaling Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. GOC:dos GOC:mah The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. signal transmission across a synapse synaptic transmission Wikipedia:Neurotransmission biological_process neurotransmission GO:0007268 chemical synaptic transmission The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:jl MeSH:D009435 neurotransmission GOC:dph The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission. GO:0010554 neurotransmitter release neurotransmitter secretory pathway biological_process GO:0007269 A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin. neurotransmitter secretion The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission. GOC:dph The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. cholinergic synaptic transmission biological_process GO:0007271 synaptic transmission, cholinergic The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:dos Wikipedia:Cholinergic The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). https://github.com/geneontology/go-ontology/issues/21234 biological_process GO:0007275 Note that this term was 'developmental process'. multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:dph GOC:ems GOC:isa_complete GOC:tb The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. GO:0009552 biological_process gametogenesis GO:0007276 gamete generation The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. GOC:ems GOC:mtg_sensu The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. germ-cell development gametogenesis primordial germ cell development biological_process GO:0007281 germ cell development The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. GOC:go_curators Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction. biological_process GO:0007292 female gamete generation Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction. GOC:dph ISBN:0198506732 Construction of a stage-1 egg chamber in the anterior part of the germarium, from the progeny of germ-line and somatic stem cells. An example of this is found in Drosophila melanogaster. biological_process GO:0007293 germarium-derived egg chamber formation Construction of a stage-1 egg chamber in the anterior part of the germarium, from the progeny of germ-line and somatic stem cells. An example of this is found in Drosophila melanogaster. GOC:mtg_sensu ISBN:0879694238 The synthesis, deposition, and organization of the materials in a cell of an ovary; where the cell can then undergo meiosis and form an ovum. An example of this is found in Drosophila melanogaster. GO:0048110 oocyte arrangement biological_process GO:0007308 oocyte construction The synthesis, deposition, and organization of the materials in a cell of an ovary; where the cell can then undergo meiosis and form an ovum. An example of this is found in Drosophila melanogaster. GOC:dph GOC:ems GOC:mtg_sensu GOC:tb ISBN:0198506732 oocyte arrangement GOC:dph GOC:tb Any process that modulates the rate or extent of progress through the mitotic cell cycle. mitotic cell cycle modulation mitotic cell cycle regulation modulation of mitotic cell cycle progression regulation of mitotic cell cycle progression regulation of progression through mitotic cell cycle biological_process mitotic cell cycle regulator GO:0007346 regulation of mitotic cell cycle Any process that modulates the rate or extent of progress through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb regulation of progression through mitotic cell cycle GOC:dph GOC:tb A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. Wikipedia:Gastrulation biological_process GO:0007369 gastrulation A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. GOC:curators ISBN:9780878933846 Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate. biological_process pattern biosynthesis pattern formation GO:0007389 pattern specification process Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate. GOC:go_curators GOC:isa_complete ISBN:0521436125 The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation. biological_process GO:0007398 ectoderm development The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation. GOC:dph GOC:tb The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. biological_process pan-neural process GO:0007399 nervous system development The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. GOC:dgh The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron. GO:0043349 GO:0043350 biological_process GO:0007405 neuroblast proliferation The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron. GOC:ai GOC:mtg_sensu GOC:sart Any process that stops, prevents, or reduces the frequency, rate or extent of the proliferation of neuroblasts. down regulation of neuroblast proliferation down-regulation of neuroblast proliferation downregulation of neuroblast proliferation suppression of neuroblast proliferation inhibition of neuroblast proliferation biological_process GO:0007406 negative regulation of neuroblast proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of the proliferation of neuroblasts. GOC:ai The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional). Wikipedia:Synaptogenesis synapse biogenesis synaptogenesis biological_process GO:0007416 synapse assembly The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional). GOC:mah synapse biogenesis GOC:mah synaptogenesis GOC:mah The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. Wikipedia:Neural_development CNS development biological_process GO:0007417 central nervous system development The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. GOC:bf GOC:jid ISBN:0582227089 The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). biological_process GO:0007420 brain development The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). GOC:dph GOC:jid GOC:tb UBERON:0000955 The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. biological_process GO:0007422 peripheral nervous system development The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. GOC:go_curators UBERON:0000010 The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure. sense organ development biological_process GO:0007423 sensory organ development The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure. GOC:go_curators sense organ development GOC:dph The process whose specific outcome is the progression of the ectodermal digestive tract over time, from its formation to the mature structure. The ectodermal digestive tract includes those portions that are derived from ectoderm. biological_process ectodermal gut development GO:0007439 ectodermal digestive tract development The process whose specific outcome is the progression of the ectodermal digestive tract over time, from its formation to the mature structure. The ectodermal digestive tract includes those portions that are derived from ectoderm. GOC:curators ectodermal gut development GOC:dph The process in which the anatomical structures of the foregut are generated and organized. biological_process GO:0007440 foregut morphogenesis The process in which the anatomical structures of the foregut are generated and organized. GOC:jid The process in which the anatomical structures of the hindgut are generated and organized. biological_process GO:0007442 hindgut morphogenesis The process in which the anatomical structures of the hindgut are generated and organized. GOC:jid The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues. biological_process GO:0007492 endoderm development The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues. GOC:dph GOC:tb The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine. biological_process GO:0007494 midgut development The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine. GOC:jid UBERON:0001045 The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue. biological_process GO:0007498 mesoderm development The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue. GOC:dph GOC:tb The process whose specific outcome is the progression of the gonadal mesoderm over time, from its formation to the mature structure. The gonadal mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism. biological_process GO:0007506 gonadal mesoderm development The process whose specific outcome is the progression of the gonadal mesoderm over time, from its formation to the mature structure. The gonadal mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism. GOC:ai The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GO:0007511 Wikipedia:Heart_development dorsal vessel development biological_process cardiac development GO:0007507 heart development The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GOC:jid UBERON:0000948 The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work. biological_process GO:0007517 muscle organ development The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work. GOC:jid ISBN:0198506732 The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers. GO:0048637 biological_process myogenesis GO:0007519 skeletal muscle tissue development The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers. GOC:mtg_muscle A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction. neuromuscular junction organization biological_process NMJ stability neuromuscular junction stability GO:0007528 neuromuscular junction development A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction. GOC:mtg_OBO2OWL_2013 NMJ stability GOC:pr neuromuscular junction stability GOC:pr The establishment of the sex of an organism by physical differentiation. Wikipedia:Sexual_differentiation biological_process GO:0007548 sex differentiation The establishment of the sex of an organism by physical differentiation. GOC:ai The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. breathing respiration biological_process GO:0007585 respiratory gaseous exchange by respiratory system The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. ISBN:0198506732 The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. Wikipedia:Digestion biological_process GO:0007586 digestion The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:isa_complete ISBN:0198506732 The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds. https://github.com/geneontology/go-ontology/issues/22368 Wikipedia:Excretion biological_process GO:0007588 excretion The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds. ISBN:0192801023 The controlled release of a fluid by a cell or tissue in an animal. biological_process GO:0007589 body fluid secretion The controlled release of a fluid by a cell or tissue in an animal. GOC:ai GOC:dph GOC:mah GOC:tb The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Wikipedia:Perception biological_process GO:0007600 sensory perception The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai GOC:dph The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. Wikipedia:Visual_perception sense of sight sensory visual perception vision biological_process GO:0007601 visual perception The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. GOC:ai The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. Wikipedia:Hearing_(sense) hearing perception of sound biological_process GO:0007605 sensory perception of sound The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. GOC:ai The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. chemosensory perception biological_process GO:0007606 sensory perception of chemical stimulus The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. jl 2012-09-20T14:06:08Z GO:0023032 GO:0044708 GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process single-organism behavior GO:0007610 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GOC:ems GOC:jl ISBN:0395448956 PMID:20160973 The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. behavior via locomotion locomotion in response to stimulus locomotory behavioral response to stimulus locomotory behaviour locomotory behavioural response to stimulus biological_process GO:0007626 locomotory behavior The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. GOC:dph The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. GO:0070261 biological_process hemolymph circulation GO:0008015 blood circulation The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. GOC:mtg_heart ISBN:0192800825 Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. regulation of cardiac contraction biological_process GO:0008016 regulation of heart contraction Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. GOC:dph GOC:go_curators GOC:tb Enables the transfer of monocarboxylic acids from one side of a membrane to the other. A monocarboxylic acid is an organic acid with one COOH group. GO:0008505 Reactome:R-HSA-429749 Reactome:R-HSA-433698 Reactome:R-HSA-5624211 Reactome:R-HSA-9645220 monocarboxylate carrier prostaglandin/thromboxane transporter activity molecular_function GO:0008028 monocarboxylic acid transmembrane transporter activity Enables the transfer of monocarboxylic acids from one side of a membrane to the other. A monocarboxylic acid is an organic acid with one COOH group. GOC:ai Reactome:R-HSA-429749 SLC5A8 transports monocarboxylates from extracellular region to cytosol Reactome:R-HSA-433698 SLC16A3,7,8 cotransport monocarboxylates, H+ from extracellular region to cytosol Reactome:R-HSA-5624211 Defective SLC16A1 does not cotransport monocarboxylates, H+ from extracellular region to cytosol Reactome:R-HSA-9645220 SLC16A1:BSG cotransports monocarboxylates, H+ from extracellular region to cytosol The directed movement of organelles or molecules along microtubules in neuron projections. Wikipedia:Axoplasmic_transport axon cargo transport axonal transport axoplasmic transport biological_process GO:0008088 axo-dendritic transport The directed movement of organelles or molecules along microtubules in neuron projections. ISBN:0815316194 Any process in which a protein is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/23112 GO:0008105 GO:0016249 GO:0034613 cellular protein localisation cellular protein localization protein localisation channel localizer activity biological_process asymmetric protein localisation asymmetric protein localization establishment and maintenance of asymmetric protein localization establishment and maintenance of protein localization GO:0008104 protein localization Any process in which a protein is transported to, or maintained in, a specific location. GOC:ai cellular protein localisation GOC:mah protein localisation GOC:mah channel localizer activity GOC:mah asymmetric protein localisation GOC:mah A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 GO:0008150 MeSH:D055705 NCIt:C17828 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. jl 2012-10-17T15:46:40Z GO:0044236 GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. Wikipedia:Steroid_metabolism steroid metabolism biological_process GO:0008202 steroid metabolic process The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. ISBN:0198547684 The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. bile acid metabolism biological_process GO:0008206 bile acid metabolic process The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. GOC:go_curators Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). https://github.com/geneontology/go-ontology/issues/24680 biological_process accidental cell death necrosis GO:0008219 This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms. cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). GOC:mah GOC:mtg_apoptosis PMID:25236395 The directed movement of sulfate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006870 sulphate transport biological_process GO:0008272 sulfate transport The directed movement of sulfate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The multiplication or reproduction of cells, resulting in the expansion of a cell population. biological_process cell proliferation GO:0008283 This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. cell population proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. GOC:mah GOC:mb Any process that activates or increases the rate or extent of cell proliferation. up regulation of cell proliferation up-regulation of cell proliferation upregulation of cell proliferation activation of cell proliferation stimulation of cell proliferation biological_process positive regulation of cell proliferation GO:0008284 positive regulation of cell population proliferation Any process that activates or increases the rate or extent of cell proliferation. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of cell proliferation. down regulation of cell proliferation down-regulation of cell proliferation downregulation of cell proliferation inhibition of cell proliferation biological_process negative regulation of cell proliferation GO:0008285 negative regulation of cell population proliferation Any process that stops, prevents or reduces the rate or extent of cell proliferation. GOC:go_curators The chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. acetylcholine metabolism biological_process GO:0008291 acetylcholine metabolic process The chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. GOC:jl GOC:nln ISBN:0192800752 The chemical reactions and pathways resulting in the formation of acetylcholine, the acetic acid ester of the organic base choline. acetylcholine anabolism acetylcholine biosynthesis acetylcholine formation acetylcholine synthesis biological_process GO:0008292 acetylcholine biosynthetic process The chemical reactions and pathways resulting in the formation of acetylcholine, the acetic acid ester of the organic base choline. GOC:jl ISBN:0192800752 Enables the transfer of a protein from one side of a membrane to the other. GO:0015266 GO:0015463 Reactome:R-HSA-1268022 Reactome:R-HSA-1299475 Reactome:R-HSA-184269 Reactome:R-HSA-3149434 Reactome:R-HSA-5205661 Reactome:R-HSA-5210943 Reactome:R-HSA-5210947 Reactome:R-HSA-5228406 Reactome:R-HSA-5229111 Reactome:R-HSA-5244404 Reactome:R-HSA-5244428 Reactome:R-HSA-5244506 Reactome:R-HSA-5246514 Reactome:R-HSA-5250616 Reactome:R-HSA-5250884 Reactome:R-HSA-5250972 Reactome:R-HSA-5336420 Reactome:R-HSA-9636375 Reactome:R-HSA-9698930 Reactome:R-HSA-9698933 molecular_function protein channel activity GO:0008320 protein transmembrane transporter activity GO_REF:0000090 Enables the transfer of a protein from one side of a membrane to the other. GOC:jl Reactome:R-HSA-1268022 TOMM40 complex translocates proteins from the cytosol to the mitochondrial intermembrane space Reactome:R-HSA-1299475 TIMM23 PAM translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix Reactome:R-HSA-184269 Monoubiquitinated N-myristoyl GAG polyprotein is targeted to the late endosomal vesicle membrane by the ESCRT-I complex Reactome:R-HSA-3149434 Transport of GAG to the Plasma Membrane Reactome:R-HSA-5205661 Pink1 is recruited from the cytoplasm to the mitochondria Reactome:R-HSA-5210943 pagA(197-794):ANTRX2 oligomer transports cya and lef (target cell endosome to cytosol) Reactome:R-HSA-5210947 pagA(197-794):ANTRX1 oligomer transports cya and lef (target cell endosome to cytosol) Reactome:R-HSA-5228406 tetX HC transports tetX LC from target cell endosome membrane into cytosol Reactome:R-HSA-5229111 AP4 transports APP from trans-Golgi network to endosome lumen Reactome:R-HSA-5244404 botB HC transports botB LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5244428 botA HC transports botA LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5244506 botE HC transports botE LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5246514 botC HC transports botC LC from target cell synaptic vesicle membrane to cytosol Reactome:R-HSA-5250616 botD HC transports botD LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5250884 botF HC transports botF LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5250972 botG HC transports botG LC from target cell synaptic vesicle membrane into cytosol Reactome:R-HSA-5336420 DT fragment B transports DT fragment A from target cell endosome membrane Reactome:R-HSA-9636375 SecA2 transports SapM from cytoplasm to cytosol Reactome:R-HSA-9698930 HCMV C Nucleocapsid Translocation Reactome:R-HSA-9698933 HCMV B Nucleocapsid Translocation Enables the transfer of cation from one side of a membrane to the other. https://github.com/geneontology/go-ontology/issues/24479 cation transmembrane transporter activity transmembrane cation transporter activity molecular_function GO:0008324 monoatomic cation transmembrane transporter activity Enables the transfer of cation from one side of a membrane to the other. GOC:dgf GOC:mtg_transport ISBN:0815340729 The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity. Wikipedia:Asymmetric_cell_division asymmetrical cell division biological_process asymmetric cytokinesis asymmetrical cytokinesis GO:0008356 asymmetric cell division The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity. PMID:11672519 The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones. gonadogenesis biological_process GO:0008406 gonad development The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones. GOC:ems ISBN:0198506732 gonadogenesis GOC:cjm Enables the transfer of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), from one side of a membrane to the other. GO:0015201 Reactome:R-HSA-372542 Reactome:R-HSA-379393 Reactome:R-HSA-380586 Reactome:R-HSA-380620 Reactome:R-HSA-444160 Reactome:R-HSA-5660706 molecular_function GO:0008504 monoamine transmembrane transporter activity Enables the transfer of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), from one side of a membrane to the other. GOC:mah Reactome:R-HSA-372542 Loading of dopamine into synaptic veiscles Reactome:R-HSA-379393 SLC6A3 cotransports DA, Na+ from extracellular region to cytosol Reactome:R-HSA-380586 loading of Serotonin in synaptic vesicles Reactome:R-HSA-380620 Reuptake of serotonin from the synapse Reactome:R-HSA-444160 VMAT1/2 can mediate the transport of biogenic amines Reactome:R-HSA-5660706 Defective SLC6A3 does not cotransport DA, Na+ from extracellular region to cytosol Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. Reactome:R-HSA-2142859 Reactome:R-HSA-561041 Reactome:R-HSA-9794830 molecular_function GO:0008514 organic anion transmembrane transporter activity Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. GOC:ai Reactome:R-HSA-2142859 Growing HA is extruded from the cell by ABCC5 Reactome:R-HSA-561041 OAT1-3 transport organic anions with antiport of dicarboxylic acids Reactome:R-HSA-9794830 SLC22A8 transports Cipro into renal cell The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species. biological_process hypodermis development GO:0008544 epidermis development The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species. GOC:go_curators UBERON:0001003 hypodermis development GOC:kmv GOC:rk The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure. GO:0061039 biological_process ovarian development ovary development GO:0008585 female gonad development The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure. GOC:dph GOC:jid GOC:tb ovarian development GOC:sl ovary development GOC:sl The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster. biological_process photoreceptor development GO:0008594 photoreceptor cell morphogenesis The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster. GOC:jid GOC:mah The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. lipid anabolism lipid biosynthesis lipid formation lipid synthesis lipogenesis biological_process GO:0008610 lipid biosynthetic process The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GOC:go_curators lipogenesis GOC:sl The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y. GO:0006861 GO:0008644 sugar transport biological_process GO:0008643 carbohydrate transport The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y. GOC:ai The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule. bf 2010-04-08T10:27:23Z GO:0008646 GO:0008647 GO:0035428 high-affinity hexose transport low-affinity hexose transport biological_process hexose membrane transport hexose transport GO:0008645 Note that this term is not intended for use in annotating lateral movement within membranes. hexose transmembrane transport The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule. GOC:vw The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. https://github.com/geneontology/go-ontology/issues/17904 Wikipedia:Amino_acid_synthesis amino acid anabolism amino acid biosynthesis amino acid formation amino acid synthesis cellular amino acid biosynthetic process biological_process GO:0008652 amino acid biosynthetic process The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. jl 2012-10-17T15:52:35Z GO:0044243 GO:0044712 Wikipedia:Catabolism breakdown catabolism degradation multicellular organismal catabolic process biological_process single-organism catabolic process GO:0009056 catabolic process The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. ISBN:0198547684 The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043285 GO:0044266 biopolymer catabolic process macromolecule breakdown macromolecule catabolism macromolecule degradation multicellular organismal macromolecule catabolic process biological_process cellular macromolecule catabolic process cellular macromolecule catabolism cellular macromolecule degradation GO:0009057 macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer catabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. jl 2012-10-17T15:52:18Z GO:0044274 GO:0044711 formation Wikipedia:Anabolism anabolism biosynthesis synthesis multicellular organismal biosynthetic process biological_process single-organism biosynthetic process GO:0009058 biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://amigo.geneontology.org/amigo/term/GO:0070589 https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis biological_process GO:0009059 macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer biosynthetic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. https://github.com/geneontology/go-ontology/issues/17904 amino acid breakdown amino acid catabolism amino acid degradation cellular amino acid catabolic process biological_process GO:0009063 amino acid catabolic process The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. GOC:ai The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. glycoprotein metabolism biological_process GO:0009100 glycoprotein metabolic process The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the formation of glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. glycoprotein anabolism glycoprotein biosynthesis glycoprotein formation glycoprotein synthesis biological_process GO:0009101 glycoprotein biosynthetic process The chemical reactions and pathways resulting in the formation of glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine. nucleobase metabolism biological_process GO:0009112 nucleobase metabolic process The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine. GOC:ma The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues. glucan anabolism glucan biosynthesis glucan formation glucan synthesis biological_process GO:0009250 glucan biosynthetic process The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues. glucan breakdown glucan catabolism glucan degradation biological_process GO:0009251 glucan catabolic process The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues. GOC:go_curators The controlled release of proteins from a cell. GO:0045166 GO:0045731 glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment biological_process GO:0009306 protein secretion The controlled release of proteins from a cell. GOC:ai The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. jl 2009-07-15T11:55:44Z GO:0044106 amine metabolism cellular amine metabolic process biological_process GO:0009308 amine metabolic process The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. amine anabolism amine biosynthesis amine formation amine synthesis biological_process GO:0009309 amine biosynthetic process The chemical reactions and pathways resulting in the formation of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. amine breakdown amine catabolism amine degradation biological_process GO:0009310 amine catabolic process The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. GOC:jl ISBN:0198506732 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. true GO:0009314 response to electromagnetic radiation stimulus response to radiation stimulus biological_process GO:0009314 Note that 'radiation' refers to electromagnetic radiation of any wavelength. response to radiation Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. GOC:jl Wikipedia:Electromagnetic_radiation Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. biological_process GO:0009416 response to light stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. GOC:go_curators ISBN:0582227089 The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). https://github.com/geneontology/go-ontology/issues/20176 Wikipedia:Fertilisation syngamy biological_process GO:0009566 fertilization The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:tb ISBN:0198506732 The series of events in which an external stimulus is received by a cell and converted into a molecular signal. biological_process perception of external stimulus GO:0009581 detection of external stimulus The series of events in which an external stimulus is received by a cell and converted into a molecular signal. GOC:hb The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal. biological_process perception of abiotic stimulus GO:0009582 detection of abiotic stimulus The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal. GOC:hb The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal. detection of light biological_process perception of light GO:0009583 detection of light stimulus The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal. GOC:go_curators The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm. biological_process perception of visible light GO:0009584 detection of visible light The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm. GOC:go_curators ISBN:0198506732 The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal. chemoperception detection of chemical substance biological_process chemoreception perception of chemical stimulus perception of chemical substance GO:0009593 detection of chemical stimulus The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal. GOC:jl Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. response to environmental stimulus biological_process GO:0009605 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to external stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism. response to biotic stress biological_process GO:0009607 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to biotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium. GO:0009618 GO:0009680 response to bacteria biological_process GO:0009617 response to bacterium Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus. GO:0009621 response to fungi biological_process GO:0009620 response to fungus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus. https://github.com/geneontology/go-ontology/issues/16572 response to abiotic stress biological_process GO:0009628 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to abiotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. detoxification response biological_process toxin resistance toxin susceptibility/resistance GO:0009636 response to toxic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. GOC:lr The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process GO:0009653 anatomical structure morphogenesis The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. GOC:go_curators ISBN:0521436125 The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent. biological_process catechol metabolic process catechol metabolism GO:0009712 catechol-containing compound metabolic process The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent. GOC:sm ISBN:0198547684 The chemical reactions and pathways resulting in the formation of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent. biological_process catechol anabolism catechol biosynthesis catechol biosynthetic process catechol formation catechol synthesis GO:0009713 catechol-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent. GOC:go_curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism. biological_process GO:0009719 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to endogenous stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism. GOC:sm Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus. response to hormone stimulus biological_process growth regulator GO:0009725 response to hormone Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus. GOC:jl response to hormone stimulus GOC:dos Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus. response to carbohydrate stimulus biological_process GO:0009743 response to carbohydrate Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus. GOC:jl response to carbohydrate stimulus GOC:dos Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus. response to hexose stimulus biological_process GO:0009746 response to hexose Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus. GOC:jl response to hexose stimulus GOC:dos Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus. response to glucose stimulus biological_process GO:0009749 response to glucose Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus. GOC:jl response to glucose stimulus GOC:dos Any process that modulates the frequency, rate or extent of asymmetric cell division. biological_process GO:0009786 regulation of asymmetric cell division Any process that modulates the frequency, rate or extent of asymmetric cell division. GOC:lr The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis embryonal development biological_process GO:0009790 embryo development The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GOC:go_curators GOC:isa_complete GOC:mtg_sensu The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. biological_process GO:0009791 post-embryonic development The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. GOC:go_curators The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. embryogenesis biological_process GO:0009792 embryo development ending in birth or egg hatching The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. GOC:go_curators GOC:isa_complete GOC:mtg_sensu The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases). alkaloid metabolism biological_process GO:0009820 alkaloid metabolic process The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases). GOC:lr ISBN:0122146743 The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases). UM-BBD_enzymeID:e0711 alkaloid anabolism alkaloid biosynthesis alkaloid formation alkaloid synthesis biological_process GO:0009821 alkaloid biosynthetic process The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases). GOC:lr ISBN:0122146743 The chemical reactions and pathways resulting in the breakdown of alkaloids, nitrogen containing natural products not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases). alkaloid breakdown alkaloid catabolism alkaloid degradation biological_process GO:0009822 alkaloid catabolic process The chemical reactions and pathways resulting in the breakdown of alkaloids, nitrogen containing natural products not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases). GOC:lr ISBN:0122146743 Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. histogenesis and organogenesis biological_process GO:0009887 animal organ morphogenesis Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:dgh GOC:go_curators ISBN:0471245208 ISBN:0721662544 The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. histogenesis and organogenesis Wikipedia:Histogenesis histogenesis biological_process GO:0009888 tissue development The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. ISBN:0471245208 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process GO:0009889 regulation of biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis inhibition of biosynthetic process biological_process GO:0009890 negative regulation of biosynthetic process Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process activation of biosynthetic process stimulation of biosynthetic process biological_process GO:0009891 positive regulation of biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process GO:0009892 negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044253 positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process positive regulation of multicellular organismal metabolic process positive regulation of organismal metabolism stimulation of metabolic process stimulation of organismal metabolic process up-regulation of organismal metabolic process biological_process GO:0009893 positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. regulation of breakdown regulation of catabolism regulation of degradation biological_process GO:0009894 regulation of catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. down regulation of catabolic process down-regulation of catabolic process downregulation of catabolic process negative regulation of breakdown negative regulation of catabolism negative regulation of degradation inhibition of catabolic process biological_process GO:0009895 negative regulation of catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. positive regulation of breakdown positive regulation of catabolism positive regulation of degradation up regulation of catabolic process up-regulation of catabolic process upregulation of catabolic process activation of catabolic process stimulation of catabolic process biological_process GO:0009896 positive regulation of catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis. GO:0043355 biological_process hypodermal cell differentiation GO:0009913 epidermal cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis. GOC:dph GOC:go_curators GOC:mtg_sensu GOC:sdb_2009 GOC:tb hypodermal cell differentiation GOC:kmv GOC:rk The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0009914 hormone transport The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:tb The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. biological_process anterior/posterior pattern formation GO:0009952 anterior/posterior pattern specification The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism. GOC:dph GOC:go_curators GOC:isa_complete GOC:tb Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway GO:0009966 regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of signal transduction. GO:0035468 up regulation of signal transduction up-regulation of signal transduction upregulation of signal transduction activation of signal transduction stimulation of signal transduction biological_process positive regulation of signaling pathway positive regulation of signalling pathway GO:0009967 positive regulation of signal transduction Any process that activates or increases the frequency, rate or extent of signal transduction. GOC:sm positive regulation of signalling pathway GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GO:0035467 down regulation of signal transduction down-regulation of signal transduction downregulation of signal transduction inhibition of signal transduction biological_process negative regulation of signaling pathway negative regulation of signalling pathway GO:0009968 negative regulation of signal transduction Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GOC:sm negative regulation of signalling pathway GOC:mah Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 NCIt:C20480 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete. oocyte cell differentiation biological_process GO:0009994 oocyte differentiation The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete. GOC:go_curators GOC:mtg_sensu The process in which a relatively unspecialized cell acquires the specialized features of a glial cell. GO:0007404 GO:0043360 glia cell differentiation neuroglia differentiation biological_process GO:0010001 glial cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a glial cell. GOC:go_curators GOC:mtg_sensu The process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. cardiac precursor cell differentiation cardioblast cell differentiation biological_process cardiomyocyte generation GO:0010002 cardioblast differentiation The process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. GOC:go_curators cardiac precursor cell differentiation GOC:mtg_heart Compaction of chromatin structure prior to meiosis in eukaryotic cells. chromosome condensation involved in meiotic cell cycle biological_process GO:0010032 meiotic chromosome condensation Compaction of chromatin structure prior to meiosis in eukaryotic cells. PMID:10072401 chromosome condensation involved in meiotic cell cycle GOC:dph GOC:tb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. GO:1990367 process resulting in tolerance to organic substance biological_process GO:0010033 response to organic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. GOC:sm PMID:23356676 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetate stimulus. biological_process GO:0010034 response to acetate Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetate stimulus. GOC:sm Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus. biological_process GO:0010035 response to inorganic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus. GOC:sm Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus. response to metal response to heavy metal biological_process heavy metal sensitivity/resistance GO:0010038 response to metal ion Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus. GOC:sm The division of the zygote into two daughter cells that will adopt developmentally distinct potentials. biological_process zygote asymmetric cytokinesis GO:0010070 zygote asymmetric cell division The division of the zygote into two daughter cells that will adopt developmentally distinct potentials. GOC:tb The regionalization process that specifies animal organ primordium boundaries resulting in a restriction of organogenesis to a limited spatial domain and keeping the organ separate from surrounding tissues. GO:0048862 organ boundary specification biological_process GO:0010160 formation of animal organ boundary The regionalization process that specifies animal organ primordium boundaries resulting in a restriction of organogenesis to a limited spatial domain and keeping the organ separate from surrounding tissues. GOC:dph GOC:isa_complete PMID:9611175 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz). response to X-ray radiation stimulus biological_process GO:0010165 response to X-ray Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz). GOC:sm Wikipedia:X-ray The process in which the anatomical structures of the soma are generated and organized. biological_process GO:0010171 body morphogenesis The process in which the anatomical structures of the soma are generated and organized. GOC:ems ISBN:0140512888 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. response to ionising radiation response to ionizing radiation stimulus biological_process GO:0010212 response to ionizing radiation Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. PMID:12509526 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. response to organic nitrogen biological_process GO:0010243 response to organonitrogen compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. PMID:9869419 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. endomembrane organization endomembrane system organisation biological_process GO:0010256 endomembrane system organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. GOC:mah GOC:sm endomembrane system organisation GOC:mah Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum. biological_process response to gamma ray response to gamma-ray photon GO:0010332 response to gamma radiation Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum. GOC:tair_curators Any process that modulates the frequency, rate or extent of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. biological_process GO:0010453 regulation of cell fate commitment Any process that modulates the frequency, rate or extent of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. GOC:dph GOC:tb Any process that stops, prevents or reduces the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. biological_process GO:0010454 negative regulation of cell fate commitment Any process that stops, prevents or reduces the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. GOC:dph GOC:tb Any process that activates, maintains or increases the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. biological_process GO:0010455 positive regulation of cell fate commitment Any process that activates, maintains or increases the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field. GOC:dph GOC:tb The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. biological_process GO:0010463 mesenchymal cell proliferation The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. biological_process GO:0010464 regulation of mesenchymal cell proliferation Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. GOC:dph GOC:tb The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. https://github.com/geneontology/go-ontology/issues/22557 https://github.com/geneontology/go-ontology/issues/25419 Wikipedia:Gene_expression biological_process GO:0010467 gene expression The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. GOC:txnOH-2018 PMID:25934543 PMID:31580950 The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. GOC:txnOH-2018 PMID:25934543 PMID:31580950 Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process gene regulation regulation of gene product expression GO:0010468 This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 gene regulation GOC:cjm Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. biological_process GO:0010470 regulation of gastrulation Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. GOC:dph GOC:tb Any process resulting in the physical partitioning and separation of an epidermal cell, any of the cells making up the epidermis, into daughter cells. biological_process hypodermal cell division GO:0010481 epidermal cell division Any process resulting in the physical partitioning and separation of an epidermal cell, any of the cells making up the epidermis, into daughter cells. PMID:17450124 hypodermal cell division GOC:kmv GOC:rk Any process that modulates the frequency, rate or extent of the physical partitioning and separation of an epidermal cell into daughter cells. An epidermal cell is any of the cells that make up the epidermis. biological_process regulation of hypodermal cell division GO:0010482 regulation of epidermal cell division Any process that modulates the frequency, rate or extent of the physical partitioning and separation of an epidermal cell into daughter cells. An epidermal cell is any of the cells that make up the epidermis. PMID:17450124 regulation of hypodermal cell division GOC:kmv GOC:rk The movement of substances between cells. jl 2013-12-19T13:24:56Z GO:1902585 biological_process single organism intercellular transport single-organism intercellular transport GO:0010496 intercellular transport The movement of substances between cells. GOC:dhl single organism intercellular transport GOC:TermGenie Any process that modulates the frequency, rate or extent of membrane disassembly. biological_process GO:0010549 regulation of membrane disassembly Any process that modulates the frequency, rate or extent of membrane disassembly. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010556 regulation of macromolecule biosynthetic process Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010557 positive regulation of macromolecule biosynthetic process Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010558 negative regulation of macromolecule biosynthetic process Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. biological_process GO:0010559 regulation of glycoprotein biosynthetic process Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. GOC:dph GOC:tb Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. biological_process GO:0010560 positive regulation of glycoprotein biosynthetic process Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. GOC:dph GOC:tb Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. biological_process GO:0010561 negative regulation of glycoprotein biosynthetic process Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010562 positive regulation of phosphorus metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010563 negative regulation of phosphorus metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. biological_process GO:0010564 regulation of cell cycle process Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. biological_process GO:0010565 regulation of cellular ketone metabolic process Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells. biological_process GO:0010566 regulation of ketone biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells. biological_process GO:0010567 regulation of ketone catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010604 positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010605 negative regulation of macromolecule metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. posttranscriptional regulation of gene expression biological_process GO:0010608 post-transcriptional regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division. biological_process GO:0010611 regulation of cardiac muscle hypertrophy Any process that modulates the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division. GOC:dph GOC:tb Any process that modulates the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. biological_process GO:0010612 regulation of cardiac muscle adaptation Any process that modulates the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division. biological_process GO:0010613 positive regulation of cardiac muscle hypertrophy Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division. biological_process GO:0010614 negative regulation of cardiac muscle hypertrophy Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division. GOC:BHF GOC:dph GOC:tb Any process that increases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. biological_process GO:0010615 positive regulation of cardiac muscle adaptation Any process that increases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. biological_process GO:0010616 negative regulation of cardiac muscle adaptation Any process that decreases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. GOC:BHF GOC:dph GOC:tb The activation of endogenous cellular processes that result in the death of a cell as part of its development. developmental programmed cell death programmed cell death involved in development biological_process GO:0010623 This process is part of the natural developmental program of some cell types, but it does not always happen as part of the development or shaping of a gross anatomical structure. programmed cell death involved in cell development The activation of endogenous cellular processes that result in the death of a cell as part of its development. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 biological_process GO:0010628 positive regulation of gene expression Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 biological_process gene silencing GO:0010629 This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. negative regulation of gene expression Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. positive regulation of organelle organisation biological_process positive regulation of organelle organization and biogenesis GO:0010638 positive regulation of organelle organization Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb positive regulation of organelle organisation GOC:mah positive regulation of organelle organization and biogenesis GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. negative regulation of organelle organisation biological_process negative regulation of organelle organization and biogenesis GO:0010639 negative regulation of organelle organization Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb negative regulation of organelle organisation GOC:mah negative regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010646 regulation of cell communication Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010647 positive regulation of cell communication Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010648 negative regulation of cell communication Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that decreases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death. negative regulation of muscle cell apoptosis biological_process GO:0010656 negative regulation of muscle cell apoptotic process Any process that decreases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death. GOC:dph GOC:mtg_apoptosis GOC:tb A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a muscle cell and result in its death. A muscle cell is a mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle. muscle cell apoptosis biological_process GO:0010657 muscle cell apoptotic process A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a muscle cell and result in its death. A muscle cell is a mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle. CL:0000187 GOC:dph GOC:mtg_apoptosis GOC:tb A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a striated muscle cell and result in its death. Striated muscle cells make up striated muscle fibers which are divided by transverse bands into striations. striated muscle cell apoptosis biological_process GO:0010658 striated muscle cell apoptotic process A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a striated muscle cell and result in its death. Striated muscle cells make up striated muscle fibers which are divided by transverse bands into striations. CL:0000737 GOC:dph GOC:mtg_apoptosis GOC:tb A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. cardiac muscle cell apoptosis biological_process GO:0010659 cardiac muscle cell apoptotic process A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. CL:0000746 GOC:dph GOC:mtg_apoptosis GOC:tb Any process that modulates the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death. regulation of muscle cell apoptosis biological_process GO:0010660 regulation of muscle cell apoptotic process Any process that modulates the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that increases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death. positive regulation of muscle cell apoptosis biological_process GO:0010661 positive regulation of muscle cell apoptotic process Any process that increases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that modulates the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death. regulation of striated muscle cell apoptosis biological_process GO:0010662 regulation of striated muscle cell apoptotic process Any process that modulates the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that increases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death. positive regulation of striated muscle cell apoptosis biological_process GO:0010663 positive regulation of striated muscle cell apoptotic process Any process that increases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that decreases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death. down regulation of striated muscle cell apoptosis down-regulation of striated muscle cell apoptosis downregulation of striated muscle cell apoptosis inhibition of striated muscle cell apoptosis negative regulation of striated muscle cell apoptosis biological_process GO:0010664 negative regulation of striated muscle cell apoptotic process Any process that decreases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death. GOC:BHF GOC:dph GOC:mtg_apoptosis GOC:rl GOC:tb down regulation of striated muscle cell apoptosis GOC:dph GOC:rl GOC:tb down-regulation of striated muscle cell apoptosis GOC:dph GOC:rl GOC:tb downregulation of striated muscle cell apoptosis GOC:dph GOC:rl GOC:tb inhibition of striated muscle cell apoptosis GOC:dph GOC:rl GOC:tb Any process that modulates the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death. regulation of cardiac muscle cell apoptosis biological_process GO:0010665 regulation of cardiac muscle cell apoptotic process Any process that modulates the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that increases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death. positive regulation of cardiac muscle cell apoptosis biological_process GO:0010666 positive regulation of cardiac muscle cell apoptotic process Any process that increases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death. down regulation of cardiac muscle cell apoptosis down-regulation of cardiac muscle cell apoptosis downregulation of cardiac muscle cell apoptosis inhibition of cardiac muscle cell apoptosis negative regulation of cardiac muscle cell apoptosis biological_process GO:0010667 negative regulation of cardiac muscle cell apoptotic process Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death. GOC:BHF GOC:dph GOC:mtg_apoptosis GOC:rl GOC:tb down regulation of cardiac muscle cell apoptosis GOC:dph GOC:rl GOC:tb down-regulation of cardiac muscle cell apoptosis GOC:dph GOC:rl GOC:tb downregulation of cardiac muscle cell apoptosis GOC:dph GOC:rl GOC:tb inhibition of cardiac muscle cell apoptosis GOC:dph GOC:rl GOC:tb The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an ectodermal cell. Differentiation includes the processes involved in commitment of a cell to a specific fate. biological_process GO:0010668 ectodermal cell differentiation The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an ectodermal cell. Differentiation includes the processes involved in commitment of a cell to a specific fate. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the regulated release of norepinephrine. biological_process GO:0010700 negative regulation of norepinephrine secretion Any process that decreases the frequency, rate or extent of the regulated release of norepinephrine. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the regulated release of norepinephrine. biological_process GO:0010701 positive regulation of norepinephrine secretion Any process that increases the frequency, rate or extent of the regulated release of norepinephrine. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix. regulation of collagen breakdown regulation of collagen catabolism regulation of collagen degradation biological_process GO:0010710 regulation of collagen catabolic process Any process that modulates the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix. GOC:BHF GOC:dph GOC:tb regulation of collagen breakdown GOC:dph GOC:tb regulation of collagen catabolism GOC:dph GOC:tb regulation of collagen degradation GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix. down regulation of collagen catabolic process down-regulation of collagen catabolic process downregulation of collagen catabolic process negative regulation of collagen breakdown negative regulation of collagen catabolism negative regulation of collagen degradation inhibition of collagen catabolic process biological_process GO:0010711 negative regulation of collagen catabolic process Any process that decreases the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix. GOC:BHF GOC:dph GOC:tb down regulation of collagen catabolic process GOC:dph GOC:tb down-regulation of collagen catabolic process GOC:dph GOC:tb downregulation of collagen catabolic process GOC:dph GOC:tb negative regulation of collagen breakdown GOC:dph GOC:tb negative regulation of collagen catabolism GOC:dph GOC:tb negative regulation of collagen degradation GOC:dph GOC:tb inhibition of collagen catabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. regulation of collagen metabolism biological_process GO:0010712 regulation of collagen metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. GOC:dph GOC:tb regulation of collagen metabolism GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. biological_process GO:0010713 negative regulation of collagen metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. positive regulation of collagen metabolism biological_process GO:0010714 positive regulation of collagen metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. GOC:dph GOC:tb positive regulation of collagen metabolism GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. regulation of extracellular matrix breakdown regulation of extracellular matrix degradation biological_process GO:0010715 regulation of extracellular matrix disassembly Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. GOC:BHF GOC:dph GOC:tb regulation of extracellular matrix breakdown GOC:dph GOC:tb regulation of extracellular matrix degradation GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. down regulation of extracellular matrix disassembly down-regulation of extracellular matrix disassembly downregulation of extracellular matrix disassembly negative regulation of extracellular matrix breakdown negative regulation of extracellular matrix degradation inhibition of extracellular matrix disassembly biological_process GO:0010716 negative regulation of extracellular matrix disassembly Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. GOC:BHF GOC:dph GOC:tb down regulation of extracellular matrix disassembly GOC:dph GOC:tb down-regulation of extracellular matrix disassembly GOC:dph GOC:tb downregulation of extracellular matrix disassembly GOC:dph GOC:tb negative regulation of extracellular matrix breakdown GOC:dph GOC:tb negative regulation of extracellular matrix degradation GOC:dph GOC:tb inhibition of extracellular matrix disassembly GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. biological_process GO:0010717 regulation of epithelial to mesenchymal transition Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. GOC:BHF GOC:dph GOC:tb Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. biological_process GO:0010718 positive regulation of epithelial to mesenchymal transition Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. biological_process GO:0010719 negative regulation of epithelial to mesenchymal transition Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell. GOC:BHF GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0010720 positive regulation of cell development Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0010721 negative regulation of cell development Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0010765 positive regulation of sodium ion transport Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0010766 negative regulation of sodium ion transport Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. https://github.com/geneontology/go-ontology/issues/24299 biological_process GO:0010770 positive regulation of cell morphogenesis Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. https://github.com/geneontology/go-ontology/issues/24299 biological_process GO:0010771 negative regulation of cell morphogenesis Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of glucose transport GO:0010827 regulation of glucose transmembrane transport Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process positive regulation of glucose transport GO:0010828 positive regulation of glucose transmembrane transport Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:BHF GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process negative regulation of glucose transport GO:0010829 negative regulation of glucose transmembrane transport Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:BHF GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. biological_process GO:0010830 regulation of myotube differentiation Any process that modulates the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. GOC:dph GOC:tb Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. biological_process GO:0010831 positive regulation of myotube differentiation Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. biological_process GO:0010832 negative regulation of myotube differentiation Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. GOC:dph GOC:tb The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia. retinal lamination retinal layer formation biological_process GO:0010842 retina layer formation The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia. GOC:ascb_2009 GOC:dph GOC:tb PMID:1270266 retinal lamination GOC:dph GOC:tb retinal layer formation GOC:dph GOC:tb Any process in which a lipid is transported to, or maintained in, a specific location. lipid localisation biological_process GO:0010876 lipid localization Any process in which a lipid is transported to, or maintained in, a specific location. GOC:BHF GOC:dph GOC:tb lipid localisation GOC:mah Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. biological_process GO:0010893 positive regulation of steroid biosynthetic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. biological_process GO:0010894 negative regulation of steroid biosynthetic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:BHF GOC:tb Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. regulation of glucose metabolism biological_process GO:0010906 regulation of glucose metabolic process Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. GOC:BHF GOC:tb regulation of glucose metabolism GOC:tb Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. positive regulation of glucose metabolism biological_process GO:0010907 positive regulation of glucose metabolic process Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. GOC:BHF GOC:tb positive regulation of glucose metabolism GOC:tb The cellular component assembly that is part of the initial shaping of the component during its developmental progression. biological_process GO:0010927 cellular component assembly involved in morphogenesis The cellular component assembly that is part of the initial shaping of the component during its developmental progression. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of cytoplasmic microtubule depolymerization. biological_process GO:0010937 regulation of cytoplasmic microtubule depolymerization Any process that modulates the frequency, rate or extent of cytoplasmic microtubule depolymerization. GOC:dph GOC:tb The removal of tubulin heterodimers from one or both ends of a cytoplasmic microtubule. biological_process GO:0010938 cytoplasmic microtubule depolymerization The removal of tubulin heterodimers from one or both ends of a cytoplasmic microtubule. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tb 2009-04-27T09:53:22Z biological_process GO:0010948 negative regulation of cell cycle process Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that modulates the frequency, rate, or extent of metal ion transport. Metal ion transport is the directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. tb 2009-05-06T11:40:55Z biological_process GO:0010959 regulation of metal ion transport Any process that modulates the frequency, rate, or extent of metal ion transport. Metal ion transport is the directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues. tb 2009-05-11T12:17:53Z biological_process GO:0010962 regulation of glucan biosynthetic process Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. tb 2009-05-20T11:42:50Z biological_process GO:0010966 regulation of phosphate transport Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell. tb 2009-05-20T11:51:21Z biological_process GO:0010968 regulation of microtubule nucleation Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell. GOC:dph GOC:tb The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. tb 2009-05-27T10:56:08Z microtubule-based transport establishment of localization by movement along microtubule movement along microtubule biological_process GO:0010970 transport along microtubule The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. GOC:dph GOC:mah GOC:tb establishment of localization by movement along microtubule GOC:dph Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). tb 2009-06-01T10:44:45Z regulation of neurite biosynthesis regulation of neurite development regulation of neurite formation regulation of neurite growth biological_process GO:0010975 regulation of neuron projection development Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). GOC:dph GOC:tb regulation of neurite biosynthesis GOC:mah regulation of neurite development GOC:mah regulation of neurite formation GOC:mah regulation of neurite growth GOC:mah Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). tb 2009-06-01T10:46:44Z positive regulation of neurite biosynthesis positive regulation of neurite development positive regulation of neurite formation positive regulation of neurite growth biological_process GO:0010976 positive regulation of neuron projection development Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). GOC:dph GOC:tb positive regulation of neurite biosynthesis GOC:mah positive regulation of neurite development GOC:mah positive regulation of neurite formation GOC:mah positive regulation of neurite growth GOC:mah Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). tb 2009-06-01T10:47:42Z negative regulation of neurite biosynthesis negative regulation of neurite development negative regulation of neurite formation negative regulation of neurite growth biological_process growth cone collapse GO:0010977 negative regulation of neuron projection development Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). GOC:dph GOC:tb negative regulation of neurite biosynthesis GOC:mah negative regulation of neurite development GOC:mah negative regulation of neurite formation GOC:mah negative regulation of neurite growth GOC:mah growth cone collapse GOC:pr A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. https://github.com/geneontology/go-ontology/issues/24835 GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death non-apoptotic programmed cell death nonapoptotic programmed cell death biological_process PCD RCD caspase-independent apoptosis GO:0012501 Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. programmed cell death A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GOC:lr GOC:mtg_apoptosis A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. Wikipedia:Endomembrane_system cellular_component GO:0012505 endomembrane system A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. GOC:lh The lipid bilayer surrounding any membrane-bounded vesicle in the cell. NIF_Subcellular:sao1153182838 cellular_component GO:0012506 vesicle membrane The lipid bilayer surrounding any membrane-bounded vesicle in the cell. GOC:mah GOC:vesicle The multiplication or reproduction of glial cells by cell division, resulting in the expansion of their population. Glial cells exist throughout the nervous system, and include Schwann cells, astrocytes, and oligodendrocytes among others. glia proliferation biological_process GO:0014009 glial cell proliferation The multiplication or reproduction of glial cells by cell division, resulting in the expansion of their population. Glial cells exist throughout the nervous system, and include Schwann cells, astrocytes, and oligodendrocytes among others. GOC:ef ISBN:0878932585 Any process that modulates the frequency, rate or extent of gliogenesis, the formation of mature glia. biological_process GO:0014013 regulation of gliogenesis Any process that modulates the frequency, rate or extent of gliogenesis, the formation of mature glia. GOC:ef Any process that stops, prevents, or reduces the frequency, rate or extent of gliogenesis, the formation of mature glia. down regulation of gliogenesis down-regulation of gliogenesis downregulation of gliogenesis inhibition of gliogenesis biological_process GO:0014014 negative regulation of gliogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of gliogenesis, the formation of mature glia. GOC:ef Any process that activates or increases the frequency, rate or extent of gliogenesis, the formation of mature glia. up regulation of gliogenesis up-regulation of gliogenesis upregulation of gliogenesis activation of gliogenesis stimulation of gliogenesis biological_process GO:0014015 positive regulation of gliogenesis Any process that activates or increases the frequency, rate or extent of gliogenesis, the formation of mature glia. GOC:ef The process in which a relatively unspecialized cell acquires specialized features of a neuroblast. There are at least four stages through which the pluripotent cells of epiblast or blastula become neuroblasts. biological_process GO:0014016 neuroblast differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuroblast. There are at least four stages through which the pluripotent cells of epiblast or blastula become neuroblasts. GOC:ef ISBN:0878932585 The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron. biological_process GO:0014019 neuroblast development The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron. GOC:ef ISBN:0878932585 The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube. GO:0014024 primary neural tube morphogenesis primary neurulation biological_process neural rod cavitation GO:0014020 primary neural tube formation The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube. GOC:ef ISBN:0878932585 PMID:15327780 primary neural tube morphogenesis GOC:dph The formation of a solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts. biological_process GO:0014023 neural rod formation The formation of a solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts. GOC:dh GOC:ef The formation of a thickened region of the neurectoderm that is roughly triangular in cross section. The neural keel develops from the neural plate and develops into the neural rod. Neural keel formation occurs during primary neurulation in teleosts. biological_process GO:0014025 neural keel formation The formation of a thickened region of the neurectoderm that is roughly triangular in cross section. The neural keel develops from the neural plate and develops into the neural rod. Neural keel formation occurs during primary neurulation in teleosts. GOC:dh GOC:ef The formation of the notochord from the chordamesoderm. The notochord is composed of large cells packed within a firm connective tissue sheath and is found in all chordates at the ventral surface of the neural tube. In vertebrates, the notochord contributes to the vertebral column. biological_process GO:0014028 notochord formation The formation of the notochord from the chordamesoderm. The notochord is composed of large cells packed within a firm connective tissue sheath and is found in all chordates at the ventral surface of the neural tube. In vertebrates, the notochord contributes to the vertebral column. GOC:dh GOC:ef The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes. biological_process GO:0014029 neural crest formation The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes. GOC:dh GOC:ef The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. biological_process GO:0014031 mesenchymal cell development The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. GOC:dh GOC:ef The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. biological_process GO:0014032 neural crest cell development The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. GOC:dh GOC:ef The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell. biological_process GO:0014033 neural crest cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell. GOC:dh GOC:ef Any process that modulates the frequency, rate or extent of neuron maturation, the process leading to the attainment of the full functional capacity of a neuron. This process is independent of morphogenetic change. biological_process GO:0014041 regulation of neuron maturation Any process that modulates the frequency, rate or extent of neuron maturation, the process leading to the attainment of the full functional capacity of a neuron. This process is independent of morphogenetic change. GOC:ef Any process that activates or increases the frequency, rate or extent of neuron maturation. up regulation of neuron maturation up-regulation of neuron maturation upregulation of neuron maturation activation of neuron maturation stimulation of neuron maturation biological_process GO:0014042 positive regulation of neuron maturation Any process that activates or increases the frequency, rate or extent of neuron maturation. GOC:ef Any process that stops, prevents, or reduces the frequency, rate or extent of neuron maturation. down regulation of neuron maturation down-regulation of neuron maturation downregulation of neuron maturation inhibition of neuron maturation biological_process GO:0014043 negative regulation of neuron maturation Any process that stops, prevents, or reduces the frequency, rate or extent of neuron maturation. GOC:ef The regulated release of acetylcholine by a cell. The acetylcholine acts as a neurotransmitter that acts in both the peripheral nervous system (PNS) and central nervous system (CNS). biological_process GO:0014055 acetylcholine secretion, neurotransmission The regulated release of acetylcholine by a cell. The acetylcholine acts as a neurotransmitter that acts in both the peripheral nervous system (PNS) and central nervous system (CNS). GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine. biological_process GO:0014056 regulation of acetylcholine secretion, neurotransmission Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that activates or increases the frequency, rate or extent of the regulated release of acetylcholine. up regulation of acetylcholine secretion up-regulation of acetylcholine secretion upregulation of acetylcholine secretion activation of acetylcholine secretion stimulation of acetylcholine secretion biological_process GO:0014057 positive regulation of acetylcholine secretion, neurotransmission Any process that activates or increases the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of acetylcholine. down regulation of acetylcholine secretion down-regulation of acetylcholine secretion downregulation of acetylcholine secretion inhibition of acetylcholine secretion biological_process GO:0014058 negative regulation of acetylcholine secretion, neurotransmission Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine. regulation of noradrenaline secretion biological_process GO:0014061 regulation of norepinephrine secretion Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of serotonin. biological_process regulation of serotonin release GO:0014062 regulation of serotonin secretion Any process that modulates the frequency, rate or extent of the regulated release of serotonin. GOC:ef regulation of serotonin release GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin. down regulation of serotonin secretion down-regulation of serotonin secretion downregulation of serotonin secretion inhibition of serotonin secretion biological_process positive regulation of serotonin release GO:0014063 negative regulation of serotonin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin. GOC:ef positive regulation of serotonin release GOC:tb Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin. up regulation of serotonin secretion up-regulation of serotonin secretion upregulation of serotonin secretion activation of serotonin secretion stimulation of serotonin secretion biological_process positive regulation of serotonin release GO:0014064 positive regulation of serotonin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin. GOC:ef positive regulation of serotonin release GOC:tb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus. response to organic cyclic substance biological_process GO:0014070 response to organic cyclic compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus. GOC:ef response to organic cyclic substance GOC:mah Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups. response to amine stimulus biological_process GO:0014075 response to amine Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups. GOC:ef response to amine stimulus GOC:dos The process whose specific outcome is the progression of a striated muscle over time, from its formation to the mature structure. Striated muscle contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. Skeletal muscle myoblasts fuse to form myotubes and eventually multinucleated muscle fibers. The fusion of cardiac cells is very rare and can only form binucleate cells. biological_process GO:0014706 striated muscle tissue development The process whose specific outcome is the progression of a striated muscle over time, from its formation to the mature structure. Striated muscle contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. Skeletal muscle myoblasts fuse to form myotubes and eventually multinucleated muscle fibers. The fusion of cardiac cells is very rare and can only form binucleate cells. CL:0000737 GOC:dph GOC:mtg_muscle Any process in which skeletal muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities. biological_process regulation of skeletal muscle plasticity GO:0014733 regulation of skeletal muscle adaptation Any process in which skeletal muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities. GOC:mtg_muscle The enlargement or overgrowth of all or part of an organ due to an increase in size (not length) of individual muscle fibers without cell division. In the case of skeletal muscle cells this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils. biological_process GO:0014734 skeletal muscle hypertrophy The enlargement or overgrowth of all or part of an organ due to an increase in size (not length) of individual muscle fibers without cell division. In the case of skeletal muscle cells this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils. GOC:mtg_muscle Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle hypertrophy. biological_process GO:0014741 negative regulation of muscle hypertrophy Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle hypertrophy. GOC:mtg_muscle Any process that activates or increases the frequency, rate or extent of muscle hypertrophy. biological_process GO:0014742 positive regulation of muscle hypertrophy Any process that activates or increases the frequency, rate or extent of muscle hypertrophy. GOC:mtg_muscle Any process that modulates the frequency, rate or extent of muscle hypertrophy. biological_process GO:0014743 regulation of muscle hypertrophy Any process that modulates the frequency, rate or extent of muscle hypertrophy. GOC:mtg_muscle Any process that activates or increases the frequency, rate or extent of muscle adaptation. biological_process positive regulation of muscle plasticity GO:0014744 positive regulation of muscle adaptation Any process that activates or increases the frequency, rate or extent of muscle adaptation. GOC:mtg_muscle Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle adaptation. biological_process negative regulation of muscle plasticity GO:0014745 negative regulation of muscle adaptation Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle adaptation. GOC:mtg_muscle Any process in which smooth muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities. biological_process smooth muscle plasticity GO:0014805 smooth muscle adaptation Any process in which smooth muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities. GOC:mtg_muscle Any process that modulates the frequency, rate or extent of somitogenesis. biological_process GO:0014807 regulation of somitogenesis Any process that modulates the frequency, rate or extent of somitogenesis. GOC:mtg_muscle Any process that modulates the frequency, rate or extent of skeletal muscle contraction. biological_process GO:0014819 regulation of skeletal muscle contraction Any process that modulates the frequency, rate or extent of skeletal muscle contraction. GOC:ef GOC:mtg_muscle A process in which force is generated within phasic smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the phasic smooth muscle, the muscle contraction occurs without an ordered sarcomeric structure. Phasic smooth muscle contraction occurs in a series of discrete contractions and relaxations. biological_process GO:0014821 phasic smooth muscle contraction A process in which force is generated within phasic smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the phasic smooth muscle, the muscle contraction occurs without an ordered sarcomeric structure. Phasic smooth muscle contraction occurs in a series of discrete contractions and relaxations. GOC:mtg_muscle A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the intestine. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The intestine is the section of the alimentary canal from the stomach to the anal canal. It includes the large intestine and small intestine. biological_process GO:0014827 intestine smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the intestine. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The intestine is the section of the alimentary canal from the stomach to the anal canal. It includes the large intestine and small intestine. GOC:mtg_muscle MA:0001539 MSH:D007422 A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the gastro-intestinal system. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The gastro-intestinal system generally refers to the digestive structures stretching from the mouth to anus, but does not include the accessory glandular organs (liver, pancreas and biliary tract). biological_process GO:0014831 gastro-intestinal system smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the gastro-intestinal system. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The gastro-intestinal system generally refers to the digestive structures stretching from the mouth to anus, but does not include the accessory glandular organs (liver, pancreas and biliary tract). GOC:mtg_muscle MA:0001523 MSH:D041981 Any process that modulates the frequency, rate or extent of skeletal muscle contraction by variation of the pattern of stimulation by nervous system. biological_process GO:0014852 regulation of skeletal muscle contraction by neural stimulation via neuromuscular junction Any process that modulates the frequency, rate or extent of skeletal muscle contraction by variation of the pattern of stimulation by nervous system. GOC:ef GOC:mtg_muscle The multiplication or reproduction of striated muscle cells, resulting in the expansion of a cell population. Striated muscles contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. biological_process GO:0014855 striated muscle cell proliferation The multiplication or reproduction of striated muscle cells, resulting in the expansion of a cell population. Striated muscles contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. CL:0000737 GOC:ef GOC:mtg_muscle The multiplication or reproduction of skeletal muscle cells, resulting in the expansion of a cell population. biological_process GO:0014856 skeletal muscle cell proliferation The multiplication or reproduction of skeletal muscle cells, resulting in the expansion of a cell population. CL:0000188 GOC:ef GOC:mtg_muscle Any process that modulates the frequency, rate or extent of skeletal muscle cell proliferation. biological_process GO:0014857 regulation of skeletal muscle cell proliferation Any process that modulates the frequency, rate or extent of skeletal muscle cell proliferation. CL:0000188 GOC:ef GOC:mtg_muscle Any process that activates or increases the frequency, rate or extent of skeletal muscle cell proliferation. biological_process GO:0014858 positive regulation of skeletal muscle cell proliferation Any process that activates or increases the frequency, rate or extent of skeletal muscle cell proliferation. CL:0000188 GOC:ef GOC:mtg_muscle Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle cell proliferation. biological_process GO:0014859 negative regulation of skeletal muscle cell proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle cell proliferation. CL:0000188 GOC:ef GOC:mtg_muscle The regulated release of neurotransmitter into the synaptic cleft involved in skeletal muscle contraction. A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin. neurotransmitter secretion involved in control of skeletal muscle contraction biological_process GO:0014860 neurotransmitter secretion involved in regulation of skeletal muscle contraction The regulated release of neurotransmitter into the synaptic cleft involved in skeletal muscle contraction. A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin. GOC:dph GOC:mtg_muscle GOC:tb neurotransmitter secretion involved in control of skeletal muscle contraction GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of skeletal muscle contraction by depolarization of muscle membrane and ionic fluxes. biological_process regulation of skeletal muscle contraction via membrane action potential GO:0014861 regulation of skeletal muscle contraction via regulation of action potential Any process that modulates the frequency, rate or extent of skeletal muscle contraction by depolarization of muscle membrane and ionic fluxes. GOC:BHF GOC:mtg_cardiac_conduct_nov11 GOC:mtg_muscle The process whose specific outcome is the progression of the skeletal myofibril over time, from its formation to the mature structure. A skeletal myofibril is a myofibril specific to skeletal muscle cells. biological_process GO:0014866 skeletal myofibril assembly The process whose specific outcome is the progression of the skeletal myofibril over time, from its formation to the mature structure. A skeletal myofibril is a myofibril specific to skeletal muscle cells. GOC:ef GOC:mtg_muscle The process resulting in the physical partitioning and separation of a myoblast into daughter cells. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. biological_process GO:0014872 myoblast division The process resulting in the physical partitioning and separation of a myoblast into daughter cells. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. CL:0000056 GOC:ef GOC:mtg_muscle Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. This occurs as part of the regulation of muscle adaptation. biological_process response to stimulus involved in regulation of muscle plasticity GO:0014874 response to stimulus involved in regulation of muscle adaptation Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. This occurs as part of the regulation of muscle adaptation. GOC:ef GOC:mtg_muscle Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus. This process occurs as part of the regulation of muscle adaptation. biological_process response to electrical stimulus involved in regulation of muscle plasticity GO:0014878 response to electrical stimulus involved in regulation of muscle adaptation Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus. This process occurs as part of the regulation of muscle adaptation. GOC:ef GOC:mtg_muscle The series of events by which an electrical stimulus is received and converted into a molecular signal. This occurs as part of the regulation of muscle adaptation. biological_process GO:0014879 detection of electrical stimulus involved in regulation of muscle adaptation The series of events by which an electrical stimulus is received and converted into a molecular signal. This occurs as part of the regulation of muscle adaptation. GOC:ef GOC:mtg_muscle The process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. biological_process cardiac muscle plasticity GO:0014887 cardiac muscle adaptation The process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. GOC:mtg_muscle Any process in which striated muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities. biological_process striated muscle plasticity GO:0014888 striated muscle adaptation Any process in which striated muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities. GOC:mtg_muscle The enlargement or overgrowth of all or part of an organ due to an increase in size of its smooth muscle cells without cell division. Physiological hypertrophy is a normal process during development, and can also occur in mature structures on demand. In the uterus, smooth muscle cells undergo hypertrophy during pregnancy. biological_process GO:0014895 smooth muscle hypertrophy The enlargement or overgrowth of all or part of an organ due to an increase in size of its smooth muscle cells without cell division. Physiological hypertrophy is a normal process during development, and can also occur in mature structures on demand. In the uterus, smooth muscle cells undergo hypertrophy during pregnancy. GOC:mtg_muscle The muscle system process that results in enlargement or overgrowth of all or part of a muscle organ due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development (it stops in cardiac muscle after adolescence) and can also be brought on in response to demand. In athletes cardiac and skeletal muscles undergo hypertrophy stimulated by increasing muscle activity on exercise. Smooth muscle cells in the uterus undergo hypertrophy during pregnancy. Wikipedia:Muscle_hypertrophy biological_process GO:0014896 muscle hypertrophy The muscle system process that results in enlargement or overgrowth of all or part of a muscle organ due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development (it stops in cardiac muscle after adolescence) and can also be brought on in response to demand. In athletes cardiac and skeletal muscles undergo hypertrophy stimulated by increasing muscle activity on exercise. Smooth muscle cells in the uterus undergo hypertrophy during pregnancy. GOC:mtg_muscle The enlargement or overgrowth of all or part of an organ due to an increase in size of muscle cells without cell division. In the case of striated muscle, this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils. biological_process GO:0014897 striated muscle hypertrophy The enlargement or overgrowth of all or part of an organ due to an increase in size of muscle cells without cell division. In the case of striated muscle, this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils. GOC:mtg_muscle The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. biological_process GO:0014902 myotube differentiation The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. GOC:mtg_muscle The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. biological_process GO:0014904 myotube cell development The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. GOC:mtg_muscle The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015831 enzyme transport biological_process GO:0015031 protein transport The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Enables the transfer of an ion from one side of a membrane to the other. https://github.com/geneontology/go-ontology/issues/24479 ion transmembrane transporter activity ion transporter activity molecular_function GO:0015075 monoatomic ion transmembrane transporter activity GO_REF:0000090 Enables the transfer of an ion from one side of a membrane to the other. GOC:dgf GOC:mtg_transport ISBN:0815340729 Enables the transfer of sodium ions (Na+) from one side of a membrane to the other. https://github.com/geneontology/go-ontology/issues/24076 GO:0022816 RHEA:34963 sodium transporter activity molecular_function GO:0015081 sodium ion transmembrane transporter activity Enables the transfer of sodium ions (Na+) from one side of a membrane to the other. GOC:BHF GOC:ai RHEA:34963 Enables the transfer of organic cations from one side of a membrane to the other. Organic cations are atoms or small molecules with a positive charge that contain carbon in covalent linkage. Reactome:R-HSA-2161500 Reactome:R-HSA-549129 Reactome:R-HSA-549279 Reactome:R-HSA-549304 Reactome:R-HSA-549322 Reactome:R-HSA-561054 Reactome:R-HSA-561072 Reactome:R-HSA-9794270 Reactome:R-HSA-9794523 Reactome:R-HSA-9795207 molecular_function GO:0015101 organic cation transmembrane transporter activity Enables the transfer of organic cations from one side of a membrane to the other. Organic cations are atoms or small molecules with a positive charge that contain carbon in covalent linkage. GOC:ai GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-2161500 abacavir [extracellular] => abacavir [cytosol] Reactome:R-HSA-549129 OCT1 transports organic cations into hepatic cells Reactome:R-HSA-549279 OCT2 mediates tubular uptake of organic cations in the kidney Reactome:R-HSA-549304 OCT3 mediates renal clearance of organic cations Reactome:R-HSA-549322 OCT1 transports organic cations out of hepatic cells Reactome:R-HSA-561054 OCT2 mediates tubular secretion of organic cations in the kidney Reactome:R-HSA-561072 OCT3 mediates renal uptake of organic cations Reactome:R-HSA-9794270 SLCO1A2 transports Cipro(1+) into the cytosol Reactome:R-HSA-9794523 SLC22A1 transports Cipro into renal cell Reactome:R-HSA-9795207 SLC22A1 transports Cipro into hepatic cell Enables the transfer of inorganic anions from one side of a membrane to the other. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage. molecular_function GO:0015103 inorganic anion transmembrane transporter activity Enables the transfer of inorganic anions from one side of a membrane to the other. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage. GOC:ai Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. RHEA:28695 Reactome:R-HSA-2752067 molecular_function GO:0015106 bicarbonate transmembrane transporter activity Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. GOC:ai Reactome:R-HSA-2752067 BESTs transport cytosolic HCO3- to extracellular region Enables the transfer of phosphate (PO4 3-) ions from one side of a membrane to the other. pr 2012-11-22T15:43:10Z GO:1901677 RHEA:32823 molecular_function phosphate transmembrane transporter activity GO:0015114 phosphate ion transmembrane transporter activity GO_REF:0000090 Enables the transfer of phosphate (PO4 3-) ions from one side of a membrane to the other. GOC:ai phosphate transmembrane transporter activity GOC:vw Enables the transfer of sulfate ions, SO4(2-), from one side of a membrane to the other. RHEA:34983 Reactome:R-HSA-3560789 Reactome:R-HSA-427555 Reactome:R-HSA-8875871 sulphate transporter activity molecular_function sulfate permease activity GO:0015116 sulfate transmembrane transporter activity GO_REF:0000090 Enables the transfer of sulfate ions, SO4(2-), from one side of a membrane to the other. GOC:ai Reactome:R-HSA-3560789 Defective SLC26A2 does not cotransport extracellular SO4(2-), H+ to cytosol Reactome:R-HSA-427555 SLC26A1,2 cotransport SO4(2-), H+ from extracellular region to cytosol Reactome:R-HSA-8875871 SLC26A11 transports SO4(2-) from extracellular region to cytosol Enables the transfer of acetate from one side of a membrane to the other. Acetate is the 2-carbon carboxylic acid ethanoic acid. molecular_function GO:0015123 acetate transmembrane transporter activity GO_REF:0000090 Enables the transfer of acetate from one side of a membrane to the other. Acetate is the 2-carbon carboxylic acid ethanoic acid. GOC:ai Enables the transfer of bile acid from one side of a membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. Reactome:R-HSA-194079 Reactome:R-HSA-194083 Reactome:R-HSA-194130 Reactome:R-HSA-5661184 Reactome:R-HSA-5661198 Reactome:R-HSA-9733964 molecular_function GO:0015125 bile acid transmembrane transporter activity Enables the transfer of bile acid from one side of a membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. GOC:ai Reactome:R-HSA-194079 SLCO1B3 transports ALB:(GCCA, TCCA) from extracellular region to cytosol Reactome:R-HSA-194083 SLCO1B1 transports ALB:(GCCA,TCCA) from extracellular region to cytosol Reactome:R-HSA-194130 Transport (influx) of bile salts and acids by OATP-A Reactome:R-HSA-5661184 Defective SLCO1B1 does not transport BIL from extracellular region (blood) to cytosol (hepatocyte) Reactome:R-HSA-5661198 Defective SLCO1B3 does not transport BIL from extracellular region (blood) to cytosol (hepatocyte) Reactome:R-HSA-9733964 SLC51A:SLC51B transports bile salts from cytosol to extracellular region Enables the transfer of bilirubin from one side of a membrane to the other. Bilirubin is a linear tetrapyrrole produced in the reticuloendothelial system from biliverdin and transported to the liver as a complex with serum albumin. In the liver, bilirubin is converted to bilirubin bisglucuronide, which is excreted in the bile. Reactome:R-HSA-5679031 Reactome:R-HSA-5679041 Reactome:R-HSA-9661417 molecular_function GO:0015127 bilirubin transmembrane transporter activity Enables the transfer of bilirubin from one side of a membrane to the other. Bilirubin is a linear tetrapyrrole produced in the reticuloendothelial system from biliverdin and transported to the liver as a complex with serum albumin. In the liver, bilirubin is converted to bilirubin bisglucuronide, which is excreted in the bile. GOC:ai ISBN:0198547684 Reactome:R-HSA-5679031 Defective ABCC2 does not transport BMG,BDG from cytosol to extracellular region Reactome:R-HSA-5679041 ABCC2 transports BMG,BDG from cytosol to extracellular region Reactome:R-HSA-9661417 ABCG2 tetramer transports BMG,BDG from cytosol to extracellular region Enables the transfer of carbohydrate from one side of a membrane to the other. GO:1901476 sugar transporter molecular_function carbohydrate transporter activity GO:0015144 carbohydrate transmembrane transporter activity GO_REF:0000090 Enables the transfer of carbohydrate from one side of a membrane to the other. GOC:jl GOC:mtg_transport ISBN:0815340729 Enables the transfer of a monosaccharide from one side of a membrane to the other. molecular_function GO:0015145 monosaccharide transmembrane transporter activity Enables the transfer of a monosaccharide from one side of a membrane to the other. GOC:jl GOC:mtg_transport ISBN:0815340729 Enables the transfer of a hexose sugar, a monosaccharide with 6 carbon atoms, from one side of a membrane to the other. Reactome:R-HSA-189242 Reactome:R-HSA-5638222 molecular_function GO:0015149 hexose transmembrane transporter activity GO_REF:0000090 Enables the transfer of a hexose sugar, a monosaccharide with 6 carbon atoms, from one side of a membrane to the other. GOC:ai GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-189242 SLC2A2 tetramer transports Fru, Gal, Glc from cytosol to extracellular region Reactome:R-HSA-5638222 Defective SLC2A2 does not transport Fru, Gal, Glc from cytosol to extracellular region Enables the transfer of polysaccharides from one side of a membrane to the other. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. molecular_function GO:0015159 polysaccharide transmembrane transporter activity Enables the transfer of polysaccharides from one side of a membrane to the other. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GOC:ai GOC:mtg_transport ISBN:0815340729 Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group. GO:0015359 amino acid transporter activity Reactome:R-HSA-210439 Reactome:R-HSA-212642 Reactome:R-HSA-351963 Reactome:R-HSA-351987 Reactome:R-HSA-352029 Reactome:R-HSA-352052 Reactome:R-HSA-352059 Reactome:R-HSA-352103 Reactome:R-HSA-352107 Reactome:R-HSA-352108 Reactome:R-HSA-352119 Reactome:R-HSA-352136 Reactome:R-HSA-352158 Reactome:R-HSA-352174 Reactome:R-HSA-352182 Reactome:R-HSA-352191 Reactome:R-HSA-352232 Reactome:R-HSA-352347 Reactome:R-HSA-352354 Reactome:R-HSA-352364 Reactome:R-HSA-352371 Reactome:R-HSA-352379 Reactome:R-HSA-352385 Reactome:R-HSA-375405 Reactome:R-HSA-375417 Reactome:R-HSA-375473 Reactome:R-HSA-375487 Reactome:R-HSA-375768 Reactome:R-HSA-375770 Reactome:R-HSA-375776 Reactome:R-HSA-375790 Reactome:R-HSA-376200 Reactome:R-HSA-378513 Reactome:R-HSA-379415 Reactome:R-HSA-379426 Reactome:R-HSA-379432 Reactome:R-HSA-5653850 Reactome:R-HSA-5655702 Reactome:R-HSA-5659674 Reactome:R-HSA-5659734 Reactome:R-HSA-5659755 Reactome:R-HSA-5660694 Reactome:R-HSA-5660890 Reactome:R-HSA-5660910 Reactome:R-HSA-888592 Reactome:R-HSA-8952726 amino acid permease activity amino acid/choline transmembrane transporter activity molecular_function general amino acid permease activity hydroxy/aromatic amino acid permease activity GO:0015171 amino acid transmembrane transporter activity GO_REF:0000090 Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group. GOC:ai GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-210439 glutamate uptake by astrocytes Reactome:R-HSA-212642 L-Glutamine transport into neurons Reactome:R-HSA-351963 SLC6A18 transports Gly from extracellular region to cytosol Reactome:R-HSA-351987 SLC6A6-mediated uptake of taurine and beta-alanine Reactome:R-HSA-352029 SLC6A12 (BGT-1)-mediated uptake of GABA and betaine Reactome:R-HSA-352052 SLC6A20 cotransports L-Pro, Na+ from the extracellular region to cytosol Reactome:R-HSA-352059 SLC6A15-mediated amino acid uptake Reactome:R-HSA-352103 SLC43A1 (LAT3)-mediated uptake of large neutral amino acids Reactome:R-HSA-352107 SLC43A2 (LAT4)-mediated uptake of large neutral amino acids Reactome:R-HSA-352108 SLC38A2 (ATA2)-mediated uptake of neutral amino acids Reactome:R-HSA-352119 SLC38A1 (ATA1)-mediated uptake of neutral amino acids Reactome:R-HSA-352136 SLC38A4 (ATA3)-mediated uptake of arginine and lysine Reactome:R-HSA-352158 SLC16A10-mediated uptake of aromatic amino acids Reactome:R-HSA-352174 SLC38A3-mediated uptake of glutamine, histidine, asparagine, and alanine Reactome:R-HSA-352182 SLC38A5-mediated uptake of glutamine, histidine, asparagine, and serine Reactome:R-HSA-352191 SLC7A8-mediated uptake of neutral amino acids Reactome:R-HSA-352232 SLC7A5:SLC3A2 transports neutral amino acids from extracellular region to cytosol Reactome:R-HSA-352347 SLC1A4-mediated exchange of extracellular serine for cytosolic alanine, threonine, or cysteine Reactome:R-HSA-352354 SLC1A4-mediated exchange of extracellular cysteine for cytosolic alanine, serine, or threonine Reactome:R-HSA-352364 SLC1A4-mediated exchange of extracellular alanine for cytosolic serine, threonine, or cysteine Reactome:R-HSA-352371 SLC1A4-mediated exchange of extracellular threonine for cytosolic alanine, serine, or cysteine Reactome:R-HSA-352379 SLC1A5-mediated exchange of alanine and glutamine across the plasma membrane Reactome:R-HSA-352385 SLC1A5-mediated exchange of glutamine and alanine across the plasma membrane Reactome:R-HSA-375405 SLC36A2 cotransports Gly, L-Pro with H+ from extracellular region to cytosol Reactome:R-HSA-375417 SLC36A1-mediated uptake of glycine, proline, and alanine Reactome:R-HSA-375473 SLC6A19 cotransports neutral amino acids, Na+ from extracellular region to cytosol Reactome:R-HSA-375487 SLC6A14 cotransports SLC6A14 ligands, Cl-, 2Na+ from extracellular region to cytosol Reactome:R-HSA-375768 SLC7A2, isoform B (CAT-2B)-mediated uptake of cationic amino acids Reactome:R-HSA-375770 SLC7A3 (CAT-3)-mediated uptake of cationic amino acids Reactome:R-HSA-375776 SLC7A1 (CAT-1)-mediated uptake of cationic amino acids Reactome:R-HSA-375790 SLC7A2, isoform A (CAT-2A)-mediated uptake of cationic amino acids Reactome:R-HSA-376200 SLC7A10-mediated uptake of small neutral amino acids Reactome:R-HSA-378513 SLC7A11-mediated exchange of extracellular cysteine and cytosolic glutamate Reactome:R-HSA-379415 SLC7A7:SLC3A2 exchanges L-Arg for L-Leu, Na+ across the plasma membrane Reactome:R-HSA-379426 SLC7A6 (y+LAT2)-mediated exchange of extracellular leucine for cytosolic arginine Reactome:R-HSA-379432 SLC7A9:SLC3A1 exchanges L-Arg, CySS-, L-Lys for L-Leu Reactome:R-HSA-5653850 Defective SLC36A2 does not cotransport Gly, L-Pro with H+ from extracellular region to cytosol Reactome:R-HSA-5655702 Defective SLC3A1 (in SLC7A9:SLC3A1) does not exchange L-Arg, CySS-, L-Lys for L-Leu Reactome:R-HSA-5659674 Variant SLC6A14 cotransports SLC6A14 ligands, Cl-, 2Na+ from extracellular region to cytosol Reactome:R-HSA-5659734 Defective SLC6A19 does not cotransport neutral amino acids, Na+ from extracellular region to cytosol Reactome:R-HSA-5659755 Defective SLC6A18 does not transport Gly from extracellular region to cytosol Reactome:R-HSA-5660694 Variant SLC6A20 does not cotransport L-Pro, Na+ from extracellulare region to cytosol Reactome:R-HSA-5660890 Defective SLC7A9 (in SLC7A9:SLC3A1) does not exchange L-Arg, CySS-, L-Lys for L-Leu Reactome:R-HSA-5660910 Defective SLC7A7 does not exchange L-Arg for L-Leu, Na+ across the plasma membrane Reactome:R-HSA-888592 Loading of GABA into clathrin sculpted GABA transport vesicle lumen Reactome:R-HSA-8952726 SLC38A9 transports L-Arg from lysosomal lumen to cytosol Enables the transfer of a nucleobase, any nitrogenous base that is a constituent of a nucleoside, nucleotide, or nucleic acidfrom one side of a membrane to the other. GO:0015392 molecular_function GO:0015205 nucleobase transmembrane transporter activity Enables the transfer of a nucleobase, any nitrogenous base that is a constituent of a nucleoside, nucleotide, or nucleic acidfrom one side of a membrane to the other. ISBN:0198506732 Enables the transfer of an inorganic molecular entity from the outside of a cell to the inside of the cell across a membrane. An inorganic molecular entity is a molecular entity that contains no carbon. https://github.com/geneontology/go-ontology/issues/14372 inorganic solute uptake transmembrane transporter activity inorganic uptake permease activity molecular_function GO:0015318 inorganic molecular entity transmembrane transporter activity Enables the transfer of an inorganic molecular entity from the outside of a cell to the inside of the cell across a membrane. An inorganic molecular entity is a molecular entity that contains no carbon. GOC:mtg_transport ISBN:0815340729 The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. cellular_component GO:0015629 actin cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. GOC:jl ISBN:0395825172 ISBN:0815316194 The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. cellular_component GO:0015630 microtubule cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. GOC:jl ISBN:0395825172 The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015669 gas transport The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015671 oxygen transport The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage. biological_process GO:0015695 organic cation transport The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage. GOC:ai The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage. biological_process GO:0015698 inorganic anion transport The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage. GOC:krc The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015701 bicarbonate transport The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. biological_process GO:0015711 organic anion transport The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. GOC:ai GOC:krc The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015718 monocarboxylic acid transport The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. bile acid transport bile salt transport biological_process GO:0015721 bile acid and bile salt transport The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:krc PMID:12663868 PMID:14699511 The directed movement of bilirubin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015723 bilirubin transport The directed movement of bilirubin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. vw 2017-02-19T10:41:27Z GO:1905950 biological_process monosaccharide transport GO:0015749 monosaccharide transmembrane transport The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. GOC:TermGenie GOC:vw GO_REF:0000069 The directed movement of polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. biological_process GO:0015774 polysaccharide transport The directed movement of polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GOC:ai The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015833 peptide transport The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process amine/polyamine transport GO:0015837 amine transport The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai ISBN:0198506732 The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015873 biological_process GO:0015844 monoamine transport The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015849 organic acid transport The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. ISBN:0198506732 The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. organic alcohol transport biological_process GO:0015850 organic hydroxy compound transport The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. GOC:ai The directed movement of a nucleobase, any nitrogenous base that is a constituent of a nucleoside, nucleotide, or nucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. nucleobase transmembrane transport biological_process GO:0015851 nucleobase transport The directed movement of a nucleobase, any nitrogenous base that is a constituent of a nucleoside, nucleotide, or nucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. ISBN:0198506732 nucleobase transmembrane transport GOC:mah The directed movement of protein-DNA complexes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. DNA-protein complex transport biological_process GO:0015869 protein-DNA complex transport The directed movement of protein-DNA complexes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai DNA-protein complex transport GOC:mah The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. biological_process GO:0015870 acetylcholine transport The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. GOC:ai The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine. levarterenol transport noradrenaline transport biological_process GO:0015874 norepinephrine transport The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine. GOC:ai ISBN:0198506732 The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process nucleobase, nucleoside, nucleotide and nucleic acid transport GO:0015931 nucleobase-containing compound transport The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb Enables the transfer of nucleobases, nucleosides, nucleotides and nucleic acids from one side of a membrane to the other. molecular_function nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity GO:0015932 nucleobase-containing compound transmembrane transporter activity Enables the transfer of nucleobases, nucleosides, nucleotides and nucleic acids from one side of a membrane to the other. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity GOC:dph GOC:tb The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released. chemoorganotrophy biological_process GO:0015980 energy derivation by oxidation of organic compounds The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released. GOC:mah A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z GO:0016021 GO:0098589 GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane integral to membrane membrane region region of membrane whole membrane cellular_component transmembrane GO:0016020 membrane A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GOC:dos GOC:mah ISBN:0815316194 transmembrane GOC:mah The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GO:0006724 GO:0044240 Wikipedia:Lipid_catabolism lipid breakdown lipid catabolism lipid degradation lipolysis multicellular organism lipid catabolic process multicellular organismal lipid catabolic process biological_process GO:0016042 lipid catabolic process The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GOC:go_curators A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. GO:0048591 cellular growth growth of cell biological_process cell expansion metabolic process resulting in cell growth metabolism resulting in cell growth non-developmental cell growth non-developmental growth of a unicellular organism GO:0016049 cell growth The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. GOC:ai non-developmental cell growth GOC:mah non-developmental growth of a unicellular organism GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. vesicle organisation biological_process vesicle organization and biogenesis GO:0016050 vesicle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. GOC:mah vesicle organization and biogenesis GOC:mah The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0006093 anabolic carbohydrate metabolic process anabolic carbohydrate metabolism carbohydrate anabolism carbohydrate biosynthesis carbohydrate formation carbohydrate synthesis biological_process GO:0016051 carbohydrate biosynthetic process The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. jl 2012-10-23T16:34:39Z GO:0006095 GO:0044276 GO:0044724 carbohydrate breakdown carbohydrate catabolism carbohydrate degradation catabolic carbohydrate metabolic process catabolic carbohydrate metabolism multicellular organismal carbohydrate catabolic process biological_process single-organism carbohydrate catabolic process GO:0016052 carbohydrate catabolic process The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. organic acid anabolism organic acid biosynthesis organic acid formation organic acid synthesis biological_process GO:0016053 organic acid biosynthetic process The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage. organic acid breakdown organic acid catabolism organic acid degradation biological_process GO:0016054 organic acid catabolic process The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 Hyperpolarization (vertebrates) or depolarization (invertebrates) of the photoreceptor cell membrane via closing/opening of cation specific channels as a result of signals generated by rhodopsin activation by a photon. changes in polarization state of photoreceptor cell membrane biological_process GO:0016057 regulation of membrane potential in photoreceptor cell Hyperpolarization (vertebrates) or depolarization (invertebrates) of the photoreceptor cell membrane via closing/opening of cation specific channels as a result of signals generated by rhodopsin activation by a photon. GOC:dph GOC:hb GOC:tb changes in polarization state of photoreceptor cell membrane GOC:dph GOC:tb The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. RNA metabolism biological_process GO:0016070 RNA metabolic process The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. ISBN:0198506732 A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. https://github.com/geneontology/go-ontology/issues/25421 GO:0006899 vesicle transport vesicular transport nonselective vesicle transport biological_process protein sorting along secretory pathway vesicle trafficking GO:0016192 vesicle-mediated transport A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. GOC:ai GOC:mah ISBN:08789310662000 vesicular transport GOC:mah Any process that modulates the frequency, rate or extent of striated muscle development. biological_process GO:0016202 regulation of striated muscle tissue development Any process that modulates the frequency, rate or extent of striated muscle development. GOC:go_curators true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity molecular_function GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. Wikipedia:Phosphorylation biological_process GO:0016310 phosphorylation The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. ISBN:0198506732 The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female. biological_process GO:0016321 female meiosis chromosome segregation The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female. GOC:ai Formation and maintenance of a polarized microtubule array originating from a microtubule-organizing center (MTOC) in the oocyte. An example of this is found in Drosophila melanogaster. GO:0048130 oocyte microtubule cytoskeleton organisation biological_process GO:0016325 oocyte microtubule cytoskeleton organization Formation and maintenance of a polarized microtubule array originating from a microtubule-organizing center (MTOC) in the oocyte. An example of this is found in Drosophila melanogaster. GOC:mtg_sensu PMID:11231123 The process in which the anatomical structures of embryonic epithelia are generated and organized. biological_process GO:0016331 morphogenesis of embryonic epithelium The process in which the anatomical structures of embryonic epithelia are generated and organized. GOC:jl The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. https://github.com/geneontology/go-ontology/issues/24787 Wikipedia:Cell_migration biological_process GO:0016477 cell migration The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. GOC:cjm GOC:dph GOC:ems GOC:pf Wikipedia:Cell_migration Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis. down regulation of angiogenesis down-regulation of angiogenesis downregulation of angiogenesis inhibition of angiogenesis biological_process GO:0016525 negative regulation of angiogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis. GOC:go_curators The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum. Wikipedia:Sarcoplasm cellular_component GO:0016528 sarcoplasm The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum. ISBN:0198547684 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2.-.-.- Reactome:R-HSA-1483089 Reactome:R-HSA-1483186 Reactome:R-HSA-5668414 Reactome:R-HSA-8868783 molecular_function GO:0016740 transferase activity Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. ISBN:0198506732 Reactome:R-HSA-1483089 PE is converted to PS by PTDSS2 Reactome:R-HSA-1483186 PC is converted to PS by PTDSS1 Reactome:R-HSA-5668414 TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK Reactome:R-HSA-8868783 TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7.-.- molecular_function GO:0016772 Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. EC:3.-.-.- Reactome:R-HSA-1236938 Reactome:R-HSA-2029475 Reactome:R-HSA-5694583 Reactome:R-HSA-5695964 Reactome:R-HSA-6786190 Reactome:R-HSA-6788295 Reactome:R-HSA-8938314 Reactome:R-HSA-8952137 molecular_function GO:0016787 hydrolase activity Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. ISBN:0198506732 Reactome:R-HSA-1236938 Partial proteolysis of antigen in phagolysosomes Reactome:R-HSA-2029475 Production of AA by iPLA2 upon FCGR activation Reactome:R-HSA-5694583 ABHD4 hydrolyses NAPE Reactome:R-HSA-5695964 ABHD14B hydrolyses PNPB Reactome:R-HSA-6786190 CMBL hydrolyses OM to OLMS Reactome:R-HSA-6788295 HDHD1:Mg2+ dephosphorylates PURIDP Reactome:R-HSA-8938314 ENPPs hydrolyse CoA-SH to PPANT, PAP Reactome:R-HSA-8952137 Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate Catalysis of the hydrolysis of any ester bond. EC:3.1.-.- Reactome:R-HSA-162729 Reactome:R-HSA-9023617 Reactome:R-HSA-9023619 Reactome:R-HSA-9749609 esterase activity molecular_function GO:0016788 hydrolase activity, acting on ester bonds Catalysis of the hydrolysis of any ester bond. GOC:jl Reactome:R-HSA-162729 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid Reactome:R-HSA-9023617 Butyrylcholinesterase hydrolyzes acyl Ghrelin Reactome:R-HSA-9023619 Platelet-activating factor acetylhydrolase (PLA2G7) hydrolyzes acyl Ghrelin Reactome:R-HSA-9749609 BCHE hydrolyzes ASA- Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insecticide stimulus. Insecticides are chemicals used to kill insects. biological_process insecticide resistance insecticide susceptibility/resistance GO:0017085 response to insecticide Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insecticide stimulus. Insecticides are chemicals used to kill insects. GOC:curators A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. nucleolus biogenesis nucleolus assembly biological_process GO:0017126 nucleologenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. GOC:jl ISBN:0198506732 nucleolus assembly GOC:mah The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. stem cell renewal biological_process GO:0017145 stem cell division The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. GOC:jid ISBN:0582227089 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0016478 down regulation of protein biosynthetic process down-regulation of protein biosynthetic process downregulation of protein biosynthetic process negative regulation of protein anabolism negative regulation of protein biosynthesis negative regulation of protein biosynthetic process negative regulation of protein formation negative regulation of protein synthesis inhibition of protein biosynthetic process biological_process protein biosynthesis inhibitor activity protein biosynthetic process inhibitor activity GO:0017148 negative regulation of translation Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:isa_complete Any process that modulates the frequency, rate or extent of exocytosis. biological_process GO:0017157 regulation of exocytosis Any process that modulates the frequency, rate or extent of exocytosis. GOC:go_curators The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle anabolism heterocycle biosynthesis heterocycle formation heterocycle synthesis biological_process GO:0018130 heterocycle biosynthetic process The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198547684 The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring. UM-BBD_pathwayID:phe carbolic acid metabolic process carbolic acid metabolism hydroxybenzene metabolic process hydroxybenzene metabolism phenol-containing compound metabolism biological_process GO:0018958 Note that phenol metabolism is not included as a child of 'xenobiotic metabolism' because although it is synthesized industrially, phenol is also found naturally in animal wastes and other organic materials. It is often formed by the activity of microorganisms, which can chemically modify a variety of xenobiotic and naturally occurring phenolic compounds. phenol-containing compound metabolic process The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring. ISBN:0198506732 The specific behavior of an organism that is associated with reproduction. https://github.com/geneontology/go-ontology/issues/23491 jl 2012-09-19T16:01:37Z GO:0033057 GO:0044704 GO:0044705 reproductive behavior in a multicellular organism reproductive behaviour multi-organism reproductive behavior multicellular organism reproductive behavior biological_process single-organism reproductive behavior GO:0019098 reproductive behavior The specific behavior of an organism that is associated with reproduction. GOC:jl GOC:pr Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. regulation of lipid metabolism biological_process GO:0019216 regulation of lipid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids. regulation of steroid metabolism biological_process GO:0019218 regulation of steroid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0019219 regulation of nucleobase-containing compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. regulation of phosphate metabolism biological_process GO:0019220 regulation of phosphate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process GO:0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators regulation of organismal metabolic process GOC:tb The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. conduction of nerve impulse signal transmission along a neuron biological_process GO:0019226 transmission of nerve impulse The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. GOC:curators ISBN:0815316194 conduction of nerve impulse GOC:dph An action potential that occurs in a neuron. biological_process generation of action potential GO:0019228 neuronal action potential An action potential that occurs in a neuron. GOC:dph GOC:isa_complete GOC:tb generation of action potential GOC:dph GOC:tb The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process. Wikipedia:Nociception perception of physiological pain biological_process nociception GO:0019233 sensory perception of pain The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process. GOC:curators The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule. hexose metabolism biological_process GO:0019318 hexose metabolic process The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of hexose, any monosaccharide with a chain of six carbon atoms in the molecule. hexose anabolism hexose biosynthesis hexose formation hexose synthesis biological_process GO:0019319 hexose biosynthetic process The chemical reactions and pathways resulting in the formation of hexose, any monosaccharide with a chain of six carbon atoms in the molecule. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule. hexose breakdown hexose catabolism hexose degradation biological_process GO:0019320 hexose catabolic process The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring. MetaCyc:PHENOLDEG-PWY phenol-containing compound breakdown phenol-containing compound catabolism phenol-containing compound degradation biological_process GO:0019336 phenol-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of acetate, the anion of acetic acid. acetate anabolism acetate biosynthesis acetate formation acetate synthesis biological_process GO:0019413 acetate biosynthetic process The chemical reactions and pathways resulting in the formation of acetate, the anion of acetic acid. GOC:go_curators The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound anabolism aromatic compound biosynthesis aromatic compound formation aromatic compound synthesis aromatic hydrocarbon biosynthesis aromatic hydrocarbon biosynthetic process biological_process GO:0019438 aromatic compound biosynthetic process The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound breakdown aromatic compound catabolism aromatic compound degradation aromatic hydrocarbon catabolic process aromatic hydrocarbon catabolism biological_process GO:0019439 aromatic compound catabolic process The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 GO:0006411 GO:0044267 GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism protein metabolic process and modification protein metabolism protein metabolism and modification multicellular organismal protein metabolic process biological_process GO:0019538 protein metabolic process The chemical reactions and pathways involving a protein. Includes protein modification. GOC:ma The chemical reactions and pathways resulting in the breakdown of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent. biological_process catechol breakdown catechol catabolic process catechol catabolism catechol degradation GO:0019614 catechol-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent. GOC:go_curators Any process involved in the maintenance of an internal steady state at the level of the cell. biological_process GO:0019725 cellular homeostasis Any process involved in the maintenance of an internal steady state at the level of the cell. GOC:isa_complete GOC:jl ISBN:0395825172 The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients. Wikipedia:Secondary_metabolism secondary metabolism secondary metabolite metabolic process secondary metabolite metabolism biological_process GO:0019748 secondary metabolic process The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients. GOC:go_curators The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). carboxylic acid metabolism biological_process GO:0019752 carboxylic acid metabolic process The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). ISBN:0198506732 The directed movement of one-carbon compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. one carbon compound transport biological_process GO:0019755 one-carbon compound transport The directed movement of one-carbon compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. cellular_component GO:0019867 outer membrane The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. GOC:go_curators A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Sexual_reproduction biological_process GO:0019953 Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times. sexual reproduction A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). Wikipedia:Sexual_reproduction The formation of the prechordal plate. The prechordal plate is a thickening of the endoderm at the cranial end of the primitive streak formed by the involution of Spemann's organizer cells. The prechordal plate and the notochord induce the formation of the neural plate from the overlying ectodermal cells. biological_process GO:0021501 prechordal plate formation The formation of the prechordal plate. The prechordal plate is a thickening of the endoderm at the cranial end of the primitive streak formed by the involution of Spemann's organizer cells. The prechordal plate and the notochord induce the formation of the neural plate from the overlying ectodermal cells. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues. biological_process GO:0021510 spinal cord development The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of ventral spinal cord interneurons. Ventral spinal cord interneurons are cells located in the ventral portion of the spinal cord that transmit signals between sensory and motor neurons and are required for reflexive responses. Differentiation includes the processes involved in commitment of a cell to a specific fate. biological_process GO:0021514 ventral spinal cord interneuron differentiation The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of ventral spinal cord interneurons. Ventral spinal cord interneurons are cells located in the ventral portion of the spinal cord that transmit signals between sensory and motor neurons and are required for reflexive responses. Differentiation includes the processes involved in commitment of a cell to a specific fate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:11262869 The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the spinal cord. Differentiation includes the processes involved in commitment of a cell to a specific fate. biological_process GO:0021515 cell differentiation in spinal cord The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the spinal cord. Differentiation includes the processes involved in commitment of a cell to a specific fate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:11262869 The process whose specific outcome is the progression of the ventral region of the spinal cord over time, from its formation to the mature structure. The neurons of the ventral region of the mature spinal cord participate in motor output. biological_process GO:0021517 ventral spinal cord development The process whose specific outcome is the progression of the ventral region of the spinal cord over time, from its formation to the mature structure. The neurons of the ventral region of the mature spinal cord participate in motor output. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of motor neurons. Motor neurons innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate. biological_process GO:0021522 spinal cord motor neuron differentiation The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of motor neurons. Motor neurons innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:11262869 The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of somatic motor neurons. Somatic motor neurons innervate skeletal muscle targets and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate. biological_process GO:0021523 somatic motor neuron differentiation The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of somatic motor neurons. Somatic motor neurons innervate skeletal muscle targets and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:11262869 The regionalization process that regulates the coordinated growth that establishes the non-random spatial arrangement of the neural tube. biological_process GO:0021532 neural tube patterning The regionalization process that regulates the coordinated growth that establishes the non-random spatial arrangement of the neural tube. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mature cells of the hindbrain. Differentiation includes the processes involved in commitment of a cell to a specific fate. biological_process GO:0021533 cell differentiation in hindbrain The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mature cells of the hindbrain. Differentiation includes the processes involved in commitment of a cell to a specific fate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The multiplication or reproduction of cells, resulting in the expansion of a cell population in the hindbrain. biological_process GO:0021534 cell proliferation in hindbrain The multiplication or reproduction of cells, resulting in the expansion of a cell population in the hindbrain. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The orderly movement of a cell that will reside in the hindbrain. biological_process GO:0021535 cell migration in hindbrain The orderly movement of a cell that will reside in the hindbrain. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions. biological_process GO:0021545 cranial nerve development The process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process whose specific outcome is the progression of the rhombomere over time, from its formation to the mature structure. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. biological_process GO:0021546 rhombomere development The process whose specific outcome is the progression of the rhombomere over time, from its formation to the mature structure. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The regionalization process that gives rise to the midbrain-hindbrain boundary. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate. MHB biosynthesis MHB formation midbrain-hindbrain boundary biosynthesis midbrain-hindbrain boundary formation biological_process isthmus biosynthesis isthmus formation GO:0021547 midbrain-hindbrain boundary initiation The regionalization process that gives rise to the midbrain-hindbrain boundary. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate. GOC:cls GOC:dgh GOC:dph GOC:isa_complete GOC:jid GO_REF:0000021 PMID:15541513 MHB biosynthesis GOC:cls MHB formation GOC:cls midbrain-hindbrain boundary biosynthesis GOC:cls midbrain-hindbrain boundary formation GOC:cls isthmus biosynthesis GOC:cls isthmus formation GOC:cls The process whose specific outcome is the progression of the pons over time, from its formation to the mature structure. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum. biological_process GO:0021548 pons development The process whose specific outcome is the progression of the pons over time, from its formation to the mature structure. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process whose specific outcome is the progression of the medulla oblongata over time, from its formation to the mature structure. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate. biological_process medulla development myelencephalon development GO:0021550 medulla oblongata development The process whose specific outcome is the progression of the medulla oblongata over time, from its formation to the mature structure. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 medulla development GOC:cls myelencephalon development GOC:cls The process in which the anatomical structure of the central nervous system is generated and organized. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. biological_process GO:0021551 central nervous system morphogenesis The process in which the anatomical structure of the central nervous system is generated and organized. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0582227089 The process in which the anatomical structure of the midbrain-hindbrain boundary is generated and organized. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate. MHB morphogenesis isthmus morphogenesis biological_process GO:0021555 midbrain-hindbrain boundary morphogenesis The process in which the anatomical structure of the midbrain-hindbrain boundary is generated and organized. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:15541513 MHB morphogenesis GOC:cls isthmus morphogenesis GOC:cls The process that gives rise to the central nervous system. This process pertains to the initial formation of a structure from unspecified parts. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. biological_process GO:0021556 central nervous system formation The process that gives rise to the central nervous system. This process pertains to the initial formation of a structure from unspecified parts. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0582227089 The process whose specific outcome is the progression of the trigeminal nerve over time, from its formation to the mature structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. cranial nerve 5 development cranial nerve V development biological_process CN V development GO:0021559 trigeminal nerve development The process whose specific outcome is the progression of the trigeminal nerve over time, from its formation to the mature structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 cranial nerve 5 development GOC:cls cranial nerve V development GOC:cls CN V development GOC:cls The process in which the anatomical structure of the hindbrain is generated and organized. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions. biological_process rhombencephalon morphogenesis GO:0021575 hindbrain morphogenesis The process in which the anatomical structure of the hindbrain is generated and organized. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to the hindbrain. This process pertains to the initial formation of a structure from unspecified parts. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions. biological_process GO:0021576 hindbrain formation The process that gives rise to the hindbrain. This process pertains to the initial formation of a structure from unspecified parts. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 A developmental process, independent of morphogenetic (shape) change, that is required for the hindbrain to attain its fully functional state. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions. biological_process GO:0021578 hindbrain maturation A developmental process, independent of morphogenetic (shape) change, that is required for the hindbrain to attain its fully functional state. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process in which the anatomical structure of the medulla oblongata is generated and organized. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate. biological_process medulla morphogenesis myelencephalon morphogenesis GO:0021579 medulla oblongata morphogenesis The process in which the anatomical structure of the medulla oblongata is generated and organized. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to the medulla oblongata. This process pertains to the initial formation of a structure from unspecified parts. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate. biological_process medulla biosynthesis medulla formation myelencephalon biosynthesis myelencephalon formation GO:0021580 medulla oblongata formation The process that gives rise to the medulla oblongata. This process pertains to the initial formation of a structure from unspecified parts. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 A developmental process, independent of morphogenetic (shape) change, that is required for the medulla oblongata to attain its fully functional state. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate. biological_process medulla maturation myelencephalon maturation GO:0021582 medulla oblongata maturation A developmental process, independent of morphogenetic (shape) change, that is required for the medulla oblongata to attain its fully functional state. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process in which the anatomical structure of the pons is generated and organized. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum. biological_process GO:0021583 pons morphogenesis The process in which the anatomical structure of the pons is generated and organized. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to the pons. This process pertains to the initial formation of a structure from unspecified parts. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum. biological_process GO:0021584 pons formation The process that gives rise to the pons. This process pertains to the initial formation of a structure from unspecified parts. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 A developmental process, independent of morphogenetic (shape) change, that is required for the pons to attain its fully functional state. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum. biological_process GO:0021586 pons maturation A developmental process, independent of morphogenetic (shape) change, that is required for the pons to attain its fully functional state. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process in which the anatomical structure of the rhombomere is generated and organized. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. biological_process GO:0021593 rhombomere morphogenesis The process in which the anatomical structure of the rhombomere is generated and organized. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to the rhombomere. This process pertains to the initial formation of a structure from unspecified parts. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. biological_process GO:0021594 rhombomere formation The process that gives rise to the rhombomere. This process pertains to the initial formation of a structure from unspecified parts. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process in which the anatomical structure of the cranial nerves are generated and organized. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions. biological_process GO:0021602 cranial nerve morphogenesis The process in which the anatomical structure of the cranial nerves are generated and organized. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to the cranial nerves. This process pertains to the initial formation of a structure from unspecified parts. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions. biological_process GO:0021603 cranial nerve formation The process that gives rise to the cranial nerves. This process pertains to the initial formation of a structure from unspecified parts. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 A developmental process, independent of morphogenetic (shape) change, that is required for a cranial nerve to attain its fully functional state. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions. biological_process GO:0021605 cranial nerve maturation A developmental process, independent of morphogenetic (shape) change, that is required for a cranial nerve to attain its fully functional state. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 A developmental process, independent of morphogenetic (shape) change, that is required for the central nervous system to attain its fully functional state. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. biological_process GO:0021626 central nervous system maturation A developmental process, independent of morphogenetic (shape) change, that is required for the central nervous system to attain its fully functional state. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0582227089 A developmental process, independent of morphogenetic (shape) change, that is required for the trigeminal nerve to attain its fully functional state. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. biological_process CN V maturation GO:0021635 trigeminal nerve maturation A developmental process, independent of morphogenetic (shape) change, that is required for the trigeminal nerve to attain its fully functional state. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process in which the anatomical structure of the trigeminal nerve is generated and organized. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. biological_process CN V morphogenesis GO:0021636 trigeminal nerve morphogenesis The process in which the anatomical structure of the trigeminal nerve is generated and organized. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to the trigeminal nerve. This process pertains to the initial formation of a structure from unspecified parts. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. biological_process CN V biosynthesis CN V formation GO:0021638 trigeminal nerve formation The process that gives rise to the trigeminal nerve. This process pertains to the initial formation of a structure from unspecified parts. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to a rhombomere boundary. This process pertains to the initial formation of a boundary delimiting a rhombomere. Rhombomeres are transverse segments of the developing rhombencephalon that are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order. biological_process GO:0021654 rhombomere boundary formation The process that gives rise to a rhombomere boundary. This process pertains to the initial formation of a boundary delimiting a rhombomere. Rhombomeres are transverse segments of the developing rhombencephalon that are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure. biological_process GO:0021675 nerve development The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 A developmental process, independent of morphogenetic (shape) change, that is required for a nerve to attain its fully functional state. biological_process GO:0021682 nerve maturation A developmental process, independent of morphogenetic (shape) change, that is required for a nerve to attain its fully functional state. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state. biological_process GO:0021700 developmental maturation A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process whose specific outcome is the progression of the locus ceruleus over time, from its formation to the mature structure. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic. locus caeruleus development locus coeruleus development biological_process GO:0021703 locus ceruleus development The process whose specific outcome is the progression of the locus ceruleus over time, from its formation to the mature structure. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process in which the anatomical structure of the locus ceruleus is generated and organized. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic. biological_process GO:0021704 locus ceruleus morphogenesis The process in which the anatomical structure of the locus ceruleus is generated and organized. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to the locus ceruleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic. biological_process GO:0021705 locus ceruleus formation The process that gives rise to the locus ceruleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 A developmental process, independent of morphogenetic (shape) change, that is required for the locus ceruleus to attain its fully functional state. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic. biological_process GO:0021706 locus ceruleus maturation A developmental process, independent of morphogenetic (shape) change, that is required for the locus ceruleus to attain its fully functional state. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process whose specific outcome is the progression of the superior olivary nucleus over time, from its formation to the mature structure. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound. biological_process superior olive development GO:0021718 superior olivary nucleus development The process whose specific outcome is the progression of the superior olivary nucleus over time, from its formation to the mature structure. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process in which the anatomical structure of the superior olivary nucleus is generated and organized. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound. biological_process superior olive morphogenesis GO:0021719 superior olivary nucleus morphogenesis The process in which the anatomical structure of the superior olivary nucleus is generated and organized. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 The process that gives rise to the superior olivary nucleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound. biological_process GO:0021720 superior olivary nucleus formation The process that gives rise to the superior olivary nucleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 A developmental process, independent of morphogenetic (shape) change, that is required for the superior olivary nucleus to attain its fully functional state. The superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound. biological_process superior olive maturation GO:0021722 superior olivary nucleus maturation A developmental process, independent of morphogenetic (shape) change, that is required for the superior olivary nucleus to attain its fully functional state. The superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0838580343 A developmental process, independent of morphogenetic (shape) change, that is required for the midbrain-hindbrain boundary to attain its fully functional state. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate. biological_process MHB maturation isthmus maturation GO:0021732 midbrain-hindbrain boundary maturation A developmental process, independent of morphogenetic (shape) change, that is required for the midbrain-hindbrain boundary to attain its fully functional state. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:15541513 The process whose specific outcome is the progression of a salivary nucleus over time, from its formation to the mature structure. biological_process GO:0021751 salivary nucleus development The process whose specific outcome is the progression of a salivary nucleus over time, from its formation to the mature structure. GOC:cls GOC:curators GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process whose specific outcome is the progression of the superior salivary nucleus over time, from its formation to the mature structure. biological_process GO:0021753 superior salivary nucleus development The process whose specific outcome is the progression of the superior salivary nucleus over time, from its formation to the mature structure. GOC:cls GOC:curators GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. biological_process GO:0021782 glial cell development The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process in which the neural tube is divided into specific regions along the rostrocaudal axis. biological_process anterior-posterior neural tube patterning GO:0021903 rostrocaudal neural tube patterning The process in which the neural tube is divided into specific regions along the rostrocaudal axis. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:11262869 anterior-posterior neural tube patterning GOC:dph The process whose specific outcome is the formation of the hindbrain-spinal cord boundary. biological_process GO:0021906 hindbrain-spinal cord boundary formation The process whose specific outcome is the formation of the hindbrain-spinal cord boundary. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:11262869 The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium. biological_process GO:0021915 neural tube development The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the central nervous system. biological_process GO:0021953 central nervous system neuron differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the central nervous system. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron. biological_process GO:0021954 central nervous system neuron development The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The formation of the flat, thickened layer of ectodermal cells known as the neural plate. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system. biological_process GO:0021990 neural plate formation The formation of the flat, thickened layer of ectodermal cells known as the neural plate. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 ISBN:0878932437 ISBN:0878932585 PMID:15806586 The process that regulates the coordinated growth and differentiation that establishes the non-random anterior-posterior spatial arrangement of the neural plate. biological_process neural plate anterior/posterior pattern formation GO:0021999 neural plate anterior/posterior regionalization The process that regulates the coordinated growth and differentiation that establishes the non-random anterior-posterior spatial arrangement of the neural plate. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 neural plate anterior/posterior pattern formation GOC:dph Generation of cells within the nervous system. Wikipedia:Neurogenesis nervous system cell generation biological_process neural cell differentiation GO:0022008 neurogenesis Generation of cells within the nervous system. GOC:cls GOC:curators GOC:dgh GOC:dph GOC:jid GO_REF:0000021 nervous system cell generation neural cell differentiation GOC:BHF GOC:dph The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier. https://github.com/geneontology/go-ontology/issues/21480 biological_process GO:0022009 central nervous system vasculogenesis The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The movement of a cell within a rhombomere. This process is known to occur as an early step in the generation of anatomical structure from a rhombomere. biological_process GO:0022035 rhombomere cell migration The movement of a cell within a rhombomere. This process is known to occur as an early step in the generation of anatomical structure from a rhombomere. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 PMID:15629700 The process whose specific outcome is the progression of the metencephalon over time, from its formation to the mature structure. biological_process GO:0022037 metencephalon development The process whose specific outcome is the progression of the metencephalon over time, from its formation to the mature structure. GOC:cls GOC:curators GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere. biological_process GO:0022406 membrane docking The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere. GOC:isa_complete PMID:27875684 A cellular process that results in the breakdown of a cellular component. GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process GO:0022411 cellular component disassembly A cellular process that results in the breakdown of a cellular component. GOC:isa_complete A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. reproductive cellular process in multicellular organism biological_process GO:0022412 cellular process involved in reproduction in multicellular organism A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. GOC:isa_complete A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. jl 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process GO:0022414 reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0022600 digestive system process A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:isa_complete GOC:jid GOC:mtg_cardio Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. regulation of morphogenesis biological_process GO:0022603 regulation of anatomical structure morphogenesis Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. GOC:mah Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized. biological_process negative regulation of cell shape and cell size positive regulation of cell shape and cell size regulation of cell shape and cell size GO:0022604 regulation of cell morphogenesis Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized. GOC:isa_complete negative regulation of cell shape and cell size GOC:dph GOC:tb positive regulation of cell shape and cell size GOC:dph GOC:tb regulation of cell shape and cell size GOC:dph GOC:tb The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process GO:0022607 cellular component assembly The aggregation, arrangement and bonding together of a cellular component. GOC:isa_complete The process in which the anatomical structures of a gland are generated and organized. biological_process GO:0022612 gland morphogenesis The process in which the anatomical structures of a gland are generated and organized. GOC:isa_complete A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. RNA-protein complex biogenesis ribonucleoprotein complex biogenesis and assembly biological_process GO:0022613 ribonucleoprotein complex biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. GOC:isa_complete GOC:mah RNA-protein complex biogenesis GOC:mah ribonucleoprotein complex biogenesis and assembly GOC:mah A process that results in the breakdown of the extracellular matrix. biological_process GO:0022617 extracellular matrix disassembly A process that results in the breakdown of the extracellular matrix. GOC:jid The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. RNA-protein complex assembly RNP complex assembly ribonucleoprotein complex assembly biological_process GO:0022618 protein-RNA complex assembly The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. GOC:jl Enables the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction. active carrier activity carrier activity permease activity pump activity molecular_function GO:0022804 active transmembrane transporter activity Enables the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction. GOC:mtg_transport ISBN:0815340729 Enables the transfer of an ion from one side of a membrane to the other up the solute's concentration gradient. This is carried out by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction. https://github.com/geneontology/go-ontology/issues/24479 active ion transmembrane transporter activity molecular_function GO:0022853 active monoatomic ion transmembrane transporter activity Enables the transfer of an ion from one side of a membrane to the other up the solute's concentration gradient. This is carried out by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction. GOC:mtg_transport ISBN:0815340729 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GO:0005386 GO:0015563 GO:0015646 GO:0022891 GO:0022892 Reactome:R-HSA-1236947 Reactome:R-HSA-429036 Reactome:R-HSA-5638209 Reactome:R-HSA-5671707 Reactome:R-HSA-6784434 Reactome:R-HSA-6784436 molecular_function substrate-specific transmembrane transporter activity substrate-specific transporter activity uptake permease activity uptake transmembrane transporter activity GO:0022857 transmembrane transporter activity Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GOC:jid GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-1236947 Egress of internalized antigen to the cytosol via sec61 Reactome:R-HSA-429036 SLC2A9 transports Fru, Glc, urate Reactome:R-HSA-5638209 Defective SLC2A9 does not transport Fru, Glc, urate Reactome:R-HSA-5671707 Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA Reactome:R-HSA-6784434 An unknown carrier transports cytosolic glyoxylate to the peroxisome Reactome:R-HSA-6784436 An unknown carrier transports mitochondrial glyoxylate to the cytosol Enables the transfer of a macromolecule from one side of a membrane to the other. molecular_function GO:0022884 macromolecule transmembrane transporter activity Enables the transfer of a macromolecule from one side of a membrane to the other. GOC:mtg_transport ISBN:0815340729 Enables the transfer of inorganic cations from one side of a membrane to the other. Inorganic cations are atoms or small molecules with a positive charge that do not contain carbon in covalent linkage. GO:0015077 GO:0015082 GO:0072509 GO:0072510 di-, tri-valent inorganic cation transmembrane transporter activity divalent inorganic cation transmembrane transporter activity monovalent inorganic cation transmembrane transporter activity trivalent inorganic cation transmembrane transporter activity molecular_function GO:0022890 inorganic cation transmembrane transporter activity Enables the transfer of inorganic cations from one side of a membrane to the other. Inorganic cations are atoms or small molecules with a positive charge that do not contain carbon in covalent linkage. GOC:ai GOC:mtg_transport ISBN:0815340729 di-, tri-valent inorganic cation transmembrane transporter activity GOC:mah Any process that modulates the frequency, rate or extent of transmembrane transporter activity. biological_process GO:0022898 regulation of transmembrane transporter activity Any process that modulates the frequency, rate or extent of transmembrane transporter activity. GOC:dph GOC:mtg_cardio GOC:mtg_transport Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. 2010-02-16T09:30:50Z biological_process regulation of gene expression as a consequence of signal transmission GO:0023019 signal transduction involved in regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. GOC:mtg_signal regulation of gene expression as a consequence of signal transmission GOC:bf Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process GO:0023051 regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. jl 2010-02-16T09:30:50Z GO:0023046 GO:0044700 biological signaling signaling process signalling biological_process signalling process single organism signaling GO:0023052 Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. signaling The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z positive regulation of signalling process biological_process positive regulation of signaling process GO:0023056 positive regulation of signaling Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. GOC:mtg_signal positive regulation of signalling process GOC:mah positive regulation of signaling process GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process negative regulation of signaling process negative regulation of signalling process GO:0023057 negative regulation of signaling Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. GOC:mtg_signal negative regulation of signaling process GOC:bf negative regulation of signalling process GOC:mah The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. 2010-02-16T09:30:50Z signal secretion biological_process GO:0023061 signal release The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. GOC:mtg_signal signal secretion GOC:bf The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. https://github.com/geneontology/go-ontology/issues/23033 mah 2009-07-31T01:07:46Z GO:0070838 GO:0070839 divalent metal ion export divalent metal ion transport heavy metal ion transport metal ion export biological_process GO:0030001 metal ion transport The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The specification and formation of anisotropic intracellular organization or cell growth patterns. GO:0000283 GO:0030468 cell polarization bud site selection/establishment of cell polarity biological_process GO:0030010 establishment of cell polarity The specification and formation of anisotropic intracellular organization or cell growth patterns. GOC:mah The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. Wikipedia:Myofibril cellular_component GO:0030016 myofibril The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. ISBN:0815316194 The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. Wikipedia:Sarcomere cellular_component GO:0030017 sarcomere The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. ISBN:0815316194 Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins. biological_process microfilament-based process GO:0030029 actin filament-based process Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. https://github.com/geneontology/go-ontology/issues/26279 cell projection organisation biological_process cell projection organization and biogenesis cell surface structure organization and biogenesis GO:0030030 cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection organization and biogenesis GOC:mah cell surface structure organization and biogenesis GOC:mah Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. formation of a cell surface projection biological_process cell projection biogenesis GO:0030031 cell projection assembly Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection biogenesis GOC:mah Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell. biological_process microvillus biogenesis GO:0030033 microvillus assembly Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell. GOC:mah ISBN:0815316194 microvillus biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. https://github.com/geneontology/go-ontology/issues/23114 actin cytoskeleton organisation biological_process actin cytoskeleton organization and biogenesis actin modulating activity GO:0030036 actin cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. GOC:dph GOC:jl GOC:mah actin cytoskeleton organization and biogenesis GOC:mah Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins. https://github.com/geneontology/go-ontology/issues/19809 biological_process GO:0030048 actin filament-based movement Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins. GOC:BHF GOC:mah Movement of a vesicle along an actin filament, mediated by motor proteins. biological_process GO:0030050 vesicle transport along actin filament Movement of a vesicle along an actin filament, mediated by motor proteins. GOC:mah A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. Wikipedia:Cell_junction cellular_component GO:0030054 cell junction A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. GOC:aruk GOC:bc GOC:mah ISBN:0198506732 PMID:26820516 PMID:28096264 http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html The regulated release of a peptide hormone from a cell. biological_process GO:0030072 peptide hormone secretion The regulated release of a peptide hormone from a cell. GOC:mah The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects. https://github.com/geneontology/go-ontology/issues/11255#issuecomment-426191045 biological_process GO:0030073 insulin secretion The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects. GOC:mah ISBN:0198506732 The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. https://github.com/geneontology/go-ontology/issues/22178 Wikipedia:Haematopoiesis blood cell biosynthesis blood cell formation haemopoiesis hematopoiesis biological_process GO:0030097 hemopoiesis The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. GOC:dgh ISBN:0198506732 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. biological_process GO:0030099 myeloid cell differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. GOC:add ISBN:0781735149 Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. NIF_Subcellular:sao885490876 constitutive secretory pathway transport vesicle Golgi to vacuole transport vesicle Golgi-vacuole transport vesicle cellular_component secretory vesicle GO:0030133 Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'. transport vesicle Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell. GOC:mah PMID:22160157 A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. secretory vesicle cellular_component GO:0030141 Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. secretory granule A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. GOC:mah ISBN:0198506732 The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. https://github.com/geneontology/go-ontology/issues/24390 Wikipedia:Cellular_differentiation biological_process GO:0030154 cell differentiation The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. https://github.com/geneontology/go-ontology/issues/23112 GO:0044254 GO:0044257 Wikipedia:Protein_catabolism cellular protein breakdown cellular protein catabolic process cellular protein catabolism cellular protein degradation protein breakdown protein catabolism protein degradation multicellular organismal protein catabolic process biological_process pheromone catabolic process pheromone catabolism GO:0030163 This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children. protein catabolic process The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GOC:mah The process in which a relatively unspecialized cell acquires specialized features of a neuron. biological_process GO:0030182 neuron differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuron. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. extracellular matrix organisation biological_process extracellular matrix organization and biogenesis GO:0030198 extracellular matrix organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. GOC:mah extracellular matrix organization and biogenesis GOC:mah Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix. collagen fibril organisation fibrillar collagen organization biological_process GO:0030199 collagen fibril organization Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix. GOC:mah ISBN:0815316194 fibrillar collagen organization GOC:mah The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. glycosaminoglycan metabolism biological_process GO:0030203 glycosaminoglycan metabolic process The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. ISBN:0192800981 The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. hyaluronan metabolism biological_process GO:0030212 hyaluronan metabolic process The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. GOC:mah ISBN:0198506732 The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. hyaluronan anabolism hyaluronan biosynthesis hyaluronan formation hyaluronan synthesis biological_process GO:0030213 hyaluronan biosynthetic process The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. GOC:mah ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. hyaluronan breakdown hyaluronan catabolism hyaluronan degradation biological_process GO:0030214 hyaluronan catabolic process The chemical reactions and pathways resulting in the breakdown of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. GOC:mah ISBN:0198506732 The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. Wikipedia:Erythropoiesis RBC differentiation erythrocyte cell differentiation erythropoiesis red blood cell differentiation biological_process GO:0030218 erythrocyte differentiation The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. GOC:mah RBC differentiation CL:0000232 erythropoiesis GOC:add GOC:dph red blood cell differentiation CL:0000232 The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. megakaryocyte cell differentiation biological_process GO:0030219 megakaryocyte differentiation The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. GOC:mah Formation of myofibrils, the repeating units of striated muscle. biological_process GO:0030239 myofibril assembly Formation of myofibrils, the repeating units of striated muscle. GOC:mah The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation biological_process GO:0030261 chromosome condensation The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:mah ISBN:0815316194 DNA condensation Wikipedia:DNA_condensation eukaryotic chromosome condensation GOC:bf nuclear chromosome condensation GOC:bf Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. apoptotic nuclear change biological_process GO:0030262 apoptotic nuclear changes Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. GOC:mah GOC:mtg_apoptosis The compaction of chromatin during apoptosis. Wikipedia:Pyknosis pyknosis biological_process GO:0030263 apoptotic chromosome condensation The compaction of chromatin during apoptosis. GOC:mah The breakdown of the nucleus into small membrane-bounded compartments, or blebs, each of which contain compacted DNA. apoptotic nuclear fragmentation nucleus fragmentation biological_process nuclear fragmentation during apoptosis GO:0030264 nuclear fragmentation involved in apoptotic nuclear change The breakdown of the nucleus into small membrane-bounded compartments, or blebs, each of which contain compacted DNA. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb ISBN:0721639976 nuclear fragmentation during apoptosis GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. regulation of bone biosynthesis regulation of bone formation biological_process GO:0030278 regulation of ossification Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. down regulation of ossification down-regulation of ossification downregulation of ossification negative regulation of bone biosynthesis negative regulation of bone formation inhibition of ossification biological_process GO:0030279 negative regulation of ossification Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators Any process that activates or increases the frequency, rate, extent or direction of cell growth. up regulation of cell growth up-regulation of cell growth upregulation of cell growth activation of cell growth stimulation of cell growth biological_process GO:0030307 positive regulation of cell growth Any process that activates or increases the frequency, rate, extent or direction of cell growth. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. down regulation of cell growth down-regulation of cell growth downregulation of cell growth inhibition of cell growth biological_process GO:0030308 negative regulation of cell growth Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. GOC:go_curators A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space. cellular_component GO:0030312 The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'. external encapsulating structure A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space. GOC:go_curators The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract. biological_process GO:0030323 respiratory tube development The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract. GOC:jid The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. biological_process GO:0030324 lung development The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. GOC:jid UBERON:0002048 Any process that modulates the frequency, rate or extent of cell migration. biological_process GO:0030334 regulation of cell migration Any process that modulates the frequency, rate or extent of cell migration. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell migration. up regulation of cell migration up-regulation of cell migration upregulation of cell migration activation of cell migration stimulation of cell migration biological_process GO:0030335 positive regulation of cell migration Any process that activates or increases the frequency, rate or extent of cell migration. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. down regulation of cell migration down-regulation of cell migration downregulation of cell migration inhibition of cell migration biological_process GO:0030336 negative regulation of cell migration Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. GOC:go_curators The controlled breakdown of any cell membrane in the context of a normal process such as autophagy. membrane breakdown membrane catabolism membrane degradation biological_process GO:0030397 membrane disassembly The controlled breakdown of any cell membrane in the context of a normal process such as autophagy. GOC:mah The expulsion of feces from the rectum. Wikipedia:Defecation biological_process GO:0030421 defecation The expulsion of feces from the rectum. GOC:mah A wavelike sequence of involuntary muscular contraction and relaxation that passes along a tubelike structure, such as the intestine, impelling the contents onwards. Wikipedia:Peristalsis biological_process GO:0030432 peristalsis A wavelike sequence of involuntary muscular contraction and relaxation that passes along a tubelike structure, such as the intestine, impelling the contents onwards. ISBN:0198506732 The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins. GO:0000065 nuclear movement, microtubule-mediated nucleus migration microtubule cytoskeleton-dependent nuclear positioning microtubule cytoskeleton-dependent nucleus positioning microtubule-dependent nuclear positioning microtubule-dependent nucleus positioning microtubule-mediated nuclear migration nuclear migration, microtubule-mediated transport of nucleus by microtubules transport of nucleus, microtubule-mediated biological_process GO:0030473 nuclear migration along microtubule The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins. GOC:mah GOC:sgd_curators The contractile fiber of smooth muscle cells. cellular_component GO:0030485 smooth muscle contractile fiber The contractile fiber of smooth muscle cells. GOC:mah The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile. GO:0019613 bile acid breakdown bile acid catabolism bile acid degradation bile acid 7alpha-dehydroxylation pathway cholate catabolic process biological_process GO:0030573 bile acid catabolic process The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile. GOC:go_curators The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells. collagen breakdown collagen catabolism collagen degradation biological_process GO:0030574 collagen catabolic process The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells. GOC:mah ISBN:0815316194 The lipid bilayer surrounding a transport vesicle. secretory vesicle membrane constitutive secretory pathway transport vesicle membrane cellular_component GO:0030658 transport vesicle membrane The lipid bilayer surrounding a transport vesicle. GOC:mah The lipid bilayer surrounding a cytoplasmic vesicle. cellular_component GO:0030659 cytoplasmic vesicle membrane The lipid bilayer surrounding a cytoplasmic vesicle. GOC:mah The lipid bilayer surrounding a vesicle associated with the Golgi apparatus. cellular_component Golgi vesicle membrane GO:0030660 Golgi-associated vesicle membrane The lipid bilayer surrounding a vesicle associated with the Golgi apparatus. GOC:mah The lipid bilayer surrounding a secretory granule. secretory vesicle membrane cellular_component GO:0030667 secretory granule membrane The lipid bilayer surrounding a secretory granule. GOC:mah The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. biological_process GO:0030705 cytoskeleton-dependent intracellular transport The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. GOC:mah Directed movement of the oocyte, following its specification, from its original central position in the cyst to a posterior position relative to the nurse cells of the egg chamber, and its maintenance in this posterior location. This is the first sign of anterior-posterior asymmetry in the developing egg chamber. establishment and maintenance of oocyte localization in egg chamber establishment and maintenance of oocyte position during oogenesis oocyte localisation involved in germarium-derived egg chamber formation oogenesis, establishment and maintenance of oocyte localization oogenesis, oocyte localization oocyte positioning during oogenesis biological_process oocyte localization during germarium-derived egg chamber formation oocyte localization during oogenesis GO:0030720 oocyte localization involved in germarium-derived egg chamber formation Directed movement of the oocyte, following its specification, from its original central position in the cyst to a posterior position relative to the nurse cells of the egg chamber, and its maintenance in this posterior location. This is the first sign of anterior-posterior asymmetry in the developing egg chamber. GOC:mtg_sensu PMID:10449356 oocyte localisation involved in germarium-derived egg chamber formation GOC:mah oocyte localization during germarium-derived egg chamber formation GOC:dph GOC:tb The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium. biological_process GO:0030855 epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium. GOC:ecd PMID:11839751 Any process that modulates the frequency, rate or extent of epithelial cell differentiation. biological_process GO:0030856 regulation of epithelial cell differentiation Any process that modulates the frequency, rate or extent of epithelial cell differentiation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell differentiation. down regulation of epithelial cell differentiation down-regulation of epithelial cell differentiation downregulation of epithelial cell differentiation inhibition of epithelial cell differentiation biological_process GO:0030857 negative regulation of epithelial cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell differentiation. GOC:mah Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation. up regulation of epithelial cell differentiation up-regulation of epithelial cell differentiation upregulation of epithelial cell differentiation activation of epithelial cell differentiation stimulation of epithelial cell differentiation biological_process GO:0030858 positive regulation of epithelial cell differentiation Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation. GOC:mah The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles). mesencephalon development biological_process GO:0030901 midbrain development The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles). http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=midbrain The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium). rhombencephalon development biological_process GO:0030902 hindbrain development The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium). http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=hindbrain The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column. biological_process GO:0030903 notochord development The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column. GOC:dgh The process whose specific outcome is the progression of the midbrain-hindbrain boundary over time, from its formation to the mature structure. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. MHB development isthmic organizer development isthmomesencephalic boundary development isthmus development midbrain-hindbrain orgainizer development biological_process GO:0030917 midbrain-hindbrain boundary development The process whose specific outcome is the progression of the midbrain-hindbrain boundary over time, from its formation to the mature structure. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. GOC:dgh Any collagen trimer that passes through a lipid bilayer membrane. MACIT cellular_component GO:0030936 transmembrane collagen trimer Any collagen trimer that passes through a lipid bilayer membrane. ISBN:0721639976 MACIT ISBN:0198599587 Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures. biological_process GO:0030951 establishment or maintenance of microtubule cytoskeleton polarity Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures. GOC:mah Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures. biological_process cytoskeleton polarization GO:0030952 establishment or maintenance of cytoskeleton polarity Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures. GOC:mah A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. intraflagellar transport complex intraflagellar transport particle cellular_component IFT complex GO:0030990 Note that we deem cilia and microtubule-based flagella to be equivalent. intraciliary transport particle A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. GOC:cilia GOC:kmv PMID:14570576 PMID:22118932 PMID:23945166 A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix matrisome cellular_component GO:0031012 extracellular matrix A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. GOC:BHF GOC:mah GOC:rph NIF_Subcellular:nlx_subcell_20090513 PMID:21123617 PMID:28089324 The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones. https://github.com/geneontology/go-ontology/issues/23777 Wikipedia:Pancreas biological_process GO:0031016 pancreas development The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones. GOC:cvs The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells. biological_process GO:0031017 exocrine pancreas development The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells. GOC:cvs The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin. biological_process GO:0031018 endocrine pancreas development The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin. GOC:cvs The directed movement of the nucleus along microfilaments within the cell, mediated by motor proteins. nuclear migration, microfilament-mediated biological_process GO:0031022 nuclear migration along microfilament The directed movement of the nucleus along microfilaments within the cell, mediated by motor proteins. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments. actomyosin organization actomyosin structure organisation biological_process actomyosin structure organization and biogenesis GO:0031032 Note that this term is a child of 'actin cytoskeleton organization and biogenesis ; GO:0030036' because the actin cytoskeleton is defined as actin filaments and associated proteins. actomyosin structure organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments. GOC:dph GOC:jl GOC:mah actomyosin structure organization and biogenesis GOC:mah Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted. NIF_Subcellular:sao772007592 dense core vesicle cellular_component GO:0031045 dense core granule Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted. NIF_Subcellular:sao772007592 PMID:14690495 dense core vesicle GOC:kmv The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure. embryonic eye development biological_process GO:0031076 embryonic camera-type eye development The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure. GOC:mah GOC:mtg_sensu A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. NIF_Subcellular:sao830981606 cellular_component intracellular membrane GO:0031090 organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GOC:dos GOC:mah intracellular membrane NIF_Subcellular:sao830981606 Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule. https://github.com/geneontology/go-ontology/issues/23195 microtubule dynamics biological_process GO:0031109 microtubule polymerization or depolymerization Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule. GOC:mah Any process that modulates the frequency, rate or extent of microtubule polymerization or depolymerization by the addition or removal of tubulin heterodimers from a microtubule. biological_process GO:0031110 regulation of microtubule polymerization or depolymerization Any process that modulates the frequency, rate or extent of microtubule polymerization or depolymerization by the addition or removal of tubulin heterodimers from a microtubule. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization. down regulation of microtubule polymerization or depolymerization down-regulation of microtubule polymerization or depolymerization downregulation of microtubule polymerization or depolymerization inhibition of microtubule polymerization or depolymerization biological_process GO:0031111 negative regulation of microtubule polymerization or depolymerization Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization. GOC:mah Any process that activates or increases the frequency, rate or extent of microtubule polymerization or depolymerization. up regulation of microtubule polymerization or depolymerization up-regulation of microtubule polymerization or depolymerization upregulation of microtubule polymerization or depolymerization activation of microtubule polymerization or depolymerization stimulation of microtubule polymerization or depolymerization biological_process GO:0031112 positive regulation of microtubule polymerization or depolymerization Any process that activates or increases the frequency, rate or extent of microtubule polymerization or depolymerization. GOC:mah Any process that modulates the frequency, rate or extent of microtubule polymerization. biological_process GO:0031113 regulation of microtubule polymerization Any process that modulates the frequency, rate or extent of microtubule polymerization. GOC:mah Any process that modulates the frequency, rate or extent of microtubule depolymerization. regulation of microtubule disassembly biological_process GO:0031114 regulation of microtubule depolymerization Any process that modulates the frequency, rate or extent of microtubule depolymerization. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization. down regulation of microtubule polymerization down-regulation of microtubule polymerization downregulation of microtubule polymerization inhibition of microtubule polymerization biological_process GO:0031115 negative regulation of microtubule polymerization Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization. GOC:mah Any process that activates or increases the frequency, rate or extent of microtubule polymerization. up regulation of microtubule polymerization up-regulation of microtubule polymerization upregulation of microtubule polymerization activation of microtubule polymerization stimulation of microtubule polymerization biological_process GO:0031116 positive regulation of microtubule polymerization Any process that activates or increases the frequency, rate or extent of microtubule polymerization. GOC:mah Any process that activates or increases the frequency, rate or extent of microtubule depolymerization. microtubule destabilization positive regulation of microtubule disassembly up regulation of microtubule depolymerization up-regulation of microtubule depolymerization upregulation of microtubule depolymerization activation of microtubule depolymerization positive regulation of microtubule catastrophe stimulation of microtubule depolymerization biological_process GO:0031117 positive regulation of microtubule depolymerization Any process that activates or increases the frequency, rate or extent of microtubule depolymerization. GOC:mah positive regulation of microtubule catastrophe GOC:dph GOC:tb A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell. cytoplasmic microtubule organisation biological_process cytoplasmic microtubule organization and biogenesis GO:0031122 cytoplasmic microtubule organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell. GOC:mah cytoplasmic microtubule organization and biogenesis GOC:mah A developmental process involving two tissues in which one tissue (the inducer) produces a signal that directs cell fate commitment of cells in the second tissue (the responder). biological_process GO:0031128 developmental induction A developmental process involving two tissues in which one tissue (the inducer) produces a signal that directs cell fate commitment of cells in the second tissue (the responder). GOC:cjm GOC:dph GOC:mah PMID:24503535 The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). neurite biosynthesis neurite development neurite formation neurite growth neurite outgrowth biological_process GO:0031175 neuron projection development The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). GOC:mah neurite development GOC:dph The area of a motile cell closest to the direction of movement. front of cell leading edge of cell cellular_component GO:0031252 cell leading edge The area of a motile cell closest to the direction of movement. GOC:pg The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection. cellular_component membrane extension membrane projection GO:0031253 cell projection membrane The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection. GOC:krc GOC:mah The portion of the plasma membrane surrounding the leading edge of a motile cell. cellular_component GO:0031256 leading edge membrane The portion of the plasma membrane surrounding the leading edge of a motile cell. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process GO:0031323 regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism inhibition of cellular metabolic process biological_process GO:0031324 negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process activation of cellular metabolic process stimulation of cellular metabolic process biological_process GO:0031325 positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. regulation of cellular anabolism regulation of cellular biosynthesis regulation of cellular formation regulation of cellular synthesis biological_process GO:0031326 regulation of cellular biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. down regulation of cellular biosynthetic process down-regulation of cellular biosynthetic process downregulation of cellular biosynthetic process negative regulation of cellular anabolism negative regulation of cellular biosynthesis negative regulation of cellular formation negative regulation of cellular synthesis inhibition of cellular biosynthetic process biological_process GO:0031327 negative regulation of cellular biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. positive regulation of cellular anabolism positive regulation of cellular biosynthesis positive regulation of cellular formation positive regulation of cellular synthesis up regulation of cellular biosynthetic process up-regulation of cellular biosynthetic process upregulation of cellular biosynthetic process activation of cellular biosynthetic process stimulation of cellular biosynthetic process biological_process GO:0031328 positive regulation of cellular biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. regulation of cellular breakdown regulation of cellular catabolism regulation of cellular degradation biological_process GO:0031329 regulation of cellular catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. down regulation of cellular catabolic process down-regulation of cellular catabolic process downregulation of cellular catabolic process negative regulation of cellular breakdown negative regulation of cellular catabolism negative regulation of cellular degradation inhibition of cellular catabolic process biological_process GO:0031330 negative regulation of cellular catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. positive regulation of cellular breakdown positive regulation of cellular catabolism positive regulation of cellular degradation up regulation of cellular catabolic process up-regulation of cellular catabolic process upregulation of cellular catabolic process activation of cellular catabolic process stimulation of cellular catabolic process biological_process GO:0031331 positive regulation of cellular catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly. down regulation of protein complex assembly down-regulation of protein complex assembly downregulation of protein complex assembly inhibition of protein complex assembly biological_process negative regulation of protein complex assembly GO:0031333 negative regulation of protein-containing complex assembly Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly. GOC:mah Any process that activates or increases the frequency, rate or extent of protein complex assembly. up regulation of protein complex assembly up-regulation of protein complex assembly upregulation of protein complex assembly activation of protein complex assembly stimulation of protein complex assembly biological_process positive regulation of protein complex assembly GO:0031334 positive regulation of protein-containing complex assembly Any process that activates or increases the frequency, rate or extent of protein complex assembly. GOC:mah Any process that modulates the frequency, rate or extent of vesicle fusion. biological_process GO:0031338 regulation of vesicle fusion Any process that modulates the frequency, rate or extent of vesicle fusion. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion. down regulation of vesicle fusion down-regulation of vesicle fusion downregulation of vesicle fusion inhibition of vesicle fusion biological_process GO:0031339 negative regulation of vesicle fusion Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion. GOC:mah Any process that activates or increases the frequency, rate or extent of vesicle fusion. up regulation of vesicle fusion up-regulation of vesicle fusion upregulation of vesicle fusion activation of vesicle fusion stimulation of vesicle fusion biological_process GO:0031340 positive regulation of vesicle fusion Any process that activates or increases the frequency, rate or extent of vesicle fusion. GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. regulation of cell projection organisation biological_process regulation of cell projection organization and biogenesis GO:0031344 regulation of cell projection organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah regulation of cell projection organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. down regulation of cell projection organization down-regulation of cell projection organization downregulation of cell projection organization negative regulation of cell projection organisation inhibition of cell projection organization biological_process negative regulation of cell projection organization and biogenesis GO:0031345 negative regulation of cell projection organization Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah down regulation of cell projection organization GOC:mah negative regulation of cell projection organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. positive regulation of cell projection organisation up regulation of cell projection organization up-regulation of cell projection organization upregulation of cell projection organization activation of cell projection organization stimulation of cell projection organization biological_process positive regulation of cell projection organization and biogenesis GO:0031346 positive regulation of cell projection organization Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah positive regulation of cell projection organization and biogenesis GOC:mah A vesicle found in the cytoplasm of a cell. GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle cytoplasmic membrane-enclosed vesicle cytoplasmic, membrane-bounded vesicle GO:0031410 cytoplasmic vesicle A vesicle found in the cytoplasm of a cell. GOC:ai GOC:mah GOC:vesicles A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/22021 GO:0034629 establishment and maintenance of protein complex localization protein complex localisation biological_process cellular protein complex localisation cellular protein complex localization cellular protein-containing complex localization establishment and maintenance of cellular protein complex localization protein complex localization GO:0031503 protein-containing complex localization A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. GOC:mah protein complex localisation GOC:mah cellular protein complex localisation GOC:mah The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential. NIF_Subcellular:sao1124888485 Wikipedia:Neuromuscular_junction cellular_component NMJ motor endplate GO:0031594 In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting skeletal muscle fibers - all of which are cholinergic and excitatory. Both inhibitory and excitatory neuromuscular junctions exist in invertebrates, utilizing a range of neurotransmitters including glutamate, GABA and 5-HT. neuromuscular junction The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential. GOC:nln NMJ GOC:ha motor endplate NIF_Subcellular:nlx_subcell_20090512 Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. regulation of neurological process regulation of neurological system process regulation of neurophysiological process biological_process GO:0031644 regulation of nervous system process Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. GOC:dph GOC:mah GOC:tb regulation of neurological process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. down regulation of neurological process down-regulation of neurological process downregulation of neurological process negative regulation of neurological process negative regulation of neurological system process negative regulation of neurophysiological process inhibition of neurological process biological_process GO:0031645 negative regulation of nervous system process Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb negative regulation of neurological process GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of a neurophysiological process. positive regulation of neurological process positive regulation of neurological system process positive regulation of neurophysiological process up regulation of neurological process up-regulation of neurological process upregulation of neurological process activation of neurological process stimulation of neurological process biological_process GO:0031646 positive regulation of nervous system process Any process that activates or increases the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb positive regulation of neurological process GOC:dph GOC:tb Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. NIF_Subcellular:sao1687101204 cellular_component GO:0031965 nuclear membrane Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. GOC:mah GOC:pz A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. cellular_component GO:0031967 organelle envelope A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. GOC:mah GOC:pz The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope. cellular_component GO:0031968 organelle outer membrane The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope. GOC:mah The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. cellular_component GO:0031974 membrane-enclosed lumen The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. GOC:add GOC:mah A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. cellular_component GO:0031975 envelope A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GOC:mah GOC:pz The volume enclosed by the nuclear inner membrane. cellular_component GO:0031981 nuclear lumen The volume enclosed by the nuclear inner membrane. GOC:mah GOC:pz Any small, fluid-filled, spherical organelle enclosed by membrane. GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component membrane-bounded vesicle membrane-enclosed vesicle GO:0031982 vesicle Any small, fluid-filled, spherical organelle enclosed by membrane. GOC:mah GOC:pz GOC:vesicles Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. locomotion during locomotory behaviour biological_process GO:0031987 locomotion involved in locomotory behavior Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of insulin. up regulation of insulin secretion up-regulation of insulin secretion upregulation of insulin secretion activation of insulin secretion stimulation of insulin secretion biological_process GO:0032024 positive regulation of insulin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of insulin. GOC:mah Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress. down regulation of translation initiation in response to stress down-regulation of translation initiation in response to stress downregulation of translation initiation in response to stress inhibition of translation initiation in response to stress biological_process GO:0032057 negative regulation of translational initiation in response to stress Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress. GOC:mah Any process that activates or increases the frequency, rate or extent of translation initiation as a result of a stimulus indicating the organism is under stress. up regulation of translation initiation in response to stress up-regulation of translation initiation in response to stress upregulation of translation initiation in response to stress activation of translation initiation in response to stress stimulation of translation initiation in response to stress biological_process GO:0032058 positive regulation of translational initiation in response to stress Any process that activates or increases the frequency, rate or extent of translation initiation as a result of a stimulus indicating the organism is under stress. GOC:mah A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. Wikipedia:Bleb_(cell_biology) plasma membrane bleb cellular_component GO:0032059 bleb A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. GOC:mtg_apoptosis PMID:12083798 PMID:16624291 Wikipedia:Bleb_(cell_biology) plasma membrane bleb GOC:pr The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. blebbing membrane blebbing cell blebbing plasma membrane bleb assembly plasma membrane blebbing biological_process GO:0032060 bleb assembly The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. GOC:mah GOC:mtg_apoptosis PMID:12083798 PMID:16624291 Wikipedia:Bleb_(cell_biology) blebbing GOC:pr membrane blebbing GOC:pr plasma membrane bleb assembly GOC:pr plasma membrane blebbing GOC:pr Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. biological_process nuclease regulator activity GO:0032069 regulation of nuclease activity Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. GOC:mah Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. biological_process DNase regulator deoxyribonuclease regulator GO:0032070 regulation of deoxyribonuclease activity Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids. down regulation of nuclease activity down-regulation of nuclease activity downregulation of nuclease activity inhibition of nuclease activity biological_process nuclease inhibitor GO:0032074 negative regulation of nuclease activity Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids. GOC:mah Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. up regulation of nuclease activity up-regulation of nuclease activity upregulation of nuclease activity activation of nuclease activity stimulation of nuclease activity biological_process nuclease activator GO:0032075 positive regulation of nuclease activity Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. GOC:mah Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. down regulation of deoxyribonuclease activity down-regulation of deoxyribonuclease activity downregulation of deoxyribonuclease activity inhibition of deoxyribonuclease activity biological_process DNase inhibitor deoxyribonuclease inhibitor GO:0032076 negative regulation of deoxyribonuclease activity Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. up regulation of deoxyribonuclease activity up-regulation of deoxyribonuclease activity upregulation of deoxyribonuclease activity activation of deoxyribonuclease activity stimulation of deoxyribonuclease activity biological_process DNase activator deoxyribonuclease activator GO:0032077 positive regulation of deoxyribonuclease activity Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah Any process that modulates the frequency, rate or extent of a response to an external stimulus. biological_process GO:0032101 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to external stimulus Any process that modulates the frequency, rate or extent of a response to an external stimulus. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus. down regulation of response to external stimulus down-regulation of response to external stimulus downregulation of response to external stimulus inhibition of response to external stimulus biological_process GO:0032102 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to external stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus. GOC:mah Any process that activates, maintains or increases the rate of a response to an external stimulus. up regulation of response to external stimulus up-regulation of response to external stimulus upregulation of response to external stimulus activation of response to external stimulus stimulation of response to external stimulus biological_process GO:0032103 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to external stimulus Any process that activates, maintains or increases the rate of a response to an external stimulus. GOC:mah The lipid bilayer surrounding a dense core granule. dense core vesicle membrane cellular_component GO:0032127 dense core granule membrane The lipid bilayer surrounding a dense core granule. GOC:mah dense core vesicle membrane GOC:kmv Any process that modulates the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. biological_process GO:0032222 regulation of synaptic transmission, cholinergic Any process that modulates the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. down regulation of synaptic transmission, cholinergic down-regulation of synaptic transmission, cholinergic downregulation of synaptic transmission, cholinergic inhibition of synaptic transmission, cholinergic biological_process GO:0032223 negative regulation of synaptic transmission, cholinergic Any process that stops, prevents, or reduces the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. up regulation of synaptic transmission, cholinergic up-regulation of synaptic transmission, cholinergic upregulation of synaptic transmission, cholinergic activation of synaptic transmission, cholinergic stimulation of synaptic transmission, cholinergic biological_process GO:0032224 positive regulation of synaptic transmission, cholinergic Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah Any process that modulates the frequency, rate or extent of the assembly of actin filament bundles. regulation of actin cable assembly biological_process regulation of actin filament bundle formation GO:0032231 regulation of actin filament bundle assembly Any process that modulates the frequency, rate or extent of the assembly of actin filament bundles. GOC:mah regulation of actin cable assembly GOC:dph GOC:tb regulation of actin filament bundle formation GOC:dph Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of actin filament bundles. down regulation of actin filament bundle formation down-regulation of actin filament bundle formation downregulation of actin filament bundle formation inhibition of actin filament bundle formation biological_process GO:0032232 negative regulation of actin filament bundle assembly Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of actin filament bundles. GOC:mah Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles. up regulation of actin filament bundle formation up-regulation of actin filament bundle formation upregulation of actin filament bundle formation activation of actin filament bundle formation stimulation of actin filament bundle formation biological_process GO:0032233 positive regulation of actin filament bundle assembly Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GO:0032239 regulation of nucleobase-containing compound transport Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport downregulation of nucleobase, nucleoside, nucleotide and nucleic acid transport inhibition of nucleobase, nucleoside, nucleotide and nucleic acid transport biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GO:0032240 negative regulation of nucleobase-containing compound transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport upregulation of nucleobase, nucleoside, nucleotide and nucleic acid transport activation of nucleobase, nucleoside, nucleotide and nucleic acid transport stimulation of nucleobase, nucleoside, nucleotide and nucleic acid transport biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GO:0032241 positive regulation of nucleobase-containing compound transport Any process that activates or increases the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport GOC:dph GOC:tb Any process in which a secretory granule is transported to, and/or maintained in, a specific location within the cell. secretory granule localisation biological_process secretory granule clustering GO:0032252 secretory granule localization Any process in which a secretory granule is transported to, and/or maintained in, a specific location within the cell. GOC:mah secretory granule localisation GOC:mah Any process in which a dense core granule is transported to, and/or maintained in, a specific location within the cell. dense core granule localisation dense core vesicle localization biological_process dense core granule clustering GO:0032253 dense core granule localization Any process in which a dense core granule is transported to, and/or maintained in, a specific location within the cell. GOC:mah dense core granule localisation GOC:mah dense core vesicle localization GOC:kmv Any process that modulates the frequency, rate or extent of the process of creating protein polymers. regulation of protein polymerisation biological_process GO:0032271 regulation of protein polymerization Any process that modulates the frequency, rate or extent of the process of creating protein polymers. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the process of creating protein polymers. down regulation of protein polymerization down-regulation of protein polymerization downregulation of protein polymerization inhibition of protein polymerization biological_process GO:0032272 negative regulation of protein polymerization Any process that stops, prevents, or reduces the frequency, rate or extent of the process of creating protein polymers. GOC:mah Any process that activates or increases the frequency, rate or extent of the process of creating protein polymers. up regulation of protein polymerization up-regulation of protein polymerization upregulation of protein polymerization activation of protein polymerization stimulation of protein polymerization biological_process GO:0032273 positive regulation of protein polymerization Any process that activates or increases the frequency, rate or extent of the process of creating protein polymers. GOC:mah Any process that modulates the frequency, rate or extent of chondrocyte differentiation. biological_process GO:0032330 regulation of chondrocyte differentiation Any process that modulates the frequency, rate or extent of chondrocyte differentiation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation. down regulation of chondrocyte differentiation down-regulation of chondrocyte differentiation downregulation of chondrocyte differentiation inhibition of chondrocyte differentiation biological_process GO:0032331 negative regulation of chondrocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation. GOC:mah Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation. up regulation of chondrocyte differentiation up-regulation of chondrocyte differentiation upregulation of chondrocyte differentiation activation of chondrocyte differentiation stimulation of chondrocyte differentiation biological_process GO:0032332 positive regulation of chondrocyte differentiation Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation. GOC:mah The directed movement of lipids within cells. biological_process GO:0032365 intracellular lipid transport The directed movement of lipids within cells. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0032368 regulation of lipid transport Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of lipid transport down-regulation of lipid transport downregulation of lipid transport inhibition of lipid transport biological_process GO:0032369 negative regulation of lipid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of lipid transport up-regulation of lipid transport upregulation of lipid transport activation of lipid transport stimulation of lipid transport biological_process GO:0032370 positive regulation of lipid transport Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells. biological_process GO:0032377 regulation of intracellular lipid transport Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells. down regulation of intracellular lipid transport down-regulation of intracellular lipid transport downregulation of intracellular lipid transport inhibition of intracellular lipid transport biological_process GO:0032378 negative regulation of intracellular lipid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells. up regulation of intracellular lipid transport up-regulation of intracellular lipid transport upregulation of intracellular lipid transport activation of intracellular lipid transport stimulation of intracellular lipid transport biological_process GO:0032379 positive regulation of intracellular lipid transport Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. biological_process GO:0032386 regulation of intracellular transport Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. down regulation of intracellular transport down-regulation of intracellular transport downregulation of intracellular transport inhibition of intracellular transport biological_process GO:0032387 negative regulation of intracellular transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. up regulation of intracellular transport up-regulation of intracellular transport upregulation of intracellular transport activation of intracellular transport stimulation of intracellular transport biological_process GO:0032388 positive regulation of intracellular transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that modulates the activity of a transporter. biological_process GO:0032409 regulation of transporter activity Any process that modulates the activity of a transporter. GOC:mah Any process that stops or reduces the activity of a transporter. down regulation of transporter activity down-regulation of transporter activity downregulation of transporter activity inhibition of transporter activity biological_process GO:0032410 negative regulation of transporter activity Any process that stops or reduces the activity of a transporter. GOC:mah Any process that activates or increases the activity of a transporter. up regulation of transporter activity up-regulation of transporter activity upregulation of transporter activity activation of transporter activity stimulation of transporter activity biological_process GO:0032411 positive regulation of transporter activity Any process that activates or increases the activity of a transporter. GOC:mah Any process that modulates the activity of an ion transporter. regulation of ion transmembrane transporter activity regulation of ion transporter activity biological_process GO:0032412 regulation of monoatomic ion transmembrane transporter activity Any process that modulates the activity of an ion transporter. GOC:mah GOC:tb regulation of ion transporter activity GOC:tb Any process that stops or reduces the activity of an ion transporter. down regulation of ion transporter activity down-regulation of ion transporter activity downregulation of ion transporter activity negative regulation of ion transporter activity inhibition of ion transporter activity biological_process GO:0032413 negative regulation of ion transmembrane transporter activity Any process that stops or reduces the activity of an ion transporter. GOC:mah GOC:tb negative regulation of ion transporter activity GOC:tb Any process that activates or increases the activity of an ion transporter. positive regulation of ion transporter activity up regulation of ion transporter activity up-regulation of ion transporter activity upregulation of ion transporter activity activation of ion transporter activity stimulation of ion transporter activity biological_process GO:0032414 positive regulation of ion transmembrane transporter activity Any process that activates or increases the activity of an ion transporter. GOC:mah GOC:tb positive regulation of ion transporter activity GOC:tb An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GO:0000141 GO:0030482 cellular_component actin cable GO:0032432 actin filament bundle An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GOC:mah actin cable GOC:mah Any biological process, occurring at the level of a multicellular organism, pertinent to its function. jl 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. jl 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. biological_process GO:0032504 multicellular organism reproduction The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:isa_complete GOC:jid A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell. microvillus organisation biological_process microvillus organization and biogenesis GO:0032528 microvillus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell. GOC:mah microvillus organisation GOC:mah microvillus organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a microvillus. regulation of microvillus organisation biological_process regulation of microvillus organization and biogenesis GO:0032530 regulation of microvillus organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a microvillus. GOC:mah regulation of microvillus organisation GOC:mah regulation of microvillus organization and biogenesis GOC:mah A process that modulates the formation of a microvillus. biological_process regulation of microvillus biogenesis GO:0032534 regulation of microvillus assembly A process that modulates the formation of a microvillus. GOC:mah regulation of microvillus biogenesis GOC:mah The portion of the plasma membrane surrounding a neuron projection. cellular_component GO:0032589 neuron projection membrane The portion of the plasma membrane surrounding a neuron projection. GOC:mah The directed movement of a protein from one location to another within a lipid bilayer. protein translocation within membrane receptor translocation within membrane receptor transport within lipid bilayer biological_process GO:0032594 protein transport within lipid bilayer The directed movement of a protein from one location to another within a lipid bilayer. GOC:mah The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. GO:0062103 RNA anabolism RNA biosynthesis RNA formation RNA synthesis double-stranded RNA biosynthesis double-stranded RNA biosynthetic process dsRNA biosynthesis dsRNA biosynthetic process biological_process GO:0032774 Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study. RNA biosynthetic process The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. GOC:mah GOC:txnOH dsRNA biosynthetic process GOC:BHF GOC:BHF_telomere GOC:nc GOC:rl The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue. biological_process GO:0032782 bile acid secretion The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue. GOC:ecd The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-). monocarboxylate metabolic process monocarboxylic acid metabolism biological_process GO:0032787 monocarboxylic acid metabolic process The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-). GOC:vk The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits. ribosome recycling biological_process ribosome dissociation factor GO:0032790 ribosome disassembly The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits. GOC:mah GOC:vk ribosome recycling GOC:db PMID:9463391 All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. cellular_component GO:0032838 plasma membrane bounded cell projection cytoplasm All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. GOC:krc GOC:mah Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms. response to insulin stimulus biological_process GO:0032868 response to insulin Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms. GOC:mah ISBN:0198506732 response to insulin stimulus GOC:dos Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion. biological_process GO:0032871 regulation of karyogamy Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion. GOC:mah Any process that modulates the frequency, rate or extent of the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. biological_process GO:0032878 regulation of establishment or maintenance of cell polarity Any process that modulates the frequency, rate or extent of the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns. GOC:mah Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. regulation of localisation biological_process GO:0032879 regulation of localization Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. GOC:mah regulation of localisation GOC:mah Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:14Z GO:1903827 regulation of cellular protein localisation regulation of cellular protein localization regulation of protein localisation biological_process GO:0032880 regulation of protein localization Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. GOC:dph GOC:mah GOC:tb regulation of cellular protein localisation GOC:TermGenie regulation of protein localisation GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides. biological_process GO:0032881 regulation of polysaccharide metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides. biological_process GO:0032885 regulation of polysaccharide biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides. GOC:mah Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton. biological_process GO:0032886 regulation of microtubule-based process Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0032890 regulation of organic acid transport Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of organic acid transport down-regulation of organic acid transport downregulation of organic acid transport inhibition of organic acid transport biological_process GO:0032891 negative regulation of organic acid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of organic acid transport up-regulation of organic acid transport upregulation of organic acid transport activation of organic acid transport stimulation of organic acid transport biological_process GO:0032892 positive regulation of organic acid transport Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The controlled release of a substance by a cell. Wikipedia:Secretion cellular secretion biological_process GO:0032940 secretion by cell The controlled release of a substance by a cell. GOC:mah The controlled release of a substance by a tissue. tissue secretion biological_process expulsion of gland contents GO:0032941 secretion by tissue The controlled release of a substance by a tissue. GOC:mah expulsion of gland contents GOC:mah The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form. PBMC proliferation peripheral blood mononuclear cell proliferation biological_process GO:0032943 mononuclear cell proliferation The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form. GOC:add Any process that modulates the frequency, rate or extent of mononuclear cell proliferation. regulation of PBMC proliferation regulation of peripheral blood mononuclear cell proliferation biological_process GO:0032944 regulation of mononuclear cell proliferation Any process that modulates the frequency, rate or extent of mononuclear cell proliferation. GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation. negative regulation of PBMC proliferation negative regulation of peripheral blood mononuclear cell proliferation biological_process GO:0032945 negative regulation of mononuclear cell proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation. GOC:add Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation. up regulation of mononuclear cell proliferation up-regulation of mononuclear cell proliferation upregulation of mononuclear cell proliferation activation of mononuclear cell proliferation positive regulation of PBMC proliferation positive regulation of peripheral blood mononuclear cell proliferation stimulation of mononuclear cell proliferation biological_process GO:0032946 positive regulation of mononuclear cell proliferation Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation. GOC:add Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. regulation of actin cytoskeleton organisation biological_process regulation of actin cytoskeleton organization and biogenesis GO:0032956 regulation of actin cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins. GOC:mah regulation of actin cytoskeleton organisation GOC:mah regulation of actin cytoskeleton organization and biogenesis GOC:mah The chemical reactions and pathways involving collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%). collagen metabolism biological_process GO:0032963 collagen metabolic process The chemical reactions and pathways involving collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%). GOC:mah ISBN:0198506732 The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%). collagen anabolism collagen biosynthesis collagen formation collagen synthesis biological_process GO:0032964 collagen biosynthetic process The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%). GOC:mah ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. regulation of collagen anabolism regulation of collagen biosynthesis regulation of collagen formation regulation of collagen synthesis biological_process GO:0032965 regulation of collagen biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. negative regulation of collagen anabolism negative regulation of collagen biosynthesis negative regulation of collagen formation negative regulation of collagen synthesis biological_process GO:0032966 negative regulation of collagen biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. positive regulation of collagen anabolism positive regulation of collagen biosynthesis positive regulation of collagen formation positive regulation of collagen synthesis biological_process GO:0032967 positive regulation of collagen biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. GOC:mah Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton. biological_process GO:0032970 regulation of actin filament-based process Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton. GOC:mah The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 GO:0034623 GO:0043241 GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly cellular protein complex disassembly macromolecule complex disassembly GO:0032984 protein-containing complex disassembly The disaggregation of a protein-containing macromolecular complex into its constituent components. GOC:mah The disaggregation of a protein-DNA complex into its constituent components. DNA-protein complex disassembly biological_process GO:0032986 protein-DNA complex disassembly The disaggregation of a protein-DNA complex into its constituent components. GOC:mah DNA-protein complex disassembly GOC:mah The disaggregation of a protein-RNA complex into its constituent components. https://github.com/geneontology/go-ontology/issues/25143 RNA-protein complex disassembly RNP complex disassembly ribonucleoprotein complex disassembly biological_process GO:0032988 protein-RNA complex disassembly The disaggregation of a protein-RNA complex into its constituent components. GOC:mah The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system. https://github.com/geneontology/go-ontology/issues/25496 https://github.com/geneontology/go-ontology/issues/26249 cellular component morphogenesis cellular structure morphogenesis biological_process GO:0032989 cellular anatomical entity morphogenesis The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system. GOC:dph GOC:mah GOC:tb cellular structure morphogenesis GOC:dph GOC:tb A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein-containing complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GOC:dos GOC:mah A macromolecular complex containing both protein and DNA molecules. DNA-protein complex cellular_component GO:0032993 Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. protein-DNA complex A macromolecular complex containing both protein and DNA molecules. GOC:mah DNA-protein complex GOC:mah The expansion of a muscle cell population by cell division. myocyte proliferation biological_process GO:0033002 muscle cell proliferation The expansion of a muscle cell population by cell division. CL:0000187 GOC:mah The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole metabolism biological_process GO:0033013 tetrapyrrole metabolic process The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. GOC:mah The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole anabolism tetrapyrrole biosynthesis tetrapyrrole formation tetrapyrrole synthesis biological_process GO:0033014 tetrapyrrole biosynthetic process The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. GOC:mah The chemical reactions and pathways leading to the breakdown of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole breakdown tetrapyrrole catabolism tetrapyrrole degradation biological_process GO:0033015 tetrapyrrole catabolic process The chemical reactions and pathways leading to the breakdown of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. GOC:mah Any apoptotic process in a myeloid cell, a cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. apoptosis of myeloid cells myeloid cell apoptosis biological_process GO:0033028 myeloid cell apoptotic process Any apoptotic process in a myeloid cell, a cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. CL:0000763 GOC:add GOC:mtg_apoptosis PMID:11292031 PMID:15330259 PMID:17133093 Any process that modulates the frequency, rate, or extent of myeloid cell apoptotic process. regulation of myeloid cell apoptosis biological_process GO:0033032 regulation of myeloid cell apoptotic process Any process that modulates the frequency, rate, or extent of myeloid cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process. down regulation of myeloid cell apoptosis down-regulation of myeloid cell apoptosis downregulation of myeloid cell apoptosis inhibition of myeloid cell apoptosis negative regulation of myeloid cell apoptosis biological_process GO:0033033 negative regulation of myeloid cell apoptotic process Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process that activates or increases the frequency, rate, or extent of myeloid cell apoptotic process. up regulation of myeloid cell apoptosis up-regulation of myeloid cell apoptosis upregulation of myeloid cell apoptosis activation of myeloid cell apoptosis positive regulation of myeloid cell apoptosis stimulation of myeloid cell apoptosis biological_process GO:0033034 positive regulation of myeloid cell apoptotic process Any process that activates or increases the frequency, rate, or extent of myeloid cell apoptotic process. GOC:add GOC:mtg_apoptosis Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localisation biological_process GO:0033036 macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. GOC:mah macromolecule localisation GOC:mah Any process in which a polysaccharide is transported to, or maintained in, a specific location. polysaccharide localisation biological_process GO:0033037 polysaccharide localization Any process in which a polysaccharide is transported to, or maintained in, a specific location. GOC:mah polysaccharide localisation GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. regulation of organelle organisation biological_process regulation of organelle organization and biogenesis GO:0033043 regulation of organelle organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:mah regulation of organelle organisation GOC:mah regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. regulation of chromosome organisation biological_process regulation of chromosome organization and biogenesis GO:0033044 regulation of chromosome organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. GOC:mah regulation of chromosome organisation GOC:mah regulation of chromosome organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of sister chromatid segregation. biological_process GO:0033045 regulation of sister chromatid segregation Any process that modulates the frequency, rate or extent of sister chromatid segregation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation. biological_process GO:0033046 negative regulation of sister chromatid segregation Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation. GOC:mah Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis. biological_process GO:0033047 regulation of mitotic sister chromatid segregation Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis. biological_process GO:0033048 negative regulation of mitotic sister chromatid segregation Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis. GOC:mah The deposition or aggregation of coloring matter in a cell. biological_process GO:0033059 cellular pigmentation The deposition or aggregation of coloring matter in a cell. GOC:mtg_MIT_16mar07 Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. biological_process GO:0033157 regulation of intracellular protein transport Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines. regulation of amine metabolism regulation of cellular amine metabolic process biological_process GO:0033238 regulation of amine metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines. negative regulation of amine metabolism negative regulation of cellular amine metabolic process biological_process GO:0033239 negative regulation of amine metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines. positive regulation of amine metabolism positive regulation of cellular amine metabolic process biological_process GO:0033240 positive regulation of amine metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. regulation of amine breakdown regulation of amine catabolism regulation of amine degradation regulation of cellular amine catabolic process biological_process GO:0033241 regulation of amine catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. negative regulation of amine breakdown negative regulation of amine catabolism negative regulation of amine degradation negative regulation of cellular amine catabolic process biological_process GO:0033242 negative regulation of amine catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. positive regulation of amine breakdown positive regulation of amine catabolism positive regulation of amine degradation biological_process GO:0033243 positive regulation of amine catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines. GOC:mah The multiplication or reproduction of cells, resulting in the expansion of a cell population in the midbrain. cell proliferation in mesencephalon biological_process mesencepahalic cell proliferation GO:0033278 cell proliferation in midbrain The multiplication or reproduction of cells, resulting in the expansion of a cell population in the midbrain. GOC:dgf GO_REF:0000021 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. secretory granule organisation biological_process secretory granule organization and biogenesis GO:0033363 secretory granule organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. GOC:mah secretory granule organisation GOC:mah secretory granule organization and biogenesis GOC:mah A process in which a protein is transported to, or maintained in, a location within an organelle. protein localisation to organelle protein localization in organelle biological_process GO:0033365 protein localization to organelle A process in which a protein is transported to, or maintained in, a location within an organelle. GOC:mah protein localisation to organelle GOC:mah protein localization in organelle GOC:mah A process in which a protein is transported to, or maintained in, a location within a secretory granule. protein localisation in secretory granule protein localization in secretory granule biological_process GO:0033366 protein localization to secretory granule A process in which a protein is transported to, or maintained in, a location within a secretory granule. GOC:mah protein localisation in secretory granule GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process GO:0033554 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stress Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine. down regulation of catecholamine secretion down-regulation of catecholamine secretion downregulation of catecholamine secretion inhibition of catecholamine secretion biological_process GO:0033604 negative regulation of catecholamine secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine. GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine. up regulation of catecholamine secretion up-regulation of catecholamine secretion upregulation of catecholamine secretion activation of catecholamine secretion stimulation of catecholamine secretion biological_process GO:0033605 positive regulation of catecholamine secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. down regulation of kinase activity down-regulation of kinase activity downregulation of kinase activity inhibition of kinase activity kinase inhibitor biological_process GO:0033673 negative regulation of kinase activity Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. up regulation of kinase activity up-regulation of kinase activity upregulation of kinase activity kinase activator stimulation of kinase activity biological_process GO:0033674 positive regulation of kinase activity Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah A process in which a ribosome is transported to, and/or maintained in, a specific location. GO:0033753 biological_process establishment of ribosome localisation establishment of ribosome localization ribosome localisation GO:0033750 ribosome localization A process in which a ribosome is transported to, and/or maintained in, a specific location. GOC:mah Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus. response to glucagon stimulus biological_process GO:0033762 response to glucagon Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus. GOC:sl response to glucagon stimulus GOC:dos Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus. biological_process GO:0033993 response to lipid Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus. GOC:sl A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus. mah 2011-02-14T02:26:36Z GO:0000042 GO:0072600 protein localisation in Golgi apparatus protein localization in Golgi apparatus establishment of protein localisation to Golgi establishment of protein localization in Golgi establishment of protein localization to Golgi establishment of protein localization to Golgi apparatus biological_process protein targeting to Golgi protein-Golgi targeting GO:0034067 protein localization to Golgi apparatus A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus. GOC:mah protein localisation in Golgi apparatus GOC:mah establishment of protein localisation to Golgi GOC:mah establishment of protein localization to Golgi apparatus GOC:mah Any process of regulating the production and elimination of erythrocytes within an organism. RBC homeostasis red blood cell homeostasis biological_process GO:0034101 erythrocyte homeostasis Any process of regulating the production and elimination of erythrocytes within an organism. GOC:add PMID:10694114 PMID:14754397 RBC homeostasis CL:0000232 red blood cell homeostasis CL:0000232 The process in which a carbohydrate is transported across a membrane. carbohydrate membrane transport transmembrane carbohydrate transport biological_process GO:0034219 Note that this term is not intended for use in annotating lateral movement within membranes. carbohydrate transmembrane transport The process in which a carbohydrate is transported across a membrane. GOC:mah transmembrane carbohydrate transport GOC:dph GOC:tb A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport ATP hydrolysis coupled ion transmembrane transport biological_process GO:0034220 Note that this term is not intended for use in annotating lateral movement within membranes. monoatomic ion transmembrane transport A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GOC:mah transmembrane ion transport GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. biological_process GO:0034242 negative regulation of syncytium formation by plasma membrane fusion Any process that decreases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides. regulation of amide metabolism regulation of cellular amide metabolic process biological_process GO:0034248 regulation of amide metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides. negative regulation of amide metabolism negative regulation of cellular amide metabolic process biological_process GO:0034249 negative regulation of amide metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides. positive regulation of amide metabolism positive regulation of cellular amide metabolic process biological_process GO:0034250 positive regulation of amide metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. regulation of amide breakdown regulation of amide catabolism regulation of amide degradation regulation of cellular amide catabolic process biological_process GO:0034251 regulation of amide catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. negative regulation of amide breakdown negative regulation of amide catabolism negative regulation of cellular amide catabolic process biological_process negative regulation of amide degradation GO:0034252 negative regulation of amide catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. positive regulation of amide breakdown positive regulation of amide catabolism positive regulation of cellular amide catabolic process biological_process positive regulation of amide degradation GO:0034253 positive regulation of amide catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides. GOC:mah Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus. response to monosaccharide stimulus biological_process GO:0034284 response to monosaccharide Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus. GOC:mah response to monosaccharide stimulus GOC:dos A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction. biological_process GO:0034329 cell junction assembly A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix. cell junction assembly and maintenance cell junction organisation biological_process cell junction biogenesis GO:0034330 cell junction organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix. GOC:dph GOC:jl GOC:mah cell junction organisation GOC:mah Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system. apoptosis of glia apoptosis of glial cells glia apoptosis glia programmed cell death by apoptosis glial cell programmed cell death by apoptosis programmed cell death of glia by apoptosis programmed cell death of glial cells by apoptosis programmed cell death, glia programmed cell death, glial cells glial cell apoptosis biological_process GO:0034349 glial cell apoptotic process Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system. CL:0000125 GOC:mtg_apoptosis GOC:sart Any process that modulates the frequency, rate, or extent of glial cell apoptotic process. biological_process regulation of glial cell apoptosis GO:0034350 regulation of glial cell apoptotic process Any process that modulates the frequency, rate, or extent of glial cell apoptotic process. GOC:mah GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate, or extent of glial cell apoptotic process. down regulation of glial cell apoptosis down-regulation of glial cell apoptosis downregulation of glial cell apoptosis inhibition of glial cell apoptosis negative regulation of glial cell apoptosis biological_process GO:0034351 negative regulation of glial cell apoptotic process Any process that stops, prevents, or reduces the frequency, rate, or extent of glial cell apoptotic process. GOC:mah GOC:mtg_apoptosis Any process that activates or increases the frequency, rate, or extent of glial cell apoptotic process. up regulation of glial cell apoptosis up-regulation of glial cell apoptosis upregulation of glial cell apoptosis activation of glial cell apoptosis positive regulation of glial cell apoptosis stimulation of glial cell apoptosis biological_process GO:0034352 positive regulation of glial cell apoptotic process Any process that activates or increases the frequency, rate, or extent of glial cell apoptotic process. GOC:mah GOC:mtg_apoptosis Any apoptotic process in a smooth muscle cell. Smooth muscle consists of non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. SMC apoptosis apoptosis of smooth muscle cells programmed cell death of smooth muscle cells by apoptosis programmed cell death, smooth muscle cells smooth muscle cell programmed cell death by apoptosis smooth muscle cell apoptosis biological_process GO:0034390 smooth muscle cell apoptotic process Any apoptotic process in a smooth muscle cell. Smooth muscle consists of non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. CL:0000192 GOC:BHF GOC:mah GOC:mtg_apoptosis GOC:rl Any process that modulates the frequency, rate, or extent of smooth muscle cell apoptotic process. regulation of SMC apoptosis regulation of smooth muscle cell apoptosis biological_process GO:0034391 regulation of smooth muscle cell apoptotic process Any process that modulates the frequency, rate, or extent of smooth muscle cell apoptotic process. GOC:BHF GOC:mtg_apoptosis GOC:rl Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process. down regulation of smooth muscle cell apoptosis down-regulation of smooth muscle cell apoptosis downregulation of smooth muscle cell apoptosis negative regulation of SMC apoptosis inhibition of smooth muscle cell apoptosis negative regulation of smooth muscle cell apoptosis biological_process GO:0034392 negative regulation of smooth muscle cell apoptotic process Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process. GOC:BHF GOC:mtg_apoptosis GOC:rl Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process. positive regulation of SMC apoptosis up regulation of smooth muscle cell apoptosis up-regulation of smooth muscle cell apoptosis upregulation of smooth muscle cell apoptosis activation of smooth muscle cell apoptosis positive regulation of smooth muscle cell apoptosis stimulation of smooth muscle cell apoptosis biological_process GO:0034393 positive regulation of smooth muscle cell apoptotic process Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process. GOC:BHF GOC:mtg_apoptosis GOC:rl The directed movement of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0034436 glycoprotein transport The directed movement of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:BHF GOC:mah GOC:rl The process in which a solute is transported from one side of the vacuolar membrane to the other. vacuolar membrane transport biological_process GO:0034486 Note that this term is not intended for use in annotating lateral movement within membranes. vacuolar transmembrane transport The process in which a solute is transported from one side of the vacuolar membrane to the other. GOC:mah The process in which an amino acid is transported from one side of the vacuolar membrane to the other. vacuolar amino acid membrane transport biological_process GO:0034487 Note that this term is not intended for use in annotating lateral movement within membranes. vacuolar amino acid transmembrane transport The process in which an amino acid is transported from one side of the vacuolar membrane to the other. GOC:mah Any process in which a protein is transported to, or maintained at, a specific location on a chromosome. protein localisation to chromosome condensin localization to chromosome biological_process GO:0034502 protein localization to chromosome Any process in which a protein is transported to, or maintained at, a specific location on a chromosome. GOC:mah protein localisation to chromosome GOC:mah A process in which a protein transports or maintains the localization of another protein to the nucleus. 2012-11-07T15:45:54Z GO:0044744 protein localisation to nucleus protein localization in cell nucleus protein localization in nucleus biological_process protein targeting to nucleus GO:0034504 protein localization to nucleus A process in which a protein transports or maintains the localization of another protein to the nucleus. GOC:ecd protein localisation to nucleus GOC:mah protein localization in nucleus GOC:mah The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. https://github.com/geneontology/go-ontology/issues/26424 cellular nitrogen compound metabolism biological_process GO:0034641 cellular nitrogen compound metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GOC:mah The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid anabolism nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis nucleobase, nucleoside, nucleotide and nucleic acid formation nucleobase, nucleoside, nucleotide and nucleic acid synthesis biological_process GO:0034654 nucleobase-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid breakdown nucleobase, nucleoside, nucleotide and nucleic acid catabolism nucleobase, nucleoside, nucleotide and nucleic acid degradation biological_process nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GO:0034655 nucleobase-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. regulation of membrane transport biological_process GO:0034762 regulation of transmembrane transport Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. down regulation of transmembrane transport down-regulation of transmembrane transport downregulation of transmembrane transport negative regulation of membrane transport inhibition of transmembrane transport biological_process GO:0034763 negative regulation of transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. positive regulation of membrane transport up regulation of transmembrane transport up-regulation of transmembrane transport upregulation of transmembrane transport activation of transmembrane transport stimulation of transmembrane transport biological_process GO:0034764 positive regulation of transmembrane transport Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. regulation of ion transmembrane transport regulation of ion membrane transport regulation of transmembrane ion transport biological_process GO:0034765 regulation of monoatomic ion transmembrane transport Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah regulation of transmembrane ion transport GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. negative regulation of ion transmembrane transport down regulation of transmembrane ion transport down-regulation of transmembrane ion transport downregulation of transmembrane ion transport negative regulation of ion membrane transport negative regulation of transmembrane ion transport inhibition of transmembrane ion transport biological_process GO:0034766 negative regulation of monoatomic ion transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah negative regulation of transmembrane ion transport GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. positive regulation of ion transmembrane transport positive regulation of ion membrane transport positive regulation of transmembrane ion transport up regulation of transmembrane ion transport up-regulation of transmembrane ion transport upregulation of transmembrane ion transport activation of transmembrane ion transport stimulation of transmembrane ion transport biological_process GO:0034767 positive regulation of monoatomic ion transmembrane transport Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah The controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion. dph 2009-08-13T11:27:24Z GO:0060881 biological_process basal lamina disassembly GO:0034769 Note that this term has no relationship to 'membrane disassembly ; GO:0030397' because the basement membrane is not a lipid bilayer. basement membrane disassembly The controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion. GOC:sart PMID:17301221 The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field. biological_process GO:0035050 embryonic heart tube development The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field. GOC:go_curators The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual. cardiac cell differentiation heart cell differentiation biological_process GO:0035051 cardiocyte differentiation The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual. GOC:bf The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GO:0035083 GO:0035084 ciliary axoneme assembly cilium axoneme assembly flagellar axoneme assembly flagellum axoneme assembly biological_process axoneme biogenesis cilium axoneme biogenesis GO:0035082 Note that cilia and eukaryotic flagella are deemed to be equivalent. axoneme assembly The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GOC:bf GOC:cilia GOC:jl ISBN:0815316194 axoneme biogenesis GOC:mah cilium axoneme biogenesis GOC:mah The process in which the anatomical structures of appendages are generated and organized. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch. biological_process GO:0035107 appendage morphogenesis The process in which the anatomical structures of appendages are generated and organized. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch. ISBN:0582227089 The process in which the anatomical structures of genitalia are generated and organized. The genitalia are the organs of reproduction or generation, external and internal. biological_process genital morphogenesis GO:0035112 genitalia morphogenesis The process in which the anatomical structures of genitalia are generated and organized. The genitalia are the organs of reproduction or generation, external and internal. GOC:bf Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow. tube lumen formation biological_process lumen formation in an anatomical structure GO:0035148 tube formation Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow. GOC:bf tube lumen formation GOC:dph GOC:mah lumen formation in an anatomical structure GOC:dph GOC:mah The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex. biological_process GO:0035190 syncytial nuclear migration The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex. GOC:bf ISBN:0879694238 PMID:8314839 Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo. programmed cell death of ectopic germ cells programmed cell death, ectopic germ cells biological_process GO:0035234 ectopic germ cell programmed cell death Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo. PMID:12814944 The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. biological_process GO:0035239 tube morphogenesis The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GOC:bf PMID:14624839 The process in which the anatomical structures of the internal genitalia are generated and organized. The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. biological_process GO:0035260 internal genitalia morphogenesis The process in which the anatomical structures of the internal genitalia are generated and organized. The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. http://www.ndif.org/Terms/genitalia.html The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals. biological_process GO:0035261 external genitalia morphogenesis The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals. http://www.ndif.org/Terms/genitalia.html The process in which the anatomical structures of the gonads are generated and organized. A gonad is an animal organ producing gametes, e.g. the testes or the ovary in mammals. biological_process GO:0035262 gonad morphogenesis The process in which the anatomical structures of the gonads are generated and organized. A gonad is an animal organ producing gametes, e.g. the testes or the ovary in mammals. ISBN:0198612001 The increase in size or mass of an entire multicellular organism, as opposed to cell growth. biological_process body growth GO:0035264 multicellular organism growth The increase in size or mass of an entire multicellular organism, as opposed to cell growth. GOC:bf GOC:curators GOC:dph GOC:tb The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function. biological_process GO:0035265 organ growth The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function. GOC:bf ISBN:0471245208 ISBN:0721662544 Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands which include the ovaries and testes. biological_process GO:0035270 endocrine system development Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands which include the ovaries and testes. GOC:bf Wikipedia:Development_of_the_endocrine_system Progression of the exocrine system over time, from its formation to a mature structure. The exocrine system is a system of hormones and glands, where the glands secrete straight to a target site via ducts or tubes. The human exocrine system includes the salivary glands, sweat glands and many glands of the digestive system. biological_process GO:0035272 exocrine system development Progression of the exocrine system over time, from its formation to a mature structure. The exocrine system is a system of hormones and glands, where the glands secrete straight to a target site via ducts or tubes. The human exocrine system includes the salivary glands, sweat glands and many glands of the digestive system. GOC:bf Wikipedia:Exocrine_gland The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis. Wikipedia:Segmentation_(biology) biological_process GO:0035282 segmentation The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis. PMID:10611687 PMID:9706689 The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. biological_process GO:0035295 tube development The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. PMID:12526790 A process in which a protein is transported to, or maintained at, a microtubule. bf 2010-03-11T11:00:56Z protein localisation to microtubule biological_process GO:0035372 protein localization to microtubule A process in which a protein is transported to, or maintained at, a microtubule. GOC:bf GOC:lb protein localisation to microtubule GOC:mah Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. bf 2010-03-29T10:58:53Z protein localisation to synapse biological_process GO:0035418 protein localization to synapse Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. GOC:bf protein localisation to synapse GOC:mah The process in which acetate is transported across a membrane. Acetate is the 2-carbon carboxylic acid ethanoic acid. bf 2010-04-08T10:59:01Z acetate membrane transport biological_process GO:0035433 Note that this term is not intended for use in annotating lateral movement within membranes. acetate transmembrane transport The process in which acetate is transported across a membrane. Acetate is the 2-carbon carboxylic acid ethanoic acid. GOC:vw The process in which a phosphate is transported across a membrane. bf 2010-04-08T11:24:06Z phosphate ion membrane transport biological_process GO:0035435 Note that this term is not intended for use in annotating lateral movement within membranes. phosphate ion transmembrane transport The process in which a phosphate is transported across a membrane. GOC:vw The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes. bf 2010-04-09T03:53:01Z biological_process GO:0035441 cell migration involved in vasculogenesis The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes. GOC:dgh The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. bf 2010-05-14T01:14:37Z GO:0007242 GO:0007243 GO:0023013 GO:0023034 intracellular signaling chain intracellular protein kinase cascade intracellular signal transduction pathway protein kinase cascade signal transmission via intracellular cascade biological_process intracellular signaling cascade intracellular signaling pathway signal transduction via intracellular signaling cascade GO:0035556 intracellular signal transduction The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. GOC:bf GOC:jl GOC:signaling ISBN:3527303782 intracellular signaling chain ISBN:3527303782 intracellular protein kinase cascade GOC:signaling protein kinase cascade GOC:signaling intracellular signaling cascade GOC:signaling The directed movement of a protein to a specific location within the extracellular region. bf 2010-11-09T10:25:08Z establishment of protein localisation in extracellular region establishment of protein localization in extracellular region biological_process GO:0035592 establishment of protein localization to extracellular region The directed movement of a protein to a specific location within the extracellular region. GOC:BHF GOC:bf establishment of protein localisation in extracellular region GOC:mah The progression of the intrahepatic bile ducts over time, from their formation to the mature structure. Intrahepatic bile ducts (bile ducts within the liver) collect bile from bile canaliculi in the liver, and connect to the extrahepatic bile ducts (bile ducts outside the liver). bf 2010-12-08T04:10:50Z IHBD development intrahepatic biliary duct development biological_process GO:0035622 intrahepatic bile duct development The progression of the intrahepatic bile ducts over time, from their formation to the mature structure. Intrahepatic bile ducts (bile ducts within the liver) collect bile from bile canaliculi in the liver, and connect to the extrahepatic bile ducts (bile ducts outside the liver). GOC:bf PMID:20614624 IHBD development PMID:20614624 intrahepatic biliary duct development PMID:20614624 The progression of the cystic duct over time, from its formation to the mature structure. The cystic duct runs from the gallbladder to the common bile duct. bf 2010-12-10T01:24:28Z biological_process GO:0035628 cystic duct development The progression of the cystic duct over time, from its formation to the mature structure. The cystic duct runs from the gallbladder to the common bile duct. PMID:20614624 The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell of the intestine. bf 2011-01-21T02:58:58Z intestinal smooth muscle cell differentiation biological_process GO:0035645 enteric smooth muscle cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell of the intestine. CL:0002504 GOC:BHF intestinal smooth muscle cell differentiation CL:0002504 A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. bf 2011-03-10T02:52:36Z sodium ion membrane transport biological_process GO:0035725 Note that this term is not intended for use in annotating lateral movement within membranes. sodium ion transmembrane transport A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. GOC:vw The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. bf 2011-03-17T10:55:42Z intraflagellar transport Reactome:R-HSA-5620924.2 biological_process intraciliary transport involved in cilium morphogenesis intraflagellar transport involved in cilium morphogenesis GO:0035735 intraciliary transport involved in cilium assembly The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. GOC:bf GOC:cilia Reactome:R-HSA-5620924.2 The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to compound eye morphogenesis. bf 2011-03-17T10:57:03Z biological_process GO:0035736 cell proliferation involved in compound eye morphogenesis The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to compound eye morphogenesis. GOC:bf GOC:sart The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an angioblast cell. Angioblasts are one of the two products formed from hemangioblast cells (the other being pluripotent hemopoietic stem cells). bf 2011-04-04T11:10:38Z angioblastic mesenchymal cell differentiation biological_process GO:0035779 angioblast cell differentiation The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an angioblast cell. Angioblasts are one of the two products formed from hemangioblast cells (the other being pluripotent hemopoietic stem cells). CL:0000566 GOC:yaf angioblastic mesenchymal cell differentiation CL:0000566 A specialized extracellular matrix that surrounds the plasma membrane of the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development. bf 2011-04-19T02:07:23Z vitelline membrane zona pellucida cellular_component GO:0035805 egg coat A specialized extracellular matrix that surrounds the plasma membrane of the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development. PMID:16944418 PMID:17163408 vitelline membrane PMID:16944418 PMID:17163408 zona pellucida PMID:16944418 PMID:17163408 The chemical reactions and pathways involving an indole alkaloid, an alkaloid containing an indole skeleton. bf 2011-05-04T03:17:44Z indole alkaloid metabolism biological_process GO:0035834 indole alkaloid metabolic process The chemical reactions and pathways involving an indole alkaloid, an alkaloid containing an indole skeleton. GOC:yaf indole alkaloid metabolism GOC:bf The chemical reactions and pathways resulting in the formation of an indole alkaloid, an alkaloid containing an indole skeleton. bf 2011-05-04T03:18:31Z indole alkaloid anabolism indole alkaloid biosynthesis indole alkaloid formation indole alkaloid synthesis biological_process GO:0035835 indole alkaloid biosynthetic process The chemical reactions and pathways resulting in the formation of an indole alkaloid, an alkaloid containing an indole skeleton. GOC:yaf indole alkaloid anabolism GOC:bf indole alkaloid biosynthesis GOC:bf indole alkaloid formation GOC:bf indole alkaloid synthesis GOC:bf The process whose specific outcome is the progression of the cloaca over time, from it's formation to the mature structure. The cloaca is the common chamber into which intestinal, genital and urinary canals open in vertebrates. bf 2011-05-06T01:54:35Z cloacal development biological_process GO:0035844 cloaca development The process whose specific outcome is the progression of the cloaca over time, from it's formation to the mature structure. The cloaca is the common chamber into which intestinal, genital and urinary canals open in vertebrates. GOC:dgh ISBN:0582227089 cloacal development GOC:bf The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow. bf 2011-05-13T01:28:06Z megakaryocyte cell development biological_process GO:0035855 megakaryocyte development The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow. CL:0000556 GOC:BHF GOC:vk megakaryocyte cell development GOC:bf A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. bf 2011-05-17T03:04:42Z site of DSB cellular_component DNA damage foci DNA damage focus IRIF ionizing radiation-induced foci GO:0035861 site of double-strand break A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. GOC:bf GOC:mah GOC:vw PMID:20096808 PMID:21035408 site of DSB PMID:21035408 DNA damage foci GOC:vw DNA damage focus GOC:mah PMID:20096808 PMID:21035408 IRIF PMID:20096808 PMID:21035408 ionizing radiation-induced foci PMID:20096808 PMID:21035408 A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. bf 2011-05-25T03:09:58Z cilial transition zone cilium transition zone cellular_component connecting cilium GO:0035869 Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone. ciliary transition zone A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. GOC:cilia GOC:kmv PMID:21422230 The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an enteroendocrine cell. Enteroendocrine cells are hormonally active epithelial cells in the gut that constitute the diffuse neuroendocrine system. bf 2011-06-06T11:48:51Z biological_process GO:0035883 enteroendocrine cell differentiation The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an enteroendocrine cell. Enteroendocrine cells are hormonally active epithelial cells in the gut that constitute the diffuse neuroendocrine system. CL:0000164 GOC:bf The process in which a relatively unspecialized cell acquires specialized features of a vascular smooth muscle cell. bf 2011-06-08T11:23:52Z VSMC differentiation vascular smooth muscle cell differentiation biological_process GO:0035886 vascular associated smooth muscle cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a vascular smooth muscle cell. GOC:sl PMID:16151017 PMID:18267954 VSMC differentiation PMID:16151017 The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell surrounding the aorta. bf 2011-06-08T11:34:26Z biological_process GO:0035887 aortic smooth muscle cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell surrounding the aorta. GOC:sl The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body. bf 2011-06-24T11:00:07Z biological_process GO:0035904 aorta development The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body. GOC:bf GOC:dgh MA:0000062 UBERON:0000947 Wikipedia:Aorta The progression of the ascending aorta over time, from its initial formation to the mature structure. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once. bf 2011-06-24T11:02:01Z biological_process GO:0035905 ascending aorta development The progression of the ascending aorta over time, from its initial formation to the mature structure. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once. GOC:bf GOC:dgh MA:0002570 UBERON:0001496 Wikipedia:Ascending_aorta The progression of the descending aorta over time, from its initial formation to the mature structure. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once. bf 2011-06-24T11:05:22Z biological_process GO:0035906 descending aorta development The progression of the descending aorta over time, from its initial formation to the mature structure. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once. GOC:bf GOC:dgh MA:0002571 UBERON:0001514 Wikipedia:Descending_aorta The progression of the dorsal aorta over time, from its initial formation to the mature structure. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. bf 2011-06-24T11:07:01Z biological_process GO:0035907 dorsal aorta development The progression of the dorsal aorta over time, from its initial formation to the mature structure. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. GOC:bf GOC:dgh UBERON:0005805 Wikipedia:Aorta ZFA:0000014 The process in which the anatomical structures of an aorta are generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body. bf 2011-06-24T11:11:11Z biological_process GO:0035909 aorta morphogenesis The process in which the anatomical structures of an aorta are generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body. GOC:bf GOC:dgh MA:0000062 UBERON:0000947 Wikipedia:Aorta The process in which the anatomical structures of the ascending aorta are generated and organized. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once. bf 2011-06-24T11:14:52Z biological_process GO:0035910 ascending aorta morphogenesis The process in which the anatomical structures of the ascending aorta are generated and organized. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once. GOC:bf GOC:dgh MA:0002570 UBERON:0001496 Wikipedia:Ascending_aorta The process in which the anatomical structures of the descending aorta are generated and organized. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once. bf 2011-06-24T11:19:24Z biological_process GO:0035911 descending aorta morphogenesis The process in which the anatomical structures of the descending aorta are generated and organized. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once. GOC:bf GOC:dgh MA:0002571 UBERON:0001514 Wikipedia:Descending_aorta The process in which the anatomical structures of the dorsal aorta are generated and organized. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. bf 2011-06-24T11:22:14Z biological_process GO:0035912 dorsal aorta morphogenesis The process in which the anatomical structures of the dorsal aorta are generated and organized. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. GOC:bf GOC:dgh UBERON:0005805 Wikipedia:Aorta ZFA:0000014 The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle. bf 2011-06-24T02:36:19Z biological_process GO:0035914 skeletal muscle cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle. CL:0000188 GOC:BHF GOC:vk The regulated release of any steroid that acts as a hormone into the circulatory system. bf 2011-07-20T01:01:00Z biological_process GO:0035929 steroid hormone secretion The regulated release of any steroid that acts as a hormone into the circulatory system. GOC:sl The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates. bf 2011-07-20T01:11:31Z biological_process GO:0035935 androgen secretion The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates. GOC:sl The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo. bf 2011-08-25T04:50:36Z endoderm cell differentiation biological_process GO:0035987 endodermal cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo. CL:0000223 GOC:yaf PMID:17624332 endoderm cell differentiation CL:0000223 The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force. bf 2011-08-26T04:14:30Z biological_process sinew development GO:0035989 tendon development The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force. GOC:yaf PMID:21412429 UBERON:0000043 sinew development UBERON:0000043 The process that gives rise to a tendon. This process pertains to the initial formation of a tendon from unspecified parts. bf 2011-08-30T01:35:10Z biological_process GO:0035992 tendon formation The process that gives rise to a tendon. This process pertains to the initial formation of a tendon from unspecified parts. GOC:yaf PMID:17567668 UBERON:0000043 The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues. bf 2011-12-19T01:47:22Z biological_process GO:0036072 direct ossification The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues. GO_REF:0000034 The multiplication or reproduction of germ cells, reproductive cells in multicellular organisms, resulting in the expansion of a cell population. bf 2012-01-17T04:06:27Z biological_process GO:0036093 germ cell proliferation The multiplication or reproduction of germ cells, reproductive cells in multicellular organisms, resulting in the expansion of a cell population. CL:0000586 GOC:kmv A prolongation or process extending from a muscle cell. A muscle cell is a mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. bf 2012-04-20T10:20:47Z myocyte projection muscle arm myopodia cellular_component GO:0036194 muscle cell projection A prolongation or process extending from a muscle cell. A muscle cell is a mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. CL:0000187 GOC:kmv PMID:15930100 PMID:22464329 myocyte projection CL:0000187 muscle arm GOC:kmv myopodia GOC:kmv The portion of the plasma membrane surrounding a muscle cell projection. bf 2012-04-20T10:21:51Z cellular_component GO:0036195 muscle cell projection membrane The portion of the plasma membrane surrounding a muscle cell projection. CL:0000187 GOC:kmv PMID:15930100 PMID:22464329 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen. bf 2012-07-20T01:05:46Z response to lowered oxygen levels biological_process GO:0036293 This term should be used when a decrease in oxygen levels is not considered a stress response. For a hypoxic stress response, consider instead 'response to hypoxia ; GO:0001666'. response to decreased oxygen levels Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen. GOC:al response to lowered oxygen levels GOC:bf Any biological process involved in the maintenance of the steady-state number of hepatocytes within a population of cells. Hepatocytes are specialized epithelial cells of the liver that are organized into interconnected plates called lobules. bf 2012-09-05T10:17:07Z biological_process GO:0036333 hepatocyte homeostasis Any biological process involved in the maintenance of the steady-state number of hepatocytes within a population of cells. Hepatocytes are specialized epithelial cells of the liver that are organized into interconnected plates called lobules. CL:0000182 GOC:nhn PMID:19878874 Any biological process involved in the maintenance of the steady-state number of epidermal stem cells within a population of cells. bf 2012-09-05T10:21:23Z biological_process GO:0036334 epidermal stem cell homeostasis Any biological process involved in the maintenance of the steady-state number of epidermal stem cells within a population of cells. CL:1000428 GOC:nhn PMID:17666529 The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance. bf 2012-09-11T13:54:49Z biological_process GO:0036342 post-anal tail morphogenesis The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance. GOC:bf GOC:kmv Wikipedia:Chordate The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon. bf 2014-07-24T10:06:19Z cellular_component GO:0036477 somatodendritic compartment The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon. GOC:PARL GOC:pad The joining of two lipid bilayers that surround the Golgi apparatus to form a single Golgi membrane. bf 2015-05-21T10:05:06Z Golgi apparatus membrane fusion membrane fusion involved in Golgi reassembly post-mitotic fusion of Golgi membranes biological_process GO:0036504 Golgi membrane fusion The joining of two lipid bilayers that surround the Golgi apparatus to form a single Golgi membrane. GOC:PARL GOC:bf PMID:12473691 membrane fusion involved in Golgi reassembly GOC:bf post-mitotic fusion of Golgi membranes PMID:10811609 The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth The increase in size or mass of an entire organism, a part of an organism or a cell. GOC:bf GOC:ma non-developmental growth GOC:mah Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. biological_process GO:0040008 regulation of growth Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. GOC:ems GOC:mah Self-propelled movement of a cell or organism from one location to another. biological_process GO:0040011 locomotion Self-propelled movement of a cell or organism from one location to another. GOC:dgh Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. biological_process GO:0040012 regulation of locomotion Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. GOC:ems Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. down regulation of locomotion down-regulation of locomotion downregulation of locomotion inhibition of locomotion biological_process GO:0040013 negative regulation of locomotion Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size. regulation of body growth regulation of body size biological_process GO:0040014 regulation of multicellular organism growth Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size. GOC:dph GOC:ems GOC:tb regulation of body growth GOC:dph GOC:tb regulation of body size GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organism to reach its usual body size. negative regulation of body growth negative regulation of body size biological_process GO:0040015 negative regulation of multicellular organism growth Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organism to reach its usual body size. GOC:dph GOC:ems GOC:tb negative regulation of body growth GOC:dph GOC:tb negative regulation of body size GOC:dph GOC:tb The first few specialized divisions of an activated animal egg. biological_process GO:0040016 embryonic cleavage The first few specialized divisions of an activated animal egg. GOC:clt ISBN:0070524300 Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. up regulation of locomotion up-regulation of locomotion upregulation of locomotion activation of locomotion stimulation of locomotion biological_process GO:0040017 positive regulation of locomotion Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size. positive regulation of body growth positive regulation of body size biological_process GO:0040018 positive regulation of multicellular organism growth Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size. GOC:dph GOC:go_curators GOC:tb positive regulation of body growth GOC:dph GOC:tb positive regulation of body size GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of embryonic development. up regulation of embryonic development up-regulation of embryonic development upregulation of embryonic development activation of embryonic development stimulation of embryonic development biological_process GO:0040019 positive regulation of embryonic development Any process that activates or increases the frequency, rate or extent of embryonic development. GOC:go_curators Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes. regulation of meiosis biological_process GO:0040020 regulation of meiotic nuclear division Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes. GOC:ems GOC:ma regulation of meiosis GOC:vw Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and the rate at which this time point is reached. heterochronic regulation of development temporal regulation of development biological_process developmental timing GO:0040034 regulation of development, heterochronic Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and the rate at which this time point is reached. PMID:9442909 The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia. glial cell generation biological_process GO:0042063 gliogenesis The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia. GOC:dgh GOC:jid glial cell generation Growth of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system. biological_process GO:0042065 glial cell growth Growth of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system. GOC:dph GOC:isa_complete GOC:jid Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catecholamines. regulation of catecholamine metabolism biological_process GO:0042069 regulation of catecholamine metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catecholamines. GOC:go_curators The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. GO:0035734 Wikipedia:Intraflagellar_transport intraflagellar transport intraflagellar transport involved in cilium organization intraflagellar transport involved in microtubule-based flagellum organisation biological_process IFT GO:0042073 Note that we deem cilium and microtubule-based flagellum to be equivalent. intraciliary transport The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. GOC:cilia GOC:kmv PMID:17981739 PMID:18180368 PMID:22869374 Reactome:R-HSA-5620924.2 The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression). biological_process GO:0042074 cell migration involved in gastrulation The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression). GOC:jl ISBN:0878932437 http://www.cellmigration.org/ The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes. GO:0048131 germ-line stem cell renewal biological_process GO:0042078 germ-line stem cell division The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes. GOC:jid PMID:2279698 Any process that modulates the frequency, rate or extent of cell proliferation. biological_process regulation of cell proliferation GO:0042127 regulation of cell population proliferation Any process that modulates the frequency, rate or extent of cell proliferation. GOC:jl The continuous network of membranes encompassing the nuclear outer membrane and the endoplasmic reticulum membrane. nuclear membrane-ER network nuclear membrane-endoplasmic reticulum continuum cellular_component NE-ER continuum NE-ER network nuclear envelope-ER network nuclear envelope-endoplasmic reticulum continuum nuclear envelope-endoplasmic reticulum network GO:0042175 nuclear outer membrane-endoplasmic reticulum membrane network The continuous network of membranes encompassing the nuclear outer membrane and the endoplasmic reticulum membrane. GOC:bf GOC:jl GOC:mah GOC:mcc GOC:pr GOC:vw nuclear membrane-ER network GOC:mah nuclear membrane-endoplasmic reticulum continuum GOC:mah nuclear envelope-endoplasmic reticulum network GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. https://github.com/geneontology/go-ontology/issues/23112 kmv 2014-08-21T15:05:45Z GO:1903362 GO:2000598 regulation of cellular protein breakdown regulation of cellular protein catabolic process regulation of cellular protein catabolism regulation of cellular protein degradation regulation of protein breakdown regulation of protein catabolism regulation of protein degradation regulation of cyclin breakdown regulation of cyclin catabolic process regulation of cyclin catabolism regulation of cyclin degradation regulation of degradation of cyclin biological_process GO:0042176 regulation of protein catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GOC:go_curators GOC:jl regulation of cellular protein breakdown GOC:TermGenie regulation of cellular protein catabolism GOC:TermGenie regulation of cellular protein degradation GOC:TermGenie regulation of cyclin breakdown GOC:obol regulation of cyclin catabolism GOC:obol regulation of cyclin degradation GOC:obol regulation of degradation of cyclin GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process. https://github.com/geneontology/go-ontology/issues/23112 GO:1903363 GO:2000599 down regulation of cellular protein breakdown down regulation of cellular protein catabolic process down regulation of cellular protein catabolism down regulation of cellular protein degradation down regulation of protein catabolic process down-regulation of cellular protein breakdown down-regulation of cellular protein catabolic process down-regulation of cellular protein catabolism down-regulation of cellular protein degradation down-regulation of protein catabolic process downregulation of cellular protein breakdown downregulation of cellular protein catabolic process downregulation of cellular protein catabolism downregulation of cellular protein degradation downregulation of protein catabolic process negative regulation of cellular protein breakdown negative regulation of cellular protein catabolic process negative regulation of cellular protein catabolism negative regulation of cellular protein degradation negative regulation of protein breakdown negative regulation of protein catabolism negative regulation of protein degradation inhibition of cellular protein breakdown inhibition of cellular protein catabolic process inhibition of cellular protein catabolism inhibition of cellular protein degradation inhibition of protein catabolic process biological_process GO:0042177 negative regulation of protein catabolic process Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process. GOC:TermGenie GOC:kmv GOC:obol GO_REF:0000058 PMID:24785082 down regulation of cellular protein breakdown GOC:TermGenie down regulation of cellular protein catabolic process GOC:TermGenie down regulation of cellular protein catabolism GOC:TermGenie down regulation of cellular protein degradation GOC:TermGenie down-regulation of cellular protein breakdown GOC:TermGenie down-regulation of cellular protein catabolic process GOC:TermGenie down-regulation of cellular protein catabolism GOC:TermGenie down-regulation of cellular protein degradation GOC:TermGenie downregulation of cellular protein breakdown GOC:TermGenie downregulation of cellular protein catabolic process GOC:TermGenie downregulation of cellular protein catabolism GOC:TermGenie downregulation of cellular protein degradation GOC:TermGenie negative regulation of cellular protein breakdown GOC:TermGenie negative regulation of cellular protein catabolism GOC:TermGenie negative regulation of cellular protein degradation GOC:TermGenie inhibition of cellular protein breakdown GOC:TermGenie inhibition of cellular protein catabolic process GOC:TermGenie inhibition of cellular protein catabolism GOC:TermGenie inhibition of cellular protein degradation GOC:TermGenie The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. ketone metabolism biological_process GO:0042180 cellular ketone metabolic process The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:jl ISBN:0787650153 The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. ketone anabolism ketone biosynthesis ketone formation ketone synthesis biological_process GO:0042181 ketone biosynthetic process The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. ketone breakdown ketone catabolism ketone degradation biological_process GO:0042182 ketone catabolic process The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:go_curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. response to chemical stimulus response to chemical substance biological_process GO:0042221 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to chemical Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:jl response to chemical stimulus GOC:dos A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis. GO:0007046 ribosome biogenesis and assembly biological_process GO:0042254 ribosome biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis. GOC:ma PMID:26404467 Wikipedia:Ribosome_biogenesis The aggregation, arrangement and bonding together of the mature ribosome and of its subunits. GO:0042257 ribosomal subunit assembly biological_process GO:0042255 ribosome assembly The aggregation, arrangement and bonding together of the mature ribosome and of its subunits. GOC:ma PMID:30467428 ribosomal subunit assembly GOC:mah GOC:vw Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. biological_process GO:0042325 regulation of phosphorylation Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. GOC:jl Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. down regulation of phosphorylation down-regulation of phosphorylation downregulation of phosphorylation inhibition of phosphorylation biological_process GO:0042326 negative regulation of phosphorylation Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. GOC:jl Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. up regulation of phosphorylation up-regulation of phosphorylation upregulation of phosphorylation activation of phosphorylation stimulation of phosphorylation biological_process GO:0042327 positive regulation of phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. GOC:jl Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. biological_process GO:0042391 regulation of membrane potential Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. GOC:jl GOC:mtg_cardio GOC:tb ISBN:0198506732 The chemical reactions and pathways occurring at the level of individual cells resulting in the formation of any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters. biogenic amine anabolism biogenic amine biosynthesis biogenic amine formation biogenic amine synthesis cellular biogenic amine biosynthetic process biological_process GO:0042401 biogenic amine biosynthetic process The chemical reactions and pathways occurring at the level of individual cells resulting in the formation of any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters. GOC:jl ISBN:0395825172 The chemical reactions and pathways occurring at the level of individual cells resulting in the breakdown of biogenic amines, any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters. biogenic amine breakdown biogenic amine catabolism biogenic amine degradation biological_process GO:0042402 cellular biogenic amine catabolic process The chemical reactions and pathways occurring at the level of individual cells resulting in the breakdown of biogenic amines, any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters. GOC:go_curators GOC:jl ISBN:0198506732 The chemical reactions and pathways involving norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine. levarterenol metabolic process levarterenol metabolism noradrenaline metabolic process noradrenaline metabolism norepinephrine metabolism biological_process GO:0042415 norepinephrine metabolic process The chemical reactions and pathways involving norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine. levarterenol biosynthesis levarterenol biosynthetic process noradrenaline biosynthesis noradrenaline biosynthetic process norepinephrine anabolism norepinephrine biosynthesis norepinephrine formation norepinephrine synthesis biological_process GO:0042421 norepinephrine biosynthetic process The chemical reactions and pathways resulting in the formation of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine. Wikipedia:Norepinephrine#Degradation levarterenol catabolic process levarterenol catabolism noradrenaline catabolic process noradrenaline catabolism norepinephrine breakdown norepinephrine catabolism norepinephrine degradation biological_process GO:0042422 norepinephrine catabolic process The chemical reactions and pathways resulting in the breakdown of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. Wikipedia:Catecholamines catecholamine anabolism catecholamine biosynthesis catecholamine formation catecholamine synthesis biological_process GO:0042423 catecholamine biosynthetic process The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. catecholamine breakdown catecholamine catabolism catecholamine degradation biological_process GO:0042424 catecholamine catabolic process The chemical reactions and pathways resulting in the breakdown of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties. Wikipedia:Serotonin serotonin anabolism serotonin biosynthesis serotonin formation serotonin synthesis biological_process GO:0042427 serotonin biosynthetic process The chemical reactions and pathways resulting in the formation of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties. serotonin metabolism biological_process GO:0042428 serotonin metabolic process The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties. serotonin breakdown serotonin catabolism serotonin degradation biological_process GO:0042429 serotonin catabolic process The chemical reactions and pathways resulting in the breakdown of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton. GO:0042434 indole and derivative metabolic process indole and derivative metabolism indole-containing compound metabolism ketole metabolic process ketole metabolism indole derivative metabolic process indole derivative metabolism biological_process GO:0042430 indole-containing compound metabolic process The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton. GOC:jl GOC:mah The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton. indole derivative biosynthesis indole derivative biosynthetic process indole-containing compound anabolism indole-containing compound biosynthesis indole-containing compound formation indole-containing compound synthesis biological_process GO:0042435 indole-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton. GOC:jl The chemical reactions and pathways resulting in the breakdown of compounds that contain an indole (2,3-benzopyrrole) skeleton. indole derivative catabolic process indole derivative catabolism indole-containing compound breakdown indole-containing compound catabolism indole-containing compound degradation biological_process GO:0042436 indole-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of compounds that contain an indole (2,3-benzopyrrole) skeleton. GOC:jl Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. GO:0046531 photoreceptor morphogenesis biological_process GO:0042461 photoreceptor cell development Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. GOC:go_curators Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve. biological_process GO:0042462 eye photoreceptor cell development Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve. GOC:jl ISBN:0192800981 Any process that modulates the frequency, rate or extent of eye photoreceptor development. regulation of eye photoreceptor development biological_process GO:0042478 regulation of eye photoreceptor cell development Any process that modulates the frequency, rate or extent of eye photoreceptor development. GOC:jl Any process that activates or increases the frequency, rate or extent of eye photoreceptor development. positive regulation of eye photoreceptor development up regulation of eye photoreceptor cell development up-regulation of eye photoreceptor cell development upregulation of eye photoreceptor cell development activation of eye photoreceptor cell development stimulation of eye photoreceptor cell development biological_process GO:0042479 positive regulation of eye photoreceptor cell development Any process that activates or increases the frequency, rate or extent of eye photoreceptor development. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of eye photoreceptor development. down regulation of eye photoreceptor cell development down-regulation of eye photoreceptor cell development downregulation of eye photoreceptor cell development negative regulation of eye photoreceptor development inhibition of eye photoreceptor cell development biological_process GO:0042480 negative regulation of eye photoreceptor cell development Any process that stops, prevents, or reduces the frequency, rate or extent of eye photoreceptor development. GOC:jl A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state. biological_process GO:0042551 neuron maturation A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state. GOC:dph GOC:jl A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme. cellular_component GO:0042588 zymogen granule A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme. GOC:jl ISBN:0198506732 The lipid bilayer surrounding a zymogen granule. cellular_component GO:0042589 zymogen granule membrane The lipid bilayer surrounding a zymogen granule. GOC:jl Any biological process involved in the maintenance of an internal steady state. GO:0032844 GO:0032845 GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process biological_process negative regulation of homeostatic process positive regulation of homeostatic process regulation of homeostatic process GO:0042592 homeostatic process Any biological process involved in the maintenance of an internal steady state. GOC:jl ISBN:0395825172 Any complex of actin, myosin, and accessory proteins. actomyosin complex actomyosin structure cellular_component GO:0042641 actomyosin Any complex of actin, myosin, and accessory proteins. GOC:go_curators The process in which a relatively unspecialized cell acquires the specialized features of a retinal cone cell. biological_process GO:0042670 retinal cone cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a retinal cone cell. GOC:go_curators The process in which a relatively unspecialized cell acquires specialized features of a muscle cell. biological_process myogenesis GO:0042692 muscle cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a muscle cell. CL:0000187 GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur. regulation of sulfur metabolism regulation of sulphur metabolic process regulation of sulphur metabolism biological_process GO:0042762 regulation of sulfur metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur. GOC:go_curators The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0042886 amide transport The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl ISBN:0198506732 Enables the transfer of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, from one side of a membrane to the other. amine/amide/polyamine channel activity molecular_function GO:0042887 amide transmembrane transporter activity Enables the transfer of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, from one side of a membrane to the other. GOC:jl ISBN:0198506732 Any process that modulates the occurrence or rate of cell death by apoptotic process. regulation of apoptosis biological_process apoptosis regulator activity GO:0042981 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. regulation of apoptotic process Any process that modulates the occurrence or rate of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis A prolongation or process extending from a cell, e.g. a flagellum or axon. cell process cellular process cellular projection cellular_component GO:0042995 cell projection A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl http://www.cogsci.princeton.edu/~wn/ Any process that modulates the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. biological_process GO:0042996 regulation of Golgi to plasma membrane protein transport Any process that modulates the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. down regulation of Golgi to plasma membrane protein transport down-regulation of Golgi to plasma membrane protein transport downregulation of Golgi to plasma membrane protein transport inhibition of Golgi to plasma membrane protein transport biological_process GO:0042997 negative regulation of Golgi to plasma membrane protein transport Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. GOC:jl Any process that activates or increases the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. up regulation of Golgi to plasma membrane protein transport up-regulation of Golgi to plasma membrane protein transport upregulation of Golgi to plasma membrane protein transport activation of Golgi to plasma membrane protein transport stimulation of Golgi to plasma membrane protein transport biological_process GO:0042998 positive regulation of Golgi to plasma membrane protein transport Any process that activates or increases the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane. GOC:jl The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane. biological_process GO:0043001 Golgi to plasma membrane protein transport The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane. ISBN:0716731363 A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. NIF_Subcellular:sao867568886 neuron process neuron protrusion neuronal cell projection neurite cellular_component nerve fiber GO:0043005 neuron projection A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. GOC:jl http://www.cogsci.princeton.edu/~wn/ neuron protrusion NIF_Subcellular:sao250931889 nerve fiber GOC:dph The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching. biological_process GO:0043009 chordate embryonic development The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching. GOC:mtg_sensu The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. GO:0001747 GO:0031075 biological_process GO:0043010 camera-type eye development The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. GOC:go_curators GOC:mtg_sensu The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. NIF_Subcellular:sao1044911821 Wikipedia:Soma_(biology) neuron cell body neuronal cell soma cellular_component GO:0043025 Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. neuronal cell body The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. GOC:go_curators The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide. peptide anabolism peptide biosynthesis peptide formation peptide synthesis biological_process GO:0043043 peptide biosynthetic process The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide. GOC:dph GOC:jl A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite. extracellular structure organisation extracellular structure organization and biogenesis biological_process GO:0043062 extracellular structure organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite. GOC:ai GOC:dph GOC:jl GOC:mah extracellular structure organization and biogenesis GOC:dph GOC:jl GOC:mah Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. up regulation of apoptosis up-regulation of apoptosis upregulation of apoptosis activation of apoptosis positive regulation of apoptosis stimulation of apoptosis biological_process pro-apoptosis GO:0043065 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. positive regulation of apoptotic process Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. GO:0006916 anti-apoptosis down regulation of apoptosis down-regulation of apoptosis downregulation of apoptosis inhibition of apoptosis negative regulation of apoptosis biological_process apoptosis inhibitor activity pro-survival GO:0043066 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. negative regulation of apoptotic process Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043070 regulation of non-apoptotic programmed cell death biological_process GO:0043067 regulation of programmed cell death Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043071 up regulation of programmed cell death up-regulation of programmed cell death upregulation of programmed cell death activation of programmed cell death positive regulation of non-apoptotic programmed cell death stimulation of programmed cell death biological_process GO:0043068 positive regulation of programmed cell death Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043072 down regulation of programmed cell death down-regulation of programmed cell death downregulation of programmed cell death inhibition of programmed cell death negative regulation of non-apoptotic programmed cell death biological_process GO:0043069 negative regulation of programmed cell death Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl The nucleus of a germ cell, a reproductive cell in multicellular organisms. germ-cell nucleus cellular_component GO:0043073 germ cell nucleus The nucleus of a germ cell, a reproductive cell in multicellular organisms. CL:0000586 GOC:go_curators Any process that activates or increases the activity of an enzyme. GO:0048554 positive regulation of enzyme activity up regulation of enzyme activity up-regulation of enzyme activity upregulation of enzyme activity activation of enzyme activity activation of metalloenzyme activity positive regulation of metalloenzyme activity stimulation of enzyme activity stimulation of metalloenzyme activity up regulation of metalloenzyme activity up-regulation of metalloenzyme activity upregulation of metalloenzyme activity biological_process GO:0043085 positive regulation of catalytic activity Any process that activates or increases the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw positive regulation of enzyme activity GOC:tb Any process that stops or reduces the activity of an enzyme. GO:0048553 down regulation of enzyme activity down-regulation of enzyme activity down-regulation of metalloenzyme activity downregulation of enzyme activity negative regulation of enzyme activity down regulation of metalloenzyme activity downregulation of metalloenzyme activity inhibition of enzyme activity inhibition of metalloenzyme activity negative regulation of metalloenzyme activity biological_process GO:0043086 negative regulation of catalytic activity Any process that stops or reduces the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw negative regulation of enzyme activity GOC:tb A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the hindgut. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The hindgut is the posterior part of the alimentary canal, including the rectum, and the large intestine. biological_process GO:0043133 hindgut contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the hindgut. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The hindgut is the posterior part of the alimentary canal, including the rectum, and the large intestine. GOC:jl GOC:mtg_muscle UBERON:0001046 Any process that modulates the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. biological_process GO:0043134 regulation of hindgut contraction Any process that modulates the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. GOC:jl UBERON:0001046 Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location. establishment and maintenance of translational machinery localization establishment and maintenance of translational protein localization regulation of translation by machinery localisation translational machinery localization translational protein localization biological_process GO:0043143 regulation of translation by machinery localization Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location. GOC:jl regulation of translation by machinery localisation GOC:mah translational machinery localization GOC:dph GOC:tb The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 GO:0034960 GO:0043283 GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process biological_process GO:0043170 macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. peptide breakdown peptide catabolism peptide degradation biological_process GO:0043171 peptide catabolic process The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. GOC:jl Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. GO:0010237 response to amino acid stimulus biological_process GO:0043200 response to amino acid Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups. GOC:ef GOC:mlg response to amino acid stimulus GOC:dos Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things. biological_process GO:0043207 response to external biotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things. GOC:go_curators Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cellular_component GO:0043229 intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. cellular_component GO:0043230 extracellular organelle Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. GOC:jl PMID:9914479 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. intracellular non-membrane-enclosed organelle cellular_component GO:0043232 intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. cellular_component GO:0043233 organelle lumen The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. GOC:jl GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. down regulation of protein complex disassembly down-regulation of protein complex disassembly downregulation of protein complex disassembly inhibition of protein complex disassembly biological_process negative regulation of protein complex disassembly GO:0043242 negative regulation of protein-containing complex disassembly Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. GOC:jl Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. up regulation of protein complex disassembly up-regulation of protein complex disassembly upregulation of protein complex disassembly activation of protein complex disassembly stimulation of protein complex disassembly biological_process positive regulation of protein complex disassembly GO:0043243 positive regulation of protein-containing complex disassembly Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. GOC:jl Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. biological_process regulation of protein complex disassembly GO:0043244 regulation of protein-containing complex disassembly Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. GOC:jl A developmental process, independent of morphogenetic (shape) change, that is required for an erythrocyte to attain its fully functional state. RBC maturation red blood cell maturation biological_process GO:0043249 erythrocyte maturation A developmental process, independent of morphogenetic (shape) change, that is required for an erythrocyte to attain its fully functional state. GOC:devbiol GOC:jl RBC maturation CL:0000232 red blood cell maturation CL:0000232 Any process that modulates the frequency, rate or extent of protein complex assembly. biological_process regulation of protein complex assembly GO:0043254 regulation of protein-containing complex assembly Any process that modulates the frequency, rate or extent of protein complex assembly. GOC:jl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates. regulation of carbohydrate anabolism regulation of carbohydrate biosynthesis regulation of carbohydrate formation regulation of carbohydrate synthesis biological_process GO:0043255 regulation of carbohydrate biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates. GOC:jl Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell. extracellular non-membrane-enclosed organelle cellular_component GO:0043264 extracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell. GOC:jl Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. regulation of ion transport biological_process GO:0043269 regulation of monoatomic ion transport Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of ion transport up-regulation of ion transport upregulation of ion transport activation of ion transport stimulation of ion transport biological_process GO:0043270 positive regulation of monoatomic ion transport Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. negative regulation of ion transport down regulation of ion transport down-regulation of ion transport downregulation of ion transport inhibition of ion transport biological_process GO:0043271 negative regulation of monoatomic ion transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an alkaloid stimulus. Alkaloids are a large group of nitrogenous substances found in naturally in plants, many of which have extracts that are pharmacologically active. biological_process GO:0043279 response to alkaloid Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an alkaloid stimulus. Alkaloids are a large group of nitrogenous substances found in naturally in plants, many of which have extracts that are pharmacologically active. GOC:jl Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. contractile fibre cellular_component GO:0043292 contractile fiber Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. GOC:go_curators ISBN:0815316194 The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus. enucleate RBC differentiation enucleate red blood cell differentiation biological_process GO:0043353 enucleate erythrocyte differentiation The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus. GOC:go_curators enucleate RBC differentiation CL:0000232 enucleate red blood cell differentiation CL:0000232 A developmental process, independent of morphogenetic (shape) change, that is required for an enucleate erythrocyte to attain its fully functional state. An enucleate erythrocyte is an erythrocyte without a nucleus. enucleate RBC maturation enucleate red blood cell maturation biological_process GO:0043354 enucleate erythrocyte maturation A developmental process, independent of morphogenetic (shape) change, that is required for an enucleate erythrocyte to attain its fully functional state. An enucleate erythrocyte is an erythrocyte without a nucleus. GOC:go_curators enucleate RBC maturation CL:0000232 enucleate red blood cell maturation CL:0000232 A developmental process, independent of morphogenetic (shape) change, that is required for a nucleate erythrocyte to attain its fully functional state. A nucleate erythrocyte is an erythrocyte with a nucleus. nucleate RBC maturation nucleate red blood cell maturation biological_process GO:0043362 nucleate erythrocyte maturation A developmental process, independent of morphogenetic (shape) change, that is required for a nucleate erythrocyte to attain its fully functional state. A nucleate erythrocyte is an erythrocyte with a nucleus. GOC:devbiol GOC:jl nucleate RBC maturation CL:0000232 nucleate red blood cell maturation CL:0000232 The process in which a myeloid precursor cell acquires specializes features of an erythrocyte with a nucleus, as found in non-mammalian vertebrates such as birds. nucleate RBC differentiation nucleate red blood cell differentiation biological_process GO:0043363 nucleate erythrocyte differentiation The process in which a myeloid precursor cell acquires specializes features of an erythrocyte with a nucleus, as found in non-mammalian vertebrates such as birds. GOC:jl nucleate RBC differentiation CL:0000232 nucleate red blood cell differentiation CL:0000232 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals. response to peptide hormone stimulus response to polypeptide hormone stimulus biological_process GO:0043434 response to peptide hormone Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals. PMID:11027914 PMID:15134857 Wikipedia:Peptide_hormone response to peptide hormone stimulus GOC:dos The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). keto acid metabolic process keto acid metabolism ketoacid metabolic process ketoacid metabolism oxo acid metabolic process oxo acid metabolism oxoacid metabolism biological_process GO:0043436 oxoacid metabolic process The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). Wikipedia:Oxyacid Any process that modulates the frequency, rate or extent of secondary metabolism, the chemical reactions and pathways involving compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. regulation of secondary metabolism biological_process GO:0043455 regulation of secondary metabolic process Any process that modulates the frequency, rate or extent of secondary metabolism, the chemical reactions and pathways involving compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. GOC:jl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. biological_process GO:0043467 regulation of generation of precursor metabolites and energy Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. GOC:jl Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates. biological_process GO:0043470 regulation of carbohydrate catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates. GOC:mlg The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. biological_process GO:0043473 pigmentation The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. GOC:jl A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities. biological_process muscle plasticity GO:0043500 muscle adaptation A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities. GOC:mtg_muscle PMID:11181628 PMID:11449884 PMID:12605307 Any process in which skeletal muscles change their phenotypic profiles in response to altered functional demands and a variety of signals. biological_process skeletal muscle plasticity GO:0043501 skeletal muscle adaptation Any process in which skeletal muscles change their phenotypic profiles in response to altered functional demands and a variety of signals. GOC:mtg_muscle PMID:11181628 PMID:11449884 PMID:12605307 Any process that modulates the frequency, rate or extent of muscle adaptation. biological_process regulation of muscle plasticity GO:0043502 regulation of muscle adaptation Any process that modulates the frequency, rate or extent of muscle adaptation. GOC:go_curators GOC:mtg_muscle Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons. regulation of apoptosis of neuronal cells regulation of apoptosis of neurons regulation of neuron programmed cell death regulation of neuronal cell programmed cell death regulation of programmed cell death of neuronal cells regulation of programmed cell death, neurons regulation of neuron apoptosis biological_process GO:0043523 regulation of neuron apoptotic process Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons. GOC:go_curators GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons. down regulation of neuron apoptosis down-regulation of neuron apoptosis downregulation of neuron apoptosis negative regulation of programmed cell death, neurons inhibition of neuron apoptosis negative regulation of neuron apoptosis neuron survival biological_process GO:0043524 negative regulation of neuron apoptotic process Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons. GOC:go_curators GOC:mtg_apoptosis Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process. positive regulation of programmed cell death, neurons up regulation of neuron apoptosis up-regulation of neuron apoptosis upregulation of neuron apoptosis activation of neuron apoptosis positive regulation of neuron apoptosis stimulation of neuron apoptosis biological_process GO:0043525 positive regulation of neuron apoptotic process Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process. GOC:go_curators GOC:mtg_apoptosis Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. biological_process GO:0043549 regulation of kinase activity Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:bf Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment. biological_process GO:0043576 regulation of respiratory gaseous exchange Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment. GOC:jl The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue. animal skin development biological_process GO:0043588 skin development The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue. GOC:jl UBERON:0002097 The process in which the anatomical structures of the skin are generated and organized. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner, sensitive and vascular dermis (cutis, corium or true skin) composed mostly of connective tissue. biological_process GO:0043589 skin morphogenesis The process in which the anatomical structures of the skin are generated and organized. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner, sensitive and vascular dermis (cutis, corium or true skin) composed mostly of connective tissue. GOC:jl UBERON:0002097 The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells. amide metabolism cellular amide metabolic process biological_process GO:0043603 amide metabolic process The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells. GOC:curators The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. biological_process GO:0043604 amide biosynthetic process The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. GOC:curators The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. cellular amide catabolic process biological_process GO:0043605 amide catabolic process The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. GOC:curators The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-). dicarboxylate metabolic process dicarboxylate metabolism dicarboxylic acid metabolism biological_process GO:0043648 dicarboxylic acid metabolic process The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-). ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups. dicarboxylate catabolic process dicarboxylate catabolism dicarboxylic acid breakdown dicarboxylic acid catabolism dicarboxylic acid degradation biological_process GO:0043649 dicarboxylic acid catabolic process The chemical reactions and pathways resulting in the breakdown of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups. dicarboxylate biosynthesis dicarboxylate biosynthetic process dicarboxylic acid anabolism dicarboxylic acid biosynthesis dicarboxylic acid formation dicarboxylic acid synthesis biological_process GO:0043650 dicarboxylic acid biosynthetic process The chemical reactions and pathways resulting in the formation of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups. ISBN:0198506732 The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state. ossification involved in skeletal development ossification involved in bone modeling biological_process GO:0043931 ossification involved in bone maturation The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state. GOC:dph GOC:mah GOC:mtg_mpo ossification involved in skeletal development GOC:dph ossification involved in bone modeling GO_REF:0000034 Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 mah 2010-09-08T10:01:42Z GO:0034600 GO:0034621 GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process cellular macromolecular complex organization cellular macromolecular complex subunit organisation cellular macromolecular complex subunit organization macromolecular complex organization macromolecular complex subunit organisation macromolecular complex subunit organization protein-containing complex subunit organization GO:0043933 protein-containing complex organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. GOC:mah protein complex subunit organisation GOC:mah The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues. glucan metabolism biological_process GO:0044042 glucan metabolic process The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues. GOC:jl Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. biological_process GO:0044057 regulation of system process Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. GOC:jl Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0044058 regulation of digestive system process Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:jl Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. regulation of endocrine system process biological_process GO:0044060 regulation of endocrine process Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. GOC:jl Any process that modulates the frequency, rate, or extent of excretion, the elimination by an organism of the waste products that arise as a result of metabolic activity. biological_process GO:0044062 regulation of excretion Any process that modulates the frequency, rate, or extent of excretion, the elimination by an organism of the waste products that arise as a result of metabolic activity. GOC:jl Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system. biological_process GO:0044065 regulation of respiratory system process Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system. GOC:jl A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 cellular component biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044087 regulation of cellular component biogenesis Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. regulation of vacuole organisation biological_process regulation of vacuole biogenesis GO:0044088 regulation of vacuole organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. GOC:jl GOC:mah regulation of vacuole organisation GOC:mah regulation of vacuole biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044089 positive regulation of cellular component biogenesis Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. positive regulation of vacuole organisation biological_process positive regulation of vacuole biogenesis GO:0044090 positive regulation of vacuole organization Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole. GOC:jl GOC:mah positive regulation of vacuole organisation GOC:mah positive regulation of vacuole biogenesis GOC:mah A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane. biological_process GO:0044091 membrane biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane. GOC:jl Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jl 2009-04-21T04:07:27Z biological_process GO:0044092 negative regulation of molecular function Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jl 2009-04-21T04:11:06Z biological_process GO:0044093 positive regulation of molecular function Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex cellular_component GO:0044207 translation initiation ternary complex A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). GOC:jl The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. https://github.com/geneontology/go-ontology/issues/26424 primary metabolism biological_process GO:0044238 primary metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators http://www.metacyc.org The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. cellular breakdown cellular catabolism cellular degradation biological_process GO:0044248 cellular catabolic process The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular anabolism cellular biosynthesis cellular formation cellular synthesis biological_process GO:0044249 cellular biosynthetic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the breakdown into fatty acids and monoglycerides of lipids in the small intestine. Lipids are broken down by lipases released by the pancreas. intestinal lipid breakdown intestinal lipid catabolism intestinal lipid degradation biological_process GO:0044258 intestinal lipid catabolic process The chemical reactions and pathways resulting in the breakdown into fatty acids and monoglycerides of lipids in the small intestine. Lipids are broken down by lipases released by the pancreas. GOC:jl http://www.emc.maricopa.edu/ The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. nitrogen compound breakdown nitrogen compound catabolism nitrogen compound degradation biological_process GO:0044270 cellular nitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. nitrogen compound anabolism nitrogen compound biosynthesis nitrogen compound formation nitrogen compound synthesis biological_process GO:0044271 cellular nitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. sulfur compound anabolism sulfur compound biosynthesis sulfur compound formation sulfur compound synthesis sulfur biosynthesis sulfur biosynthetic process biological_process GO:0044272 sulfur compound biosynthetic process The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. GOC:jl The chemical reactions and pathways resulting in the breakdown of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. sulfur compound breakdown sulfur compound catabolism sulfur compound degradation sulfur catabolic process sulfur catabolism biological_process GO:0044273 sulfur compound catabolic process The chemical reactions and pathways resulting in the breakdown of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. GOC:jl The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. jl 2010-01-26T12:05:20Z small molecule metabolism biological_process GO:0044281 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule metabolic process The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:vw The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. jl 2010-01-26T12:06:10Z small molecule catabolism biological_process GO:0044282 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule catabolic process The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:vw The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. jl 2010-01-26T12:06:49Z small molecule biosynthesis biological_process GO:0044283 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule biosynthetic process The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:vw The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. jl 2010-02-05T10:37:16Z FBbt:00005107 FMA:67301 Wikipedia:Cell_body cell soma cellular_component GO:0044297 Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. cell body The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. GOC:go_curators The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin. jl 2010-08-25T01:44:51Z pancreatic B cell proliferation pancreatic beta cell proliferation biological_process GO:0044342 type B pancreatic cell proliferation The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin. GOC:jl GOC:yaf pancreatic B cell proliferation GOC:mah Any apoptotic process in a fibroblast, a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. jl 2010-09-23T11:33:38Z fibroblast apoptosis biological_process GO:0044346 fibroblast apoptotic process Any apoptotic process in a fibroblast, a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. CL:0000057 GOC:jl GOC:mtg_apoptosis GOC:yaf A process in which a protein is transported to, or maintained in, a location within the cytoskeleton. jl 2011-12-13T11:43:24Z protein localisation to cytoskeleton biological_process GO:0044380 protein localization to cytoskeleton A process in which a protein is transported to, or maintained in, a location within the cytoskeleton. GOC:jl protein localisation to cytoskeleton GOC:mah Any process evolved to enable an interaction with an organism of a different species. https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 biological process involved in interspecies interaction between organisms Any process evolved to enable an interaction with an organism of a different species. GOC:cc The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. jl 2012-03-29T01:55:18Z secondary metabolite biosynthesis biological_process GO:0044550 secondary metabolite biosynthetic process The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. GOC:jl A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. jl 2013-03-27T15:09:58Z microtubule-based flagellum organization biological_process GO:0044782 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:cilia GOC:jl The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. GO:0006947 cell fusion cell-cell fusion biological_process GO:0045026 plasma membrane fusion The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. GOC:elh GOC:mtg_muscle The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle. biological_process GO:0045132 meiotic chromosome segregation The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle. GOC:ai GOC:mah The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion. biological_process GO:0045137 development of primary sexual characteristics The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion. GOC:ai The cellular developmental process by which a cell establishes the intrinsic character of a cell or tissue region irreversibly committing it to a particular fate. https://github.com/geneontology/go-ontology/issues/24390 biological_process GO:0045165 Note that this term was 'cell fate determination' but the term name was changed to better match its existing definition and the child term 'cell fate determination; GO:0001709' was also created. cell fate commitment The cellular developmental process by which a cell establishes the intrinsic character of a cell or tissue region irreversibly committing it to a particular fate. ISBN:0716731185 Signaling at long or short range between cells that results in the commitment of a cell to a certain fate. cell fate commitment, cell-cell signaling cell fate commitment, cell-cell signalling cell-cell signaling during in cell fate commitment cell-cell signaling resulting in cell fate commitment cell-cell signalling during cell fate commitment cell-cell signalling resulting in cell fate commitment cell-cell signalling involved in cell fate specification biological_process GO:0045168 cell-cell signaling involved in cell fate commitment Signaling at long or short range between cells that results in the commitment of a cell to a certain fate. GOC:dph GOC:go_curators GOC:tb cell-cell signalling involved in cell fate specification GOC:dph GOC:tb The directed movement of a protein to a specific location. establishment of protein localisation protein positioning protein recruitment biological_process GO:0045184 establishment of protein localization The directed movement of a protein to a specific location. GOC:bf establishment of protein localisation GOC:mah Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system. GO:0043339 GO:0043342 establishment and/or maintenance of neuroblast cell polarity biological_process GO:0045196 establishment or maintenance of neuroblast polarity Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system. GOC:bf GOC:mah GOC:mtg_sensu PMID:19375318 PMID:20066083 The specification and formation of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system. GO:0043340 GO:0043343 establishment of neuroblast cell polarity biological_process GO:0045200 establishment of neuroblast polarity The specification and formation of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system. GOC:bf GOC:mtg_sensu The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. NIF_Subcellular:sao914572699 Wikipedia:Chemical_synapse synaptic junction mixed synapse cellular_component electrotonic synapse GO:0045202 synapse The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. GOC:aruk ISBN:0198506732 PMID:24619342 PMID:29383328 PMID:31998110 mixed synapse NIF_Subcellular:sao1506103497 electrotonic synapse NIF_Subcellular:sao1311109124 The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. GO:0006938 sarcomere alignment sarcomere organisation biological_process GO:0045214 sarcomere organization The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. GOC:bf A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells. cell-cell junction assembly and maintenance cell-cell junction organisation intercellular junction assembly and maintenance biological_process cell-cell junction biogenesis GO:0045216 cell-cell junction organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells. GOC:ai GOC:dph GOC:jl GOC:mah cell-cell junction organisation GOC:mah The chemical reactions and pathways resulting in the formation of CD4, a CD marker that occurs on T-helper cells and is involved in MHC class II restricted interactions. CD4 anabolism CD4 biosynthesis CD4 formation CD4 synthesis biological_process GO:0045222 CD4 biosynthetic process The chemical reactions and pathways resulting in the formation of CD4, a CD marker that occurs on T-helper cells and is involved in MHC class II restricted interactions. GOC:go_curators ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4. regulation of CD4 anabolism regulation of CD4 biosynthesis regulation of CD4 biosynthetic process regulation of CD4 formation regulation of CD4 synthesis biological_process GO:0045223 regulation of CD4 production Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4. positive regulation of CD4 anabolism positive regulation of CD4 biosynthesis positive regulation of CD4 biosynthetic process positive regulation of CD4 formation positive regulation of CD4 synthesis up regulation of CD4 biosynthetic process up-regulation of CD4 biosynthetic process upregulation of CD4 biosynthetic process activation of CD4 biosynthetic process stimulation of CD4 biosynthetic process biological_process GO:0045224 positive regulation of CD4 production Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4. down regulation of CD4 biosynthetic process down-regulation of CD4 biosynthetic process downregulation of CD4 biosynthetic process negative regulation of CD4 anabolism negative regulation of CD4 biosynthesis negative regulation of CD4 biosynthetic process negative regulation of CD4 formation negative regulation of CD4 synthesis inhibition of CD4 biosynthetic process biological_process GO:0045225 negative regulation of CD4 production Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4. GOC:go_curators A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell. external encapsulating structure organisation external encapsulating structure organization and biogenesis biological_process GO:0045229 external encapsulating structure organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell. GOC:ai GOC:dph GOC:jl GOC:mah external encapsulating structure organization and biogenesis GOC:dph GOC:jl GOC:mah The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat. adipocyte cell differentiation adipocyte differentiation adipose cell differentiation biological_process adipogenesis GO:0045444 fat cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat. CL:0000136 GOC:go_curators The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers. myoblast cell differentiation biological_process GO:0045445 myoblast differentiation The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers. CL:0000056 GOC:go_curators GOC:mtg_muscle The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium. biological_process GO:0045446 endothelial cell differentiation The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium. CL:0000115 GOC:go_curators Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. biological_process GO:0045595 regulation of cell differentiation Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. down regulation of cell differentiation down-regulation of cell differentiation downregulation of cell differentiation inhibition of cell differentiation biological_process GO:0045596 negative regulation of cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell differentiation. up regulation of cell differentiation up-regulation of cell differentiation upregulation of cell differentiation activation of cell differentiation stimulation of cell differentiation biological_process GO:0045597 positive regulation of cell differentiation Any process that activates or increases the frequency, rate or extent of cell differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of adipocyte differentiation. regulation of adipocyte cell differentiation regulation of adipocyte differentiation biological_process GO:0045598 regulation of fat cell differentiation Any process that modulates the frequency, rate or extent of adipocyte differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation. down regulation of fat cell differentiation down-regulation of fat cell differentiation downregulation of fat cell differentiation negative regulation of adipocyte cell differentiation negative regulation of adipocyte differentiation inhibition of fat cell differentiation biological_process GO:0045599 negative regulation of fat cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of adipocyte differentiation. positive regulation of adipocyte cell differentiation positive regulation of adipocyte differentiation up regulation of fat cell differentiation up-regulation of fat cell differentiation upregulation of fat cell differentiation activation of fat cell differentiation stimulation of fat cell differentiation biological_process GO:0045600 positive regulation of fat cell differentiation Any process that activates or increases the frequency, rate or extent of adipocyte differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of endothelial cell differentiation. biological_process GO:0045601 regulation of endothelial cell differentiation Any process that modulates the frequency, rate or extent of endothelial cell differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of endothelial cell differentiation. down regulation of endothelial cell differentiation down-regulation of endothelial cell differentiation downregulation of endothelial cell differentiation inhibition of endothelial cell differentiation biological_process GO:0045602 negative regulation of endothelial cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of endothelial cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation. up regulation of endothelial cell differentiation up-regulation of endothelial cell differentiation upregulation of endothelial cell differentiation activation of endothelial cell differentiation stimulation of endothelial cell differentiation biological_process GO:0045603 positive regulation of endothelial cell differentiation Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of epidermal cell differentiation. biological_process regulation of hypodermal cell differentiation GO:0045604 regulation of epidermal cell differentiation Any process that modulates the frequency, rate or extent of epidermal cell differentiation. GOC:go_curators regulation of hypodermal cell differentiation GOC:kmv GOC:rk Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal cell differentiation. down regulation of epidermal cell differentiation down-regulation of epidermal cell differentiation downregulation of epidermal cell differentiation inhibition of epidermal cell differentiation biological_process negative regulation of hypodermal cell differentiation GO:0045605 negative regulation of epidermal cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal cell differentiation. GOC:go_curators negative regulation of hypodermal cell differentiation GOC:kmv GOC:rk Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation. up regulation of epidermal cell differentiation up-regulation of epidermal cell differentiation upregulation of epidermal cell differentiation activation of epidermal cell differentiation stimulation of epidermal cell differentiation biological_process positive regulation of hypodermal cell differentiation GO:0045606 positive regulation of epidermal cell differentiation Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation. GOC:go_curators positive regulation of hypodermal cell differentiation GOC:kmv GOC:rk Any process that modulates the frequency, rate or extent of myeloid cell differentiation. biological_process GO:0045637 regulation of myeloid cell differentiation Any process that modulates the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation. down regulation of myeloid cell differentiation down-regulation of myeloid cell differentiation downregulation of myeloid cell differentiation inhibition of myeloid cell differentiation biological_process GO:0045638 negative regulation of myeloid cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation. up regulation of myeloid cell differentiation up-regulation of myeloid cell differentiation upregulation of myeloid cell differentiation activation of myeloid cell differentiation stimulation of myeloid cell differentiation biological_process GO:0045639 positive regulation of myeloid cell differentiation Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of erythrocyte differentiation. regulation of RBC differentiation regulation of red blood cell differentiation biological_process GO:0045646 regulation of erythrocyte differentiation Any process that modulates the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators regulation of RBC differentiation CL:0000232 regulation of red blood cell differentiation CL:0000232 Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation. down regulation of erythrocyte differentiation down-regulation of erythrocyte differentiation downregulation of erythrocyte differentiation negative regulation of RBC differentiation negative regulation of red blood cell differentiation inhibition of erythrocyte differentiation biological_process GO:0045647 negative regulation of erythrocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators negative regulation of RBC differentiation CL:0000232 negative regulation of red blood cell differentiation CL:0000232 Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation. positive regulation of RBC differentiation positive regulation of red blood cell differentiation up regulation of erythrocyte differentiation up-regulation of erythrocyte differentiation upregulation of erythrocyte differentiation activation of erythrocyte differentiation stimulation of erythrocyte differentiation biological_process GO:0045648 positive regulation of erythrocyte differentiation Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators positive regulation of RBC differentiation CL:0000232 positive regulation of red blood cell differentiation CL:0000232 Any process that modulates the frequency, rate or extent of megakaryocyte differentiation. biological_process GO:0045652 regulation of megakaryocyte differentiation Any process that modulates the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation. down regulation of megakaryocyte differentiation down-regulation of megakaryocyte differentiation downregulation of megakaryocyte differentiation inhibition of megakaryocyte differentiation biological_process GO:0045653 negative regulation of megakaryocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation. up regulation of megakaryocyte differentiation up-regulation of megakaryocyte differentiation upregulation of megakaryocyte differentiation activation of megakaryocyte differentiation stimulation of megakaryocyte differentiation biological_process GO:0045654 positive regulation of megakaryocyte differentiation Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. biological_process GO:0045661 regulation of myoblast differentiation Any process that modulates the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. CL:0000056 GOC:go_curators GOC:mtg_muscle Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. down regulation of myoblast differentiation down-regulation of myoblast differentiation downregulation of myoblast differentiation inhibition of myoblast differentiation biological_process GO:0045662 negative regulation of myoblast differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. CL:0000056 GOC:go_curators GOC:mtg_muscle Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. up regulation of myoblast differentiation up-regulation of myoblast differentiation upregulation of myoblast differentiation activation of myoblast differentiation stimulation of myoblast differentiation biological_process GO:0045663 positive regulation of myoblast differentiation Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. CL:0000056 GOC:go_curators GOC:mtg_muscle Any process that modulates the frequency, rate or extent of neuron differentiation. biological_process GO:0045664 regulation of neuron differentiation Any process that modulates the frequency, rate or extent of neuron differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation. down regulation of neuron differentiation down-regulation of neuron differentiation downregulation of neuron differentiation inhibition of neuron differentiation biological_process GO:0045665 negative regulation of neuron differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of neuron differentiation. up regulation of neuron differentiation up-regulation of neuron differentiation upregulation of neuron differentiation activation of neuron differentiation stimulation of neuron differentiation biological_process GO:0045666 positive regulation of neuron differentiation Any process that activates or increases the frequency, rate or extent of neuron differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of epidermis development. regulation of epidermal development biological_process regulation of hypodermis development GO:0045682 regulation of epidermis development Any process that modulates the frequency, rate or extent of epidermis development. GOC:go_curators regulation of hypodermis development GOC:kmv GOC:rk Any process that stops, prevents, or reduces the frequency, rate or extent of epidermis development. down regulation of epidermis development down-regulation of epidermis development downregulation of epidermis development negative regulation of epidermal development inhibition of epidermis development biological_process negative regulation of hypodermis development GO:0045683 negative regulation of epidermis development Any process that stops, prevents, or reduces the frequency, rate or extent of epidermis development. GOC:go_curators negative regulation of hypodermis development GOC:kmv GOC:rk Any process that activates or increases the frequency, rate or extent of epidermis development. positive regulation of epidermal development up regulation of epidermis development up-regulation of epidermis development upregulation of epidermis development activation of epidermis development stimulation of epidermis development biological_process positive regulation of hypodermis development GO:0045684 positive regulation of epidermis development Any process that activates or increases the frequency, rate or extent of epidermis development. GOC:go_curators positive regulation of hypodermis development GOC:kmv GOC:rk Any process that modulates the frequency, rate or extent of glia cell differentiation. regulation of glia cell differentiation regulation of neuroglia differentiation biological_process GO:0045685 regulation of glial cell differentiation Any process that modulates the frequency, rate or extent of glia cell differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation. down regulation of glial cell differentiation down-regulation of glial cell differentiation downregulation of glial cell differentiation negative regulation of glia cell differentiation negative regulation of neuroglia differentiation inhibition of glial cell differentiation biological_process GO:0045686 negative regulation of glial cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of glia cell differentiation. positive regulation of glia cell differentiation positive regulation of neuroglia differentiation up regulation of glial cell differentiation up-regulation of glial cell differentiation upregulation of glial cell differentiation activation of glial cell differentiation stimulation of glial cell differentiation biological_process GO:0045687 positive regulation of glial cell differentiation Any process that activates or increases the frequency, rate or extent of glia cell differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. down regulation of glycogen biosynthetic process down-regulation of glycogen biosynthetic process downregulation of glycogen biosynthetic process negative regulation of glycogen anabolism negative regulation of glycogen biosynthesis negative regulation of glycogen formation negative regulation of glycogen synthesis inhibition of glycogen biosynthetic process biological_process GO:0045719 negative regulation of glycogen biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of gluconeogenesis. down regulation of gluconeogenesis down-regulation of gluconeogenesis downregulation of gluconeogenesis inhibition of gluconeogenesis biological_process GO:0045721 negative regulation of gluconeogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of gluconeogenesis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of gluconeogenesis. up regulation of gluconeogenesis up-regulation of gluconeogenesis upregulation of gluconeogenesis activation of gluconeogenesis stimulation of gluconeogenesis biological_process GO:0045722 positive regulation of gluconeogenesis Any process that activates or increases the frequency, rate or extent of gluconeogenesis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the formation of a cilium. positive regulation of flagellum assembly up regulation of cilium assembly up-regulation of cilium assembly upregulation of cilium assembly activation of cilium assembly stimulation of cilium assembly biological_process positive regulation of flagellum biogenesis GO:0045724 positive regulation of cilium assembly Any process that activates or increases the frequency, rate or extent of the formation of a cilium. GOC:cilia GOC:go_curators positive regulation of flagellum biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. positive regulation of glycogen anabolism positive regulation of glycogen biosynthesis positive regulation of glycogen formation positive regulation of glycogen synthesis up regulation of glycogen biosynthetic process up-regulation of glycogen biosynthetic process upregulation of glycogen biosynthetic process activation of glycogen biosynthetic process stimulation of glycogen biosynthetic process biological_process GO:0045725 positive regulation of glycogen biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0045946 positive regulation of protein anabolism positive regulation of protein biosynthesis positive regulation of protein biosynthetic process positive regulation of protein formation positive regulation of protein synthesis up regulation of protein biosynthetic process up-regulation of protein biosynthetic process upregulation of protein biosynthetic process activation of protein biosynthetic process stimulation of protein biosynthetic process biological_process GO:0045727 positive regulation of translation Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:dph GOC:go_curators GOC:tb positive regulation of protein biosynthetic process GOC:tb Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. https://github.com/geneontology/go-ontology/issues/23112 GO:1903364 GO:2000600 positive regulation of cellular protein breakdown positive regulation of cellular protein catabolic process positive regulation of cellular protein catabolism positive regulation of cellular protein degradation positive regulation of protein breakdown positive regulation of protein catabolism positive regulation of protein degradation up regulation of cellular protein breakdown up regulation of cellular protein catabolic process up regulation of cellular protein catabolism up regulation of cellular protein degradation up regulation of protein catabolic process up-regulation of cellular protein breakdown up-regulation of cellular protein catabolic process up-regulation of cellular protein catabolism up-regulation of cellular protein degradation up-regulation of protein catabolic process upregulation of cellular protein breakdown upregulation of cellular protein catabolic process upregulation of cellular protein catabolism upregulation of cellular protein degradation upregulation of protein catabolic process activation of cellular protein breakdown activation of cellular protein catabolic process activation of cellular protein catabolism activation of cellular protein degradation activation of protein catabolic process positive regulation of cyclin breakdown positive regulation of cyclin catabolic process positive regulation of cyclin catabolism positive regulation of cyclin degradation positive regulation of degradation of cyclin stimulation of protein catabolic process biological_process GO:0045732 positive regulation of protein catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. GOC:go_curators positive regulation of cellular protein breakdown GOC:TermGenie positive regulation of cellular protein catabolism GOC:TermGenie positive regulation of cellular protein degradation GOC:TermGenie up regulation of cellular protein breakdown GOC:TermGenie up regulation of cellular protein catabolic process GOC:TermGenie up regulation of cellular protein catabolism GOC:TermGenie up regulation of cellular protein degradation GOC:TermGenie up-regulation of cellular protein breakdown GOC:TermGenie up-regulation of cellular protein catabolic process GOC:TermGenie up-regulation of cellular protein catabolism GOC:TermGenie up-regulation of cellular protein degradation GOC:TermGenie upregulation of cellular protein breakdown GOC:TermGenie upregulation of cellular protein catabolic process GOC:TermGenie upregulation of cellular protein catabolism GOC:TermGenie upregulation of cellular protein degradation GOC:TermGenie activation of cellular protein breakdown GOC:TermGenie activation of cellular protein catabolic process GOC:TermGenie activation of cellular protein catabolism GOC:TermGenie activation of cellular protein degradation GOC:TermGenie positive regulation of cyclin breakdown GOC:obol positive regulation of cyclin catabolism GOC:obol positive regulation of cyclin degradation GOC:obol positive regulation of degradation of cyclin GOC:obol The chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid. GO:0019663 acetate breakdown acetate catabolism acetate degradation biological_process homoacetate catabolic process GO:0045733 acetate catabolic process The chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid. regulation of acetate breakdown regulation of acetate catabolism regulation of acetate degradation biological_process GO:0045734 regulation of acetate catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of DNA repair. down regulation of DNA repair down-regulation of DNA repair downregulation of DNA repair inhibition of DNA repair biological_process GO:0045738 negative regulation of DNA repair Any process that stops, prevents, or reduces the frequency, rate or extent of DNA repair. GOC:go_curators Any process that activates or increases the frequency, rate or extent of DNA repair. up regulation of DNA repair up-regulation of DNA repair upregulation of DNA repair activation of DNA repair stimulation of DNA repair biological_process GO:0045739 positive regulation of DNA repair Any process that activates or increases the frequency, rate or extent of DNA repair. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate. down regulation of acetate catabolic process down-regulation of acetate catabolic process downregulation of acetate catabolic process negative regulation of acetate breakdown negative regulation of acetate catabolism negative regulation of acetate degradation inhibition of acetate catabolic process biological_process GO:0045753 negative regulation of acetate catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate. positive regulation of acetate breakdown positive regulation of acetate catabolism positive regulation of acetate degradation up regulation of acetate catabolic process up-regulation of acetate catabolic process upregulation of acetate catabolic process activation of acetate catabolic process stimulation of acetate catabolic process biological_process GO:0045754 positive regulation of acetate catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. down regulation of action potential down-regulation of action potential downregulation of action potential inhibition of action potential biological_process GO:0045759 negative regulation of action potential Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:go_curators Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. up regulation of action potential up-regulation of action potential upregulation of action potential activation of action potential stimulation of action potential biological_process GO:0045760 positive regulation of action potential Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid. down regulation of amino acid metabolic process down-regulation of amino acid metabolic process downregulation of amino acid metabolic process negative regulation of amino acid metabolism inhibition of amino acid metabolic process biological_process GO:0045763 negative regulation of cellular amino acid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. positive regulation of amino acid metabolism positive regulation of cellular amino acid metabolic process up regulation of amino acid metabolic process up-regulation of amino acid metabolic process upregulation of amino acid metabolic process activation of amino acid metabolic process stimulation of amino acid metabolic process biological_process GO:0045764 positive regulation of amino acid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GOC:go_curators Any process that modulates the frequency, rate or extent of angiogenesis. biological_process GO:0045765 regulation of angiogenesis Any process that modulates the frequency, rate or extent of angiogenesis. GOC:go_curators Any process that activates or increases angiogenesis. up regulation of angiogenesis up-regulation of angiogenesis upregulation of angiogenesis activation of angiogenesis stimulation of angiogenesis biological_process GO:0045766 positive regulation of angiogenesis Any process that activates or increases angiogenesis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of asymmetric cell division. down regulation of asymmetric cell division down-regulation of asymmetric cell division downregulation of asymmetric cell division inhibition of asymmetric cell division biological_process GO:0045769 negative regulation of asymmetric cell division Any process that stops, prevents, or reduces the frequency, rate or extent of asymmetric cell division. GOC:go_curators Any process that activates or increases the frequency, rate or extent of asymmetric cell division. up regulation of asymmetric cell division up-regulation of asymmetric cell division upregulation of asymmetric cell division activation of asymmetric cell division stimulation of asymmetric cell division biological_process GO:0045770 positive regulation of asymmetric cell division Any process that activates or increases the frequency, rate or extent of asymmetric cell division. GOC:go_curators Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. positive regulation of bone biosynthesis positive regulation of bone formation up regulation of ossification up-regulation of ossification upregulation of ossification activation of ossification stimulation of ossification biological_process GO:0045778 positive regulation of ossification Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. down regulation of progression through cell cycle down-regulation of progression through cell cycle downregulation of progression through cell cycle negative regulation of cell cycle progression negative regulation of progression through cell cycle inhibition of progression through cell cycle biological_process GO:0045786 negative regulation of cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the rate or extent of progression through the cell cycle. positive regulation of cell cycle progression positive regulation of progression through cell cycle up regulation of progression through cell cycle up-regulation of progression through cell cycle upregulation of progression through cell cycle activation of progression through cell cycle stimulation of progression through cell cycle biological_process GO:0045787 positive regulation of cell cycle Any process that activates or increases the rate or extent of progression through the cell cycle. GOC:go_curators positive regulation of progression through cell cycle GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. down regulation of glycogen catabolic process down-regulation of glycogen catabolic process downregulation of glycogen catabolic process negative regulation of glycogen breakdown negative regulation of glycogen catabolism negative regulation of glycogen degradation negative regulation of glycogenolysis inhibition of glycogen catabolic process biological_process GO:0045818 negative regulation of glycogen catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. GOC:go_curators negative regulation of glycogenolysis GOC:sl Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. positive regulation of glycogen breakdown positive regulation of glycogen catabolism positive regulation of glycogen degradation positive regulation of glycogenolysis up regulation of glycogen catabolic process up-regulation of glycogen catabolic process upregulation of glycogen catabolic process activation of glycogen catabolic process stimulation of glycogen catabolic process biological_process GO:0045819 positive regulation of glycogen catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. GOC:go_curators positive regulation of glycogenolysis GOC:sl Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction. down regulation of heart contraction down-regulation of heart contraction downregulation of heart contraction inhibition of heart contraction biological_process negative regulation of cardiac contraction GO:0045822 negative regulation of heart contraction Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of heart contraction. positive regulation of cardiac contraction up regulation of heart contraction up-regulation of heart contraction upregulation of heart contraction activation of heart contraction stimulation of heart contraction biological_process GO:0045823 positive regulation of heart contraction Any process that activates or increases the frequency, rate or extent of heart contraction. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. down regulation of lipid metabolic process down-regulation of lipid metabolic process downregulation of lipid metabolic process negative regulation of lipid metabolism inhibition of lipid metabolic process biological_process GO:0045833 negative regulation of lipid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. positive regulation of lipid metabolism up regulation of lipid metabolic process up-regulation of lipid metabolic process upregulation of lipid metabolic process activation of lipid metabolic process stimulation of lipid metabolic process biological_process GO:0045834 positive regulation of lipid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis. down regulation of meiosis down-regulation of meiosis downregulation of meiosis negative regulation of meiosis inhibition of meiosis biological_process GO:0045835 negative regulation of meiotic nuclear division Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of meiosis. positive regulation of meiosis up regulation of meiosis up-regulation of meiosis upregulation of meiosis activation of meiosis stimulation of meiosis biological_process GO:0045836 positive regulation of meiotic nuclear division Any process that activates or increases the frequency, rate or extent of meiosis. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother. down regulation of mitosis down-regulation of mitosis downregulation of mitosis negative regulation of mitosis inhibition of mitosis biological_process GO:0045839 negative regulation of mitotic nuclear division Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the frequency, rate or extent of mitosis. positive regulation of mitosis up regulation of mitosis up-regulation of mitosis upregulation of mitosis activation of mitosis mitogenic activity stimulation of mitosis biological_process GO:0045840 positive regulation of mitotic nuclear division Any process that activates or increases the frequency, rate or extent of mitosis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development. down regulation of striated muscle development down-regulation of striated muscle development downregulation of striated muscle development inhibition of striated muscle development biological_process GO:0045843 negative regulation of striated muscle tissue development Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development. GOC:go_curators Any process that activates or increases the frequency, rate or extent of striated muscle development. up regulation of striated muscle development up-regulation of striated muscle development upregulation of striated muscle development activation of striated muscle development stimulation of striated muscle development biological_process GO:0045844 positive regulation of striated muscle tissue development Any process that activates or increases the frequency, rate or extent of striated muscle development. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation. down regulation of translational elongation down-regulation of translational elongation downregulation of translational elongation inhibition of translational elongation biological_process GO:0045900 negative regulation of translational elongation Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of translational elongation. up regulation of translational elongation up-regulation of translational elongation upregulation of translational elongation activation of translational elongation stimulation of translational elongation biological_process GO:0045901 positive regulation of translational elongation Any process that activates or increases the frequency, rate or extent of translational elongation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination. down regulation of translational termination down-regulation of translational termination downregulation of translational termination inhibition of translational termination biological_process GO:0045904 negative regulation of translational termination Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination. GOC:go_curators Any process that activates or increases the frequency, rate or extent of translational termination. up regulation of translational termination up-regulation of translational termination upregulation of translational termination activation of translational termination stimulation of translational termination biological_process GO:0045905 positive regulation of translational termination Any process that activates or increases the frequency, rate or extent of translational termination. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. down regulation of carbohydrate metabolic process down-regulation of carbohydrate metabolic process downregulation of carbohydrate metabolic process negative regulation of carbohydrate metabolism inhibition of carbohydrate metabolic process biological_process GO:0045912 negative regulation of carbohydrate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. positive regulation of carbohydrate metabolism up regulation of carbohydrate metabolic process up-regulation of carbohydrate metabolic process upregulation of carbohydrate metabolic process activation of carbohydrate metabolic process stimulation of carbohydrate metabolic process biological_process GO:0045913 positive regulation of carbohydrate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catecholamine. down regulation of catecholamine metabolic process down-regulation of catecholamine metabolic process downregulation of catecholamine metabolic process negative regulation of catecholamine metabolism inhibition of catecholamine metabolic process biological_process GO:0045914 negative regulation of catecholamine metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catecholamine. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catecholamine. positive regulation of catecholamine metabolism up regulation of catecholamine metabolic process up-regulation of catecholamine metabolic process upregulation of catecholamine metabolic process activation of catecholamine metabolic process stimulation of catecholamine metabolic process biological_process GO:0045915 positive regulation of catecholamine metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catecholamine. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. down regulation of exocytosis down-regulation of exocytosis downregulation of exocytosis inhibition of exocytosis biological_process GO:0045920 negative regulation of exocytosis Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of exocytosis. up regulation of exocytosis up-regulation of exocytosis upregulation of exocytosis activation of exocytosis stimulation of exocytosis biological_process GO:0045921 positive regulation of exocytosis Any process that activates or increases the frequency, rate or extent of exocytosis. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. down regulation of growth down-regulation of growth downregulation of growth inhibition of growth biological_process GO:0045926 negative regulation of growth Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. GOC:go_curators Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. up regulation of growth up-regulation of growth upregulation of growth activation of growth stimulation of growth biological_process GO:0045927 positive regulation of growth Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle. down regulation of progression through mitotic cell cycle down-regulation of progression through mitotic cell cycle downregulation of progression through mitotic cell cycle negative regulation of mitotic cell cycle progression negative regulation of progression through mitotic cell cycle inhibition of progression through mitotic cell cycle biological_process GO:0045930 negative regulation of mitotic cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb negative regulation of progression through mitotic cell cycle GOC:dph GOC:tb Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. positive regulation of mitotic cell cycle progression positive regulation of progression through mitotic cell cycle up regulation of progression through mitotic cell cycle up-regulation of progression through mitotic cell cycle upregulation of progression through mitotic cell cycle activation of progression through mitotic cell cycle stimulation of progression through mitotic cell cycle biological_process GO:0045931 positive regulation of mitotic cell cycle Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb positive regulation of progression through mitotic cell cycle GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction. down regulation of muscle contraction down-regulation of muscle contraction downregulation of muscle contraction inhibition of muscle contraction biological_process GO:0045932 negative regulation of muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of muscle contraction. up regulation of muscle contraction up-regulation of muscle contraction upregulation of muscle contraction activation of muscle contraction stimulation of muscle contraction biological_process GO:0045933 positive regulation of muscle contraction Any process that activates or increases the frequency, rate or extent of muscle contraction. GOC:go_curators Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045934 negative regulation of nucleobase-containing compound metabolic process Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045935 positive regulation of nucleobase-containing compound metabolic process Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. down regulation of phosphate metabolic process down-regulation of phosphate metabolic process downregulation of phosphate metabolic process negative regulation of phosphate metabolism inhibition of phosphate metabolic process biological_process GO:0045936 negative regulation of phosphate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. positive regulation of phosphate metabolism up regulation of phosphate metabolic process up-regulation of phosphate metabolic process upregulation of phosphate metabolic process activation of phosphate metabolic process stimulation of phosphate metabolic process biological_process GO:0045937 positive regulation of phosphate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids. down regulation of steroid metabolic process down-regulation of steroid metabolic process downregulation of steroid metabolic process negative regulation of steroid metabolism inhibition of steroid metabolic process biological_process GO:0045939 negative regulation of steroid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids. positive regulation of steroid metabolism up regulation of steroid metabolic process up-regulation of steroid metabolic process upregulation of steroid metabolic process activation of steroid metabolic process stimulation of steroid metabolic process biological_process GO:0045940 positive regulation of steroid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation. down regulation of translational initiation down-regulation of translational initiation downregulation of translational initiation inhibition of translational initiation biological_process GO:0045947 negative regulation of translational initiation Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of translational initiation. up regulation of translational initiation up-regulation of translational initiation upregulation of translational initiation activation of translational initiation stimulation of translational initiation biological_process GO:0045948 positive regulation of translational initiation Any process that activates or increases the frequency, rate or extent of translational initiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction. down regulation of smooth muscle contraction down-regulation of smooth muscle contraction downregulation of smooth muscle contraction inhibition of smooth muscle contraction biological_process smooth muscle relaxation GO:0045986 negative regulation of smooth muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of smooth muscle contraction. up regulation of smooth muscle contraction up-regulation of smooth muscle contraction upregulation of smooth muscle contraction activation of smooth muscle contraction stimulation of smooth muscle contraction biological_process GO:0045987 positive regulation of smooth muscle contraction Any process that activates or increases the frequency, rate or extent of smooth muscle contraction. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction. down regulation of striated muscle contraction down-regulation of striated muscle contraction downregulation of striated muscle contraction inhibition of striated muscle contraction biological_process GO:0045988 negative regulation of striated muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of striated muscle contraction. up regulation of striated muscle contraction up-regulation of striated muscle contraction upregulation of striated muscle contraction activation of striated muscle contraction stimulation of striated muscle contraction biological_process GO:0045989 positive regulation of striated muscle contraction Any process that activates or increases the frequency, rate or extent of striated muscle contraction. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. down regulation of embryonic development down-regulation of embryonic development downregulation of embryonic development inhibition of embryonic development biological_process GO:0045992 negative regulation of embryonic development Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. GOC:go_curators Any process that modulates the frequency, rate or extent of embryonic development. biological_process GO:0045995 regulation of embryonic development Any process that modulates the frequency, rate or extent of embryonic development. GOC:go_curators The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. nucleobase anabolism nucleobase biosynthesis nucleobase formation nucleobase synthesis biological_process GO:0046112 nucleobase biosynthetic process The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. GOC:ai The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. nucleobase breakdown nucleobase catabolism nucleobase degradation biological_process GO:0046113 nucleobase catabolic process The chemical reactions and pathways resulting in the breakdown of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid. GOC:ai The chemical reactions and pathways resulting in the formation of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring. phenol-containing compound anabolism phenol-containing compound biosynthesis phenol-containing compound formation phenol-containing compound synthesis biological_process GO:0046189 phenol-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring. GOC:ai The chemical reactions and pathways resulting in the formation of indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group. indolalkylamine anabolism indolalkylamine biosynthesis indolalkylamine formation indolalkylamine synthesis biological_process GO:0046219 indolalkylamine biosynthetic process The chemical reactions and pathways resulting in the formation of indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group. GOC:curators The chemical reactions and pathways resulting in the formation of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. monosaccharide anabolism monosaccharide biosynthesis monosaccharide formation monosaccharide synthesis biological_process GO:0046364 monosaccharide biosynthetic process The chemical reactions and pathways resulting in the formation of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. monosaccharide breakdown monosaccharide catabolism monosaccharide degradation biological_process GO:0046365 monosaccharide catabolic process The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. carboxylic acid anabolism carboxylic acid biosynthesis carboxylic acid formation carboxylic acid synthesis biological_process GO:0046394 carboxylic acid biosynthetic process The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. carboxylic acid breakdown carboxylic acid catabolism carboxylic acid degradation biological_process GO:0046395 carboxylic acid catabolic process The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. ISBN:0198506732 The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolism biological_process GO:0046483 heterocycle metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198506732 The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster. GO:0007467 biological_process GO:0046530 photoreceptor cell differentiation The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster. GOC:ai ISBN:0198506732 Any process that modulates the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster. GO:0045673 regulation of photoreceptor differentiation biological_process GO:0046532 regulation of photoreceptor cell differentiation Any process that modulates the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster. GO:0045674 down regulation of photoreceptor cell differentiation down regulation of photoreceptor differentiation down-regulation of photoreceptor cell differentiation down-regulation of photoreceptor differentiation downregulation of photoreceptor cell differentiation downregulation of photoreceptor differentiation negative regulation of photoreceptor differentiation inhibition of photoreceptor cell differentiation inhibition of photoreceptor differentiation biological_process GO:0046533 negative regulation of photoreceptor cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster. GOC:go_curators Any process that activates or increases the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster. GO:0045675 positive regulation of photoreceptor differentiation up regulation of photoreceptor cell differentiation up regulation of photoreceptor differentiation up-regulation of photoreceptor cell differentiation up-regulation of photoreceptor differentiation upregulation of photoreceptor cell differentiation upregulation of photoreceptor differentiation activation of photoreceptor cell differentiation activation of photoreceptor differentiation stimulation of photoreceptor cell differentiation stimulation of photoreceptor differentiation biological_process GO:0046534 positive regulation of photoreceptor cell differentiation Any process that activates or increases the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster. GOC:go_curators The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion. biological_process GO:0046545 development of primary female sexual characteristics The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion. GOC:ai Development of a rod cell, one of the sensory cells in the eye that reacts to the presence of light. Rod cells contain the photopigment rhodopsin or porphyropsin and are responsible for vision in dim light. biological_process GO:0046548 retinal rod cell development Development of a rod cell, one of the sensory cells in the eye that reacts to the presence of light. Rod cells contain the photopigment rhodopsin or porphyropsin and are responsible for vision in dim light. ISBN:0198506732 Development of a cone cell, one of the sensory cells in the eye that reacts to the presence of light. Cone cells contain the photopigment iodopsin or cyanopsin and are responsible for photopic (daylight) vision. biological_process GO:0046549 retinal cone cell development Development of a cone cell, one of the sensory cells in the eye that reacts to the presence of light. Cone cells contain the photopigment iodopsin or cyanopsin and are responsible for photopic (daylight) vision. ISBN:0198506732 Any process that modulates the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046620 regulation of organ growth Any process that modulates the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046621 negative regulation of organ growth Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046622 positive regulation of organ growth Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb The establishment of the sex of a female organism by physical differentiation. biological_process GO:0046660 female sex differentiation The establishment of the sex of a female organism by physical differentiation. GOC:bf Programmed cell death that occurs in the developing retina. programmed cell death, retina cells programmed cell death, retinal cells retina cell programmed cell death retina programmed cell death retinal programmed cell death biological_process GO:0046666 retinal cell programmed cell death Programmed cell death that occurs in the developing retina. GOC:bf Programmed cell death that occurs in the retina to remove excess cells between ommatidia, thus resulting in a hexagonal lattice, precise with respect to cell number and position surrounding each ommatidium. biological_process GO:0046667 compound eye retinal cell programmed cell death Programmed cell death that occurs in the retina to remove excess cells between ommatidia, thus resulting in a hexagonal lattice, precise with respect to cell number and position surrounding each ommatidium. PMID:12006672 Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina. regulation of retinal programmed cell death biological_process GO:0046668 regulation of retinal cell programmed cell death Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina. GOC:ai GOC:tb regulation of retinal programmed cell death GOC:tb Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the compound eye retina. regulation of retinal cell programmed cell death biological_process GO:0046669 regulation of compound eye retinal cell programmed cell death Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the compound eye retina. GOC:ai Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the retina. positive regulation of retinal programmed cell death up regulation of retinal programmed cell death up-regulation of retinal programmed cell death upregulation of retinal programmed cell death activation of retinal programmed cell death stimulation of retinal programmed cell death biological_process GO:0046670 positive regulation of retinal cell programmed cell death Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the retina. GOC:ai GOC:tb positive regulation of retinal programmed cell death GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the retina. down regulation of retinal programmed cell death down-regulation of retinal programmed cell death downregulation of retinal programmed cell death negative regulation of retinal programmed cell death inhibition of retinal programmed cell death biological_process GO:0046671 negative regulation of retinal cell programmed cell death Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the retina. GOC:ai GOC:tb negative regulation of retinal programmed cell death GOC:tb Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the compound eye retina. activation of retinal cell programmed cell death positive regulation of retinal cell programmed cell death stimulation of retinal cell programmed cell death up regulation of retinal cell programmed cell death up-regulation of retinal cell programmed cell death upregulation of retinal cell programmed cell death biological_process GO:0046672 positive regulation of compound eye retinal cell programmed cell death Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the compound eye retina. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the compound eye retina. down regulation of retinal cell programmed cell death down-regulation of retinal cell programmed cell death downregulation of retinal cell programmed cell death inhibition of retinal cell programmed cell death negative regulation of retina cell programmed cell death negative regulation of retinal cell programmed cell death biological_process GO:0046673 negative regulation of compound eye retinal cell programmed cell death Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the compound eye retina. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin. down regulation of insulin secretion down-regulation of insulin secretion downregulation of insulin secretion inhibition of insulin secretion biological_process GO:0046676 negative regulation of insulin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin. GOC:ai Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbamate stimulus. Carbamates are a group of insecticides and parasiticides that act by inhibiting cholinesterase. biological_process carbamate resistance carbamate susceptibility/resistance GO:0046681 response to carbamate Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbamate stimulus. Carbamates are a group of insecticides and parasiticides that act by inhibiting cholinesterase. ISBN:0721662544 The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle breakdown heterocycle catabolism heterocycle degradation biological_process GO:0046700 heterocycle catabolic process The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). GOC:ai The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state. https://github.com/geneontology/go-ontology/issues/24218 muscle fiber maintenance biological_process muscle homeostasis GO:0046716 muscle cell cellular homeostasis The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state. GOC:mah PMID:3091429 PMID:7781901 muscle fiber maintenance GOC:dph GOC:tb muscle homeostasis GOC:dph The controlled release of acid by a cell or a tissue. biological_process GO:0046717 acid secretion The controlled release of acid by a cell or a tissue. GOC:ai The addition of tubulin heterodimers to one or both ends of a microtubule. microtubule assembly biological_process microtubule formation GO:0046785 microtubule polymerization The addition of tubulin heterodimers to one or both ends of a microtubule. GOC:ai GOC:go_curators Enables the transfer of metal ions from one side of a membrane to the other. heavy metal ion porter activity heavy metal ion transporter activity heavy metal ion:hydrogen symporter activity heavy metal-exporting ATPase activity high affinity metal ion uptake transporter activity low affinity metal ion uptake transporter activity molecular_function GO:0046873 metal ion transmembrane transporter activity Enables the transfer of metal ions from one side of a membrane to the other. GOC:ai The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. biological_process GO:0046879 hormone secretion The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell. biological_process GO:0046883 regulation of hormone secretion Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell. up regulation of hormone secretion up-regulation of hormone secretion upregulation of hormone secretion activation of hormone secretion stimulation of hormone secretion biological_process GO:0046887 positive regulation of hormone secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell. down regulation of hormone secretion down-regulation of hormone secretion downregulation of hormone secretion inhibition of hormone secretion biological_process GO:0046888 negative regulation of hormone secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. positive regulation of lipid anabolism positive regulation of lipid biosynthesis positive regulation of lipid formation positive regulation of lipid synthesis positive regulation of lipogenesis up regulation of lipid biosynthetic process up-regulation of lipid biosynthetic process upregulation of lipid biosynthetic process activation of lipid biosynthetic process stimulation of lipid biosynthetic process biological_process GO:0046889 positive regulation of lipid biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai positive regulation of lipogenesis GOC:sl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. regulation of lipid anabolism regulation of lipid biosynthesis regulation of lipid formation regulation of lipid synthesis regulation of lipogenesis biological_process GO:0046890 regulation of lipid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai regulation of lipogenesis GOC:sl The controlled release of a substance by a cell or a tissue. biological_process GO:0046903 secretion The controlled release of a substance by a cell or a tissue. GOC:ai The directed movement of substances within a cell. jl 2013-12-18T14:04:50Z GO:1902582 biological_process single organism intracellular transport single-organism intracellular transport GO:0046907 intracellular transport The directed movement of substances within a cell. GOC:ai single organism intracellular transport GOC:TermGenie Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell. biological_process GO:0046928 regulation of neurotransmitter secretion Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter. down regulation of neurotransmitter secretion down-regulation of neurotransmitter secretion downregulation of neurotransmitter secretion conotoxin activity inhibition of neurotransmitter secretion biological_process GO:0046929 negative regulation of neurotransmitter secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter. GOC:ai The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). biological_process GO:0046942 carboxylic acid transport The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). GOC:ai Enables the transfer of carboxylic acids from one side of a membrane to the other. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). Reactome:R-HSA-390347 molecular_function GO:0046943 carboxylic acid transmembrane transporter activity Enables the transfer of carboxylic acids from one side of a membrane to the other. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). GOC:ai Reactome:R-HSA-390347 Exchange of isocitrate and 2-oxoglutarate across the peroxisomal membrane The directed movement of a vesicle along a microtubule, mediated by motor proteins. This process begins with the attachment of a vesicle to a microtubule, and ends when the vesicle reaches its final destination. microtubule-based vesicle localization biological_process GO:0047496 vesicle transport along microtubule The directed movement of a vesicle along a microtubule, mediated by motor proteins. This process begins with the attachment of a vesicle to a microtubule, and ends when the vesicle reaches its final destination. GOC:ecd GOC:rl microtubule-based vesicle localization GOC:rl The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized. biological_process GO:0048048 embryonic eye morphogenesis The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized. GOC:jid The developmental process that results in the deposition of coloring matter in an organism, tissue or cell. biological_process pigmentation during development GO:0048066 developmental pigmentation The developmental process that results in the deposition of coloring matter in an organism, tissue or cell. ISBN:0582227089 Any process that modulates the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism. regulation of pigmentation during development biological_process GO:0048070 regulation of developmental pigmentation Any process that modulates the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism. GOC:dph GOC:jid GOC:tb regulation of pigmentation during development GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism. down regulation of developmental pigmentation down-regulation of developmental pigmentation downregulation of developmental pigmentation inhibition of pigmentation biological_process GO:0048086 negative regulation of developmental pigmentation Any process that decreases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism. GOC:dph GOC:jid GOC:tb down regulation of developmental pigmentation GOC:dph GOC:tb down-regulation of developmental pigmentation GOC:dph GOC:tb downregulation of developmental pigmentation GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism. up regulation of developmental pigmentation up-regulation of developmental pigmentation upregulation of developmental pigmentation activation of developmental pigmentation stimulation of developmental pigmentation biological_process GO:0048087 positive regulation of developmental pigmentation Any process that increases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism. GOC:dph GOC:jid GOC:tb up regulation of developmental pigmentation GOC:dph up-regulation of developmental pigmentation GOC:dph GOC:tb upregulation of developmental pigmentation GOC:dph GOC:tb activation of developmental pigmentation GOC:dph GOC:tb stimulation of developmental pigmentation GOC:dph GOC:tb The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. somatic stem cell renewal biological_process GO:0048103 somatic stem cell division The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. GOC:jid ISBN:0582227089 The self-renewing division of a germline stem cell in the female gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the female gametes. GO:0048141 female germ-line stem cell renewal biological_process GO:0048132 female germ-line stem cell asymmetric division The self-renewing division of a germline stem cell in the female gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the female gametes. GOC:jid GOC:mtg_sensu The multiplication or reproduction of fibroblast cells, resulting in the expansion of the fibroblast population. biological_process GO:0048144 fibroblast proliferation The multiplication or reproduction of fibroblast cells, resulting in the expansion of the fibroblast population. GOC:jid Any process that modulates the frequency, rate or extent of multiplication or reproduction of fibroblast cells. biological_process GO:0048145 regulation of fibroblast proliferation Any process that modulates the frequency, rate or extent of multiplication or reproduction of fibroblast cells. GOC:jid Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells. up regulation of fibroblast proliferation up-regulation of fibroblast proliferation upregulation of fibroblast proliferation activation of fibroblast proliferation stimulation of fibroblast proliferation biological_process GO:0048146 positive regulation of fibroblast proliferation Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells. down regulation of fibroblast proliferation down-regulation of fibroblast proliferation downregulation of fibroblast proliferation inhibition of fibroblast proliferation biological_process GO:0048147 negative regulation of fibroblast proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells. GOC:jid The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. biological_process Golgi-derived vesicle transport GO:0048193 Golgi vesicle transport The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. GOC:jid ISBN:0716731363 PMID:10219233 The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. Golgi vesicle targeting dictyosome vesicle targeting vesicle targeting, to, from or within dictyosome biological_process GO:0048199 vesicle targeting, to, from or within Golgi The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. GOC:jid GOC:mah ISBN:0716731363 PMID:10219233 Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus. regulation of Golgi vesicle targeting biological_process GO:0048209 regulation of vesicle targeting, to, from or within Golgi Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus. GOC:jid GOC:mah ISBN:0716731363 PMID:10219233 The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system. noradrenaline secretion biological_process GO:0048243 norepinephrine secretion The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system. GOC:ef GOC:jid Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching. elastic fibre assembly elastin fiber assembly elastin fibre assembly biological_process GO:0048251 elastic fiber assembly Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching. GOC:jid PMID:10841810 PMID:12615674 elastin fiber assembly GOC:BHF elastin fibre assembly GOC:BHF The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi. biological_process GO:0048280 vesicle fusion with Golgi apparatus The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi. GOC:jid The creation of a single organelle from two or more organelles. biological_process GO:0048284 organelle fusion The creation of a single organelle from two or more organelles. GOC:jid The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission The creation of two or more organelles by division of one organelle. GOC:jid The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei. biological_process nuclear membrane fusion during karyogamy GO:0048288 nuclear membrane fusion involved in karyogamy The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei. GOC:jid nuclear membrane fusion during karyogamy GOC:dph GOC:tb The partitioning of organelles between daughter cells at cell division. biological_process GO:0048308 organelle inheritance The partitioning of organelles between daughter cells at cell division. GOC:jid The partitioning of Golgi apparatus between daughter cells at cell division. Golgi apparatus inheritance Golgi division Golgi partitioning biological_process GO:0048313 Golgi inheritance The partitioning of Golgi apparatus between daughter cells at cell division. GOC:jid PMID:12851069 Golgi division GOC:ascb_2009 GOC:dph GOC:tb The process whose specific outcome is the progression of the axial mesoderm over time, from its formation to the mature structure. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. biological_process GO:0048318 axial mesoderm development The process whose specific outcome is the progression of the axial mesoderm over time, from its formation to the mature structure. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. GOC:dgh The process in which the anatomical structures of the axial mesoderm are generated and organized. biological_process GO:0048319 axial mesoderm morphogenesis The process in which the anatomical structures of the axial mesoderm are generated and organized. GOC:go_curators The process that gives rise to the axial mesoderm. This process pertains to the initial formation of the structure from unspecified parts. biological_process GO:0048320 axial mesoderm formation The process that gives rise to the axial mesoderm. This process pertains to the initial formation of the structure from unspecified parts. GOC:dgh The process in which the anatomical structures of the mesoderm are generated and organized. biological_process GO:0048332 mesoderm morphogenesis The process in which the anatomical structures of the mesoderm are generated and organized. GOC:go_curators The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell. mesoderm cell differentiation biological_process GO:0048333 mesodermal cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell. GOC:dgh The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube. biological_process GO:0048339 paraxial mesoderm development The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube. GOC:dgh The process in which the anatomical structures of the paraxial mesoderm are generated and organized. biological_process GO:0048340 paraxial mesoderm morphogenesis The process in which the anatomical structures of the paraxial mesoderm are generated and organized. GOC:go_curators The process that gives rise to the paraxial mesoderm. This process pertains to the initial formation of the structure from unspecified parts. biological_process GO:0048341 paraxial mesoderm formation The process that gives rise to the paraxial mesoderm. This process pertains to the initial formation of the structure from unspecified parts. GOC:dgh The process whose specific outcome is the progression of the lateral mesoderm over time, from its formation to the mature structure. lateral plate mesoderm development biological_process GO:0048368 lateral mesoderm development The process whose specific outcome is the progression of the lateral mesoderm over time, from its formation to the mature structure. GOC:go_curators The process in which the anatomical structures of the lateral mesoderm are generated and organized. lateral plate mesoderm morphogenesis biological_process GO:0048369 lateral mesoderm morphogenesis The process in which the anatomical structures of the lateral mesoderm are generated and organized. GOC:go_curators The process that gives rise to the lateral mesoderm. This process pertains to the initial formation of the structure from unspecified parts. lateral plate mesoderm biosynthesis lateral plate mesoderm formation biological_process GO:0048370 lateral mesoderm formation The process that gives rise to the lateral mesoderm. This process pertains to the initial formation of the structure from unspecified parts. GOC:jid The process whose specific outcome is the progression of the intermediate mesoderm over time, from its formation to the mature structure. The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. biological_process GO:0048389 intermediate mesoderm development The process whose specific outcome is the progression of the intermediate mesoderm over time, from its formation to the mature structure. The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. GOC:dgh The process in which the anatomical structures of the intermediate mesoderm are generated and organized. biological_process GO:0048390 intermediate mesoderm morphogenesis The process in which the anatomical structures of the intermediate mesoderm are generated and organized. GOC:go_curators The process that gives rise to the intermediate mesoderm. This process pertains to the initial formation of the structure from unspecified parts. biological_process GO:0048391 intermediate mesoderm formation The process that gives rise to the intermediate mesoderm. This process pertains to the initial formation of the structure from unspecified parts. GOC:dgh The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. https://github.com/geneontology/go-ontology/issues/24390 biological_process terminal differentiation GO:0048468 cell development The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. GOC:go_curators terminal differentiation GOC:dph GOC:tb The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state. https://github.com/geneontology/go-ontology/issues/24390 biological_process functional differentiation GO:0048469 cell maturation The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state. GOC:go_curators functional differentiation GOC:dph The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. GO:0009993 GO:0048157 Wikipedia:Oogenesis ovum development biological_process GO:0048477 oogenesis The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. GOC:kmv GOC:mtg_sensu GOC:pr ovum development The process whose specific outcome is the progression of the autonomic nervous system over time, from its formation to the mature structure. The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands. biological_process GO:0048483 autonomic nervous system development The process whose specific outcome is the progression of the autonomic nervous system over time, from its formation to the mature structure. The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands. FMA:9905 GOC:jid GOC:sr The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter. biological_process GO:0048485 sympathetic nervous system development The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter. FMA:9906 GOC:jid GOC:sr The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development. biological_process timing of cell differentiation GO:0048505 regulation of timing of cell differentiation The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development. GOC:bf GOC:dph GOC:jid GOC:tb Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. https://github.com/geneontology/go-ontology/issues/25943 Wikipedia:Organogenesis development of an organ organogenesis biological_process GO:0048513 animal organ development Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:dph GOC:jid The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood. biological_process GO:0048514 blood vessel morphogenesis The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood. GOC:jid Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. up regulation of behavior up-regulation of behavior upregulation of behavior activation of behavior stimulation of behavior biological_process GO:0048520 positive regulation of behavior Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. GOC:jid GOC:pr Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. down regulation of behavior down-regulation of behavior downregulation of behavior inhibition of behavior biological_process GO:0048521 negative regulation of behavior Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. GOC:jid GOC:pr Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process GO:0048522 positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process GO:0048523 negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation. haematopoietic or lymphoid organ development haemopoietic or lymphoid organ development hemopoietic or lymphoid organ development biological_process GO:0048534 hematopoietic or lymphoid organ development The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation. GOC:add GOC:rl ISBN:0781735149 The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions. biological_process GO:0048536 spleen development The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions. GOC:add ISBN:0781735149 The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure. biological_process GO:0048539 bone marrow development The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure. GOC:add ISBN:0781735149 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus. response to steroid hormone stimulus biological_process GO:0048545 response to steroid hormone Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus. GOC:go_curators response to steroid hormone stimulus GOC:dos The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed. GO:0048547 gut morphogenesis alimentary canal morphogenesis digestive tube morphogenesis gastrointestinal tract morphogenesis intestinal morphogenesis biological_process GO:0048546 digestive tract morphogenesis The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed. GOC:dph GOC:go_curators PMID:12618131 gut morphogenesis GOC:dph Morphogenesis, during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. biological_process GO:0048562 embryonic organ morphogenesis Morphogenesis, during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:jid The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed. gut development intestinal development intestine development biological_process GO:0048565 digestive tract development The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed. GOC:go_curators gut development GOC:dph Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. embryonic organogenesis biological_process GO:0048568 embryonic organ development Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:jid The process in which the anatomical structures of the notochord are generated and organized. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column. biological_process GO:0048570 notochord morphogenesis The process in which the anatomical structures of the notochord are generated and organized. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column. GOC:jid Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. biological_process GO:0048580 regulation of post-embryonic development Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. down regulation of post-embryonic development down-regulation of post-embryonic development downregulation of post-embryonic development inhibition of post-embryonic development biological_process GO:0048581 negative regulation of post-embryonic development Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. GOC:jid Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. up regulation of post-embryonic development up-regulation of post-embryonic development upregulation of post-embryonic development activation of post-embryonic development stimulation of post-embryonic development biological_process GO:0048582 positive regulation of post-embryonic development Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. GOC:jid Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. biological_process GO:0048583 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus activation of response to stimulus stimulation of response to stimulus biological_process GO:0048584 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to stimulus Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. down regulation of response to stimulus down-regulation of response to stimulus downregulation of response to stimulus inhibition of response to stimulus biological_process GO:0048585 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another. developmental growth of a unicellular organism biological_process GO:0048588 developmental cell growth The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another. GOC:go_curators GOC:isa_complete The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. biological_process GO:0048589 developmental growth The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. GOC:go_curators The process in which the anatomical structures of the eye are generated and organized. GO:0048748 biological_process GO:0048592 eye morphogenesis The process in which the anatomical structures of the eye are generated and organized. GOC:jid GOC:mtg_sensu The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. GO:0048594 GO:0048595 camera-style eye morphogenesis biological_process GO:0048593 camera-type eye morphogenesis The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field. GOC:jid GOC:mtg_sensu camera-style eye morphogenesis GOC:dph The process in which the anatomical structures of the eye are generated and organized during embryonic development. embryonic eye morphogenesis biological_process GO:0048596 embryonic camera-type eye morphogenesis The process in which the anatomical structures of the eye are generated and organized during embryonic development. GOC:jid GOC:mtg_sensu The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 embryonic morphogenesis The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. GOC:jid GOC:mtg_sensu embryonic anatomical structure morphogenesis GOC:dph GOC:tb The process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. biological_process GO:0048599 oocyte development The process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. GOC:go_curators The process in which the structures of an oocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of an oocyte. oocyte morphogenesis during differentiation biological_process GO:0048601 oocyte morphogenesis The process in which the structures of an oocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of an oocyte. GOC:go_curators The reproductive developmental process whose specific outcome is the progression of somatic structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures. https://github.com/geneontology/go-ontology/issues/23445 biological_process GO:0048608 reproductive structure development The reproductive developmental process whose specific outcome is the progression of somatic structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures. GOC:dph GOC:isa_complete GOC:jid The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. organismal reproductive process reproductive process in a multicellular organism biological_process GO:0048609 multicellular organismal reproductive process The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. GOC:dph GOC:jid GOC:tb The process whose specific outcome is the progression of the myoblast over time, from its formation to the mature structure. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. biological_process GO:0048627 myoblast development The process whose specific outcome is the progression of the myoblast over time, from its formation to the mature structure. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. CL:0000056 GOC:dph GOC:mtg_muscle A developmental process, independent of morphogenetic (shape) change, that is required for a myoblast to attain its fully functional state. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. biological_process GO:0048628 myoblast maturation A developmental process, independent of morphogenetic (shape) change, that is required for a myoblast to attain its fully functional state. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. CL:0000056 GOC:dph GOC:mtg_muscle The increase in size or mass of a skeletal muscle. This may be due to a change in the fiber number or size. biological_process GO:0048630 skeletal muscle tissue growth The increase in size or mass of a skeletal muscle. This may be due to a change in the fiber number or size. GOC:lm PMID:15726494 PMID:15907921 Any process that modulates the frequency, rate or extent of skeletal muscle growth. biological_process GO:0048631 regulation of skeletal muscle tissue growth Any process that modulates the frequency, rate or extent of skeletal muscle growth. GOC:lm PMID:15726494 PMID:15907921 Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle growth. down regulation of skeletal muscle growth down-regulation of skeletal muscle growth downregulation of skeletal muscle growth inhibition of skeletal muscle growth biological_process GO:0048632 negative regulation of skeletal muscle tissue growth Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle growth. GOC:lm PMID:15726494 PMID:15907921 Any process that activates, maintains or increases the rate of skeletal muscle growth. up regulation of skeletal muscle growth up-regulation of skeletal muscle growth upregulation of skeletal muscle growth activation of skeletal muscle growth stimulation of skeletal muscle growth biological_process GO:0048633 positive regulation of skeletal muscle tissue growth Any process that activates, maintains or increases the rate of skeletal muscle growth. GOC:lm PMID:15726494 PMID:15907921 Any process that modulates the frequency, rate or extent of muscle development. biological_process GO:0048634 regulation of muscle organ development Any process that modulates the frequency, rate or extent of muscle development. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of muscle development. down regulation of muscle development down-regulation of muscle development downregulation of muscle development inhibition of muscle development biological_process GO:0048635 negative regulation of muscle organ development Any process that stops, prevents, or reduces the frequency, rate or extent of muscle development. GOC:go_curators Any process that activates, maintains or increases the rate of muscle development. up regulation of muscle development up-regulation of muscle development upregulation of muscle development activation of muscle development stimulation of muscle development biological_process GO:0048636 positive regulation of muscle organ development Any process that activates, maintains or increases the rate of muscle development. GOC:go_curators Any process that modulates the frequency, rate or extent of developmental growth. biological_process GO:0048638 regulation of developmental growth Any process that modulates the frequency, rate or extent of developmental growth. GOC:go_curators Any process that activates, maintains or increases the rate of developmental growth. up regulation of developmental growth up-regulation of developmental growth upregulation of developmental growth activation of developmental growth stimulation of developmental growth biological_process GO:0048639 positive regulation of developmental growth Any process that activates, maintains or increases the rate of developmental growth. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth. down regulation of developmental growth down-regulation of developmental growth downregulation of developmental growth inhibition of developmental growth biological_process GO:0048640 negative regulation of developmental growth Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth. GOC:go_curators Any process that modulates the frequency, rate or extent of skeletal muscle tissue development. biological_process GO:0048641 regulation of skeletal muscle tissue development Any process that modulates the frequency, rate or extent of skeletal muscle tissue development. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development. down regulation of skeletal muscle development down-regulation of skeletal muscle development downregulation of skeletal muscle development inhibition of skeletal muscle development biological_process GO:0048642 negative regulation of skeletal muscle tissue development Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development. GOC:go_curators Any process that activates, maintains or increases the rate of skeletal muscle tissue development. up regulation of skeletal muscle development up-regulation of skeletal muscle development upregulation of skeletal muscle development activation of skeletal muscle development stimulation of skeletal muscle development biological_process GO:0048643 positive regulation of skeletal muscle tissue development Any process that activates, maintains or increases the rate of skeletal muscle tissue development. GOC:go_curators The process in which the anatomical structures of muscle are generated and organized. biological_process GO:0048644 muscle organ morphogenesis The process in which the anatomical structures of muscle are generated and organized. GOC:jid The process pertaining to the initial formation of an animal organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ. animal organ primordium initiation initiation of an animal organ primordium biological_process GO:0048645 animal organ formation The process pertaining to the initial formation of an animal organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ. GOC:dph GOC:jid The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. formation of an anatomical structure involved in morphogenesis biological_process GO:0048646 Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. anatomical structure formation involved in morphogenesis The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GOC:dph GOC:jid GOC:tb formation of an anatomical structure involved in morphogenesis GOC:dph GOC:tb The multiplication or reproduction of smooth muscle cells, resulting in the expansion of a cell population. SMC proliferation biological_process GO:0048659 smooth muscle cell proliferation The multiplication or reproduction of smooth muscle cells, resulting in the expansion of a cell population. CL:0000192 GOC:ebc PMID:1840698 Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation. regulation of SMC proliferation biological_process GO:0048660 regulation of smooth muscle cell proliferation Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation. CL:0000192 GOC:ebc Any process that activates or increases the rate or extent of smooth muscle cell proliferation. positive regulation of SMC proliferation up regulation of smooth muscle cell proliferation up-regulation of smooth muscle cell proliferation upregulation of smooth muscle cell proliferation activation of smooth muscle cell proliferation stimulation of smooth muscle cell proliferation biological_process GO:0048661 positive regulation of smooth muscle cell proliferation Any process that activates or increases the rate or extent of smooth muscle cell proliferation. CL:0000192 GOC:ebc Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation. down regulation of smooth muscle cell proliferation down-regulation of smooth muscle cell proliferation downregulation of smooth muscle cell proliferation negative regulation of SMC proliferation inhibition of smooth muscle cell proliferation biological_process GO:0048662 negative regulation of smooth muscle cell proliferation Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation. CL:0000192 GOC:ebc The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. biological_process GO:0048666 neuron development The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. GOC:dph The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron. neuron morphogenesis involved in differentiation biological_process GO:0048667 cell morphogenesis involved in neuron differentiation The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron. GOC:dph GOC:tb neuron morphogenesis involved in differentiation GOC:dph GOC:tb The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons. neuron generation biological_process GO:0048699 generation of neurons The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons. GOC:nln The process in which the anatomical structures of the skeleton are generated and organized. skeletal morphogenesis biological_process GO:0048705 skeletal system morphogenesis The process in which the anatomical structures of the skeleton are generated and organized. GOC:dph GOC:dsf GOC:jid GOC:tb skeletal morphogenesis GOC:dph GOC:tb The process in which the anatomical structures of a tissue are generated and organized. biological_process GO:0048729 tissue morphogenesis The process in which the anatomical structures of a tissue are generated and organized. GOC:dph GOC:jid The process in which the anatomical structures of the epidermis are generated and organized. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species. biological_process hypodermis morphogenesis GO:0048730 epidermis morphogenesis The process in which the anatomical structures of the epidermis are generated and organized. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species. GOC:jid UBERON:0001003 hypodermis morphogenesis GOC:kmv GOC:rk The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. biological_process GO:0048731 system development The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. GOC:dph GOC:jid The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion. biological_process GO:0048732 gland development The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion. GOC:jid The process whose specific outcome is the progression of an appendage over time, from its formation to the mature structure. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch. biological_process GO:0048736 appendage development The process whose specific outcome is the progression of an appendage over time, from its formation to the mature structure. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch. GOC:jid GOC:rc The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure. heart muscle development biological_process GO:0048738 cardiac muscle tissue development The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure. GOC:dph GOC:jid GOC:lm The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. skeletal muscle fibre development skeletal myofiber development skeletal myofibre development biological_process GO:0048741 skeletal muscle fiber development The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. GOC:dph GOC:ef GOC:jid GOC:lm GOC:mtg_muscle Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. regulation of skeletal muscle fibre development regulation of skeletal myofiber development regulation of skeletal myofibre development biological_process GO:0048742 regulation of skeletal muscle fiber development Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. GOC:dph GOC:jid GOC:mtg_muscle GOC:sm Any process that activates, maintains or increases the rate of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. positive regulation of skeletal muscle fibre development positive regulation of skeletal myofiber development positive regulation of skeletal myofibre development up regulation of skeletal muscle fiber development up-regulation of skeletal muscle fiber development upregulation of skeletal muscle fiber development activation of skeletal muscle fiber development stimulation of skeletal muscle fiber development biological_process GO:0048743 positive regulation of skeletal muscle fiber development Any process that activates, maintains or increases the rate of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. GOC:dph GOC:jid GOC:lm GOC:mtg_muscle Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. down regulation of skeletal muscle fiber development down-regulation of skeletal muscle fiber development downregulation of skeletal muscle fiber development negative regulation of skeletal muscle fibre development negative regulation of skeletal myofiber development negative regulation of skeletal myofibre development inhibition of skeletal muscle fiber development biological_process GO:0048744 negative regulation of skeletal muscle fiber development Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast. GOC:dph GOC:jid GOC:lm GOC:mtg_muscle The process whose specific outcome is the progression of smooth muscle over time, from its formation to the mature structure. biological_process GO:0048745 smooth muscle tissue development The process whose specific outcome is the progression of smooth muscle over time, from its formation to the mature structure. GOC:dph GOC:jid GOC:lm The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye. GO:0007456 insect-type retina development biological_process GO:0048749 compound eye development The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye. GOC:jid GOC:mtg_sensu Wikipedia:Eye insect-type retina development PMID:11735386 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule. pigment granule organisation biological_process pigment granule organization and biogenesis GO:0048753 pigment granule organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule. GOC:rc pigment granule organization and biogenesis GOC:mah The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder. biological_process tubulogenesis GO:0048754 branching morphogenesis of an epithelial tube The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder. GOC:dgh GOC:dph GOC:jid tubulogenesis GOC:dph GOC:tb The process in which the anatomical structures of branches in a nerve are generated and organized. This term refers to an anatomical structure (nerve) not a cell (neuron). biological_process GO:0048755 branching morphogenesis of a nerve The process in which the anatomical structures of branches in a nerve are generated and organized. This term refers to an anatomical structure (nerve) not a cell (neuron). GOC:dgh GOC:dph GOC:jid The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types. biological_process GO:0048762 mesenchymal cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types. GOC:dph GOC:jid A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. cellular_component GO:0048770 pigment granule A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. GOC:jid GOC:mh A developmental process, independent of morphogenetic (shape) change, that is required for an animal organ to attain its fully functional state. An organ is a tissue or set of tissues that work together to perform a specific function or functions. biological_process GO:0048799 animal organ maturation A developmental process, independent of morphogenetic (shape) change, that is required for an animal organ to attain its fully functional state. An organ is a tissue or set of tissues that work together to perform a specific function or functions. GOC:curators The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure. genital development biological_process GO:0048806 genitalia development The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure. GOC:jid The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites. neurite biosynthesis neurite formation neurite growth biological_process neurite morphogenesis GO:0048812 neuron projection morphogenesis The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites. GOC:mah neurite morphogenesis GOC:dph GOC:tb The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure. RBC development red blood cell development biological_process GO:0048821 erythrocyte development The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure. GOC:devbiol RBC development CL:0000232 red blood cell development CL:0000232 The process aimed at the progression of an enucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. enucleate RBC development enucleate red blood cell development biological_process GO:0048822 enucleate erythrocyte development The process aimed at the progression of an enucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. GOC:devbiol enucleate RBC development CL:0000232 enucleate red blood cell development CL:0000232 The process aimed at the progression of a nucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. nucleate RBC development nucleate red blood cell development biological_process GO:0048823 nucleate erythrocyte development The process aimed at the progression of a nucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. GOC:devbiol nucleate RBC development CL:0000232 nucleate red blood cell development CL:0000232 The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs. arterial morphogenesis arteriogenesis biological_process GO:0048844 artery morphogenesis The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs. GOC:dsf PMID:16740480 arteriogenesis GOC:mtg_heart The process in which the anatomical structures of venous blood vessels are generated and organized. Veins are blood vessels that transport blood from the body and its organs to the heart. vein morphogenesis venous morphogenesis biological_process GO:0048845 venous blood vessel morphogenesis The process in which the anatomical structures of venous blood vessels are generated and organized. Veins are blood vessels that transport blood from the body and its organs to the heart. GOC:dsf PMID:16740480 The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). biological_process GO:0048854 brain morphogenesis The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). GOC:dgh GOC:jid The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure biological_process GO:0048856 anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 The biological process whose specific outcome is the progression of a neural nucleus from its initial condition to its mature state. A neural nucleus is an anatomical structure consisting of a discrete aggregate of neuronal soma. biological_process GO:0048857 neural nucleus development The biological process whose specific outcome is the progression of a neural nucleus from its initial condition to its mature state. A neural nucleus is an anatomical structure consisting of a discrete aggregate of neuronal soma. GO_REF:0000021 The process in which the anatomical structures of a cell projection are generated and organized. biological_process GO:0048858 cell projection morphogenesis The process in which the anatomical structures of a cell projection are generated and organized. GO_REF:0000021 The process in which the limits of an anatomical structure are generated. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. biological_process GO:0048859 formation of anatomical boundary The process in which the limits of an anatomical structure are generated. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. Wikipedia:Stem_cell_differentiation biological_process GO:0048863 stem cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CL:0000034 GOC:isa_complete The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate. biological_process GO:0048864 stem cell development The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate. CL:0000034 GOC:isa_complete A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process GO:0048869 cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GOC:isa_complete Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. https://github.com/geneontology/go-ontology/issues/19809 cell locomotion movement of a cell biological_process cell movement GO:0048870 cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GOC:dgh GOC:dph GOC:isa_complete GOC:mlg Any process involved in the maintenance of an internal steady state at the level of the multicellular organism. biological_process GO:0048871 multicellular organismal-level homeostasis Any process involved in the maintenance of an internal steady state at the level of the multicellular organism. GOC:isa_complete Any biological process involved in the maintenance of the steady-state number of cells within a population of cells. https://github.com/geneontology/go-ontology/issues/24218 cell population homeostasis homeostasis of cell number biological_process GO:0048872 homeostasis of number of cells Any biological process involved in the maintenance of the steady-state number of cells within a population of cells. GOC:isa_complete homeostasis of cell number GOC:dph The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure. biological_process GO:0048880 sensory system development The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure. GOC:dgh The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the peripheral nervous system. biological_process GO:0048934 peripheral nervous system neuron differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the peripheral nervous system. GOC:dgh The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron. biological_process GO:0048935 peripheral nervous system neuron development The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron. GOC:dgh Any process in which a chromosome is transported to, or maintained in, a specific location. chromosome localisation establishment and maintenance of chromosome localization establishment and maintenance of chromosome position biological_process GO:0050000 chromosome localization Any process in which a chromosome is transported to, or maintained in, a specific location. GOC:ai chromosome localisation GOC:mah The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. biological_process GO:0050432 catecholamine secretion The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:ai GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of catecholamines. biological_process GO:0050433 regulation of catecholamine secretion Any process that modulates the frequency, rate or extent of the regulated release of catecholamines. GOC:ai The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0050657 nucleic acid transport The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai ISBN:0198506732 The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0050658 RNA transport The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances. biological_process GO:0050673 epithelial cell proliferation The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances. ISBN:0721662544 Any process that modulates the frequency, rate or extent of epithelial cell proliferation. biological_process GO:0050678 regulation of epithelial cell proliferation Any process that modulates the frequency, rate or extent of epithelial cell proliferation. GOC:ai Any process that activates or increases the rate or extent of epithelial cell proliferation. up regulation of epithelial cell proliferation up-regulation of epithelial cell proliferation upregulation of epithelial cell proliferation activation of epithelial cell proliferation stimulation of epithelial cell proliferation biological_process GO:0050679 positive regulation of epithelial cell proliferation Any process that activates or increases the rate or extent of epithelial cell proliferation. GOC:ai Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation. down regulation of epithelial cell proliferation down-regulation of epithelial cell proliferation downregulation of epithelial cell proliferation inhibition of epithelial cell proliferation biological_process GO:0050680 negative regulation of epithelial cell proliferation Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation. GOC:ai Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. biological_process GO:0050708 regulation of protein secretion Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. down regulation of protein secretion down-regulation of protein secretion downregulation of protein secretion inhibition of protein secretion biological_process GO:0050709 negative regulation of protein secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. up regulation of protein secretion up-regulation of protein secretion upregulation of protein secretion activation of protein secretion stimulation of protein secretion biological_process GO:0050714 positive regulation of protein secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that modulates the frequency, rate or extent of neurogenesis, the generation of cells in the nervous system. biological_process GO:0050767 regulation of neurogenesis Any process that modulates the frequency, rate or extent of neurogenesis, the generation of cells in the nervous system. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system. down regulation of neurogenesis down-regulation of neurogenesis downregulation of neurogenesis inhibition of neurogenesis biological_process GO:0050768 negative regulation of neurogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system. GOC:ai Any process that activates or increases the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system. up regulation of neurogenesis up-regulation of neurogenesis upregulation of neurogenesis activation of neurogenesis stimulation of neurogenesis biological_process GO:0050769 positive regulation of neurogenesis Any process that activates or increases the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system. GOC:ai Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. biological_process GO:0050776 regulation of immune response Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. down regulation of immune response down-regulation of immune response downregulation of immune response inhibition of immune response biological_process GO:0050777 negative regulation of immune response Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. up regulation of immune response up-regulation of immune response upregulation of immune response stimulation of immune response biological_process GO:0050778 positive regulation of immune response Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators Any process that modulates the activity of an enzyme. GO:0048552 regulation of enzyme activity regulation of metalloenzyme activity biological_process GO:0050790 regulation of catalytic activity Any process that modulates the activity of an enzyme. GOC:ai GOC:ebc GOC:vw Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). biological_process GO:0050793 regulation of developmental process Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:go_curators Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. regulation of behaviour biological_process GO:0050795 regulation of behavior Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. GOC:go_curators GOC:pr Any process that modulates the frequency, rate or extent of the regulated release of insulin. biological_process GO:0050796 regulation of insulin secretion Any process that modulates the frequency, rate or extent of the regulated release of insulin. GOC:ai Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). biological_process GO:0050803 regulation of synapse structure or activity Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). GOC:ai Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission. modulation of synaptic transmission regulation of chemical synaptic transmission regulation of synaptic transmission biological_process GO:0050804 modulation of chemical synaptic transmission Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. down regulation of synaptic transmission down-regulation of synaptic transmission downregulation of synaptic transmission inhibition of synaptic transmission biological_process GO:0050805 negative regulation of synaptic transmission Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. GOC:ai Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. up regulation of synaptic transmission up-regulation of synaptic transmission upregulation of synaptic transmission activation of synaptic transmission stimulation of synaptic transmission biological_process GO:0050806 positive regulation of synaptic transmission Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. GOC:ai Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). regulation of synapse organisation regulation of synapse structure biological_process regulation of synapse organization and biogenesis GO:0050807 regulation of synapse organization Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). GOC:ai GOC:dph GOC:tb regulation of synapse organisation GOC:mah regulation of synapse organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). synapse organisation biological_process synapse development synapse morphogenesis synapse organization and biogenesis GO:0050808 synapse organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell). GOC:ai GOC:pr synapse development GOC:aruk synapse morphogenesis GOC:BHF synapse organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. regulation of steroid anabolism regulation of steroid biosynthesis regulation of steroid formation regulation of steroid synthesis regulation of steroidogenesis biological_process GO:0050810 regulation of steroid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:ai A organ system process carried out by any of the organs or tissues of neurological system. https://github.com/geneontology/go-ontology/issues/13824 neurological system process neurophysiological process biological_process pan-neural process GO:0050877 nervous system process A organ system process carried out by any of the organs or tissues of neurological system. GOC:ai GOC:mtg_cardio Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism. biological_process GO:0050879 multicellular organismal movement Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism. GOC:dph GOC:mtg_muscle GOC:tb The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system. biological_process GO:0050881 musculoskeletal movement The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system. GOC:dph The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. endocrine physiological process endocrine physiology biological_process GO:0050886 endocrine process The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. ISBN:0721662544 The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory. Wikipedia:Cognition biological_process GO:0050890 cognition The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory. ISBN:0721619908 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 GO:0050896 SNOMEDCT:248237001 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf Any process pertaining to the functions of the nervous and muscular systems of an organism. neuromotor process neuromuscular physiological process biological_process GO:0050905 neuromuscular process Any process pertaining to the functions of the nervous and muscular systems of an organism. GOC:ai The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal. Wikipedia:Transduction_(physiology) sensory detection of stimulus sensory perception, sensory transduction of stimulus sensory perception, stimulus detection sensory transduction biological_process GO:0050906 detection of stimulus involved in sensory perception The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal. GOC:ai GOC:dos GOC:dph The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of chemical stimulus sensory detection of chemical stimulus during sensory perception sensory perception, sensory detection of chemical stimulus sensory perception, sensory transduction of chemical stimulus sensory transduction of chemical stimulus sensory transduction of chemical stimulus during sensory perception biological_process GO:0050907 detection of chemical stimulus involved in sensory perception The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. sensory detection of light during visual perception sensory detection of light stimulus during visual perception sensory transduction of light during visual perception sensory transduction of light stimulus during visual perception visual perception, detection of light stimulus visual perception, sensory transduction during perception of light visual perception, sensory transduction of light stimulus biological_process GO:0050908 detection of light stimulus involved in visual perception The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. GOC:ai GOC:dos The process in which a relatively unspecialized cell acquires the specialized features of a pigmented cell, such as a melanocyte. GO:0043357 GO:0043358 chromatophore differentiation pigmented cell differentiation biological_process GO:0050931 Note that the chromatophore mentioned here is distinct from the pigment bearing structure found in certain photosynthetic bacteria and cyanobacteria. It is also different from the plant chromoplast, which is also sometimes called a chromatophore. pigment cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a pigmented cell, such as a melanocyte. GOC:dgh Any process that modulates the frequency, rate or extent of pigmented cell differentiation. biological_process GO:0050932 regulation of pigment cell differentiation Any process that modulates the frequency, rate or extent of pigmented cell differentiation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of pigment cell differentiation. down regulation of pigment cell differentiation down-regulation of pigment cell differentiation downregulation of pigment cell differentiation inhibition of pigment cell differentiation biological_process GO:0050941 negative regulation of pigment cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of pigment cell differentiation. GOC:ai Any process that activates or increases the frequency, rate or extent of pigment cell differentiation. up regulation of pigment cell differentiation up-regulation of pigment cell differentiation upregulation of pigment cell differentiation activation of pigment cell differentiation stimulation of pigment cell differentiation biological_process GO:0050942 positive regulation of pigment cell differentiation Any process that activates or increases the frequency, rate or extent of pigment cell differentiation. GOC:ai The series of events required for an organism to receive a sensory electrical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. biological_process GO:0050952 sensory perception of electrical stimulus The series of events required for an organism to receive a sensory electrical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. biological_process GO:0050953 sensory perception of light stimulus The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. mechanosensory perception perception of mechanical stimulus biological_process chemi-mechanical coupling GO:0050954 sensory perception of mechanical stimulus The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive an electrical stimulus, convert it to a molecular signal, and recognize and characterize the signal. Many fish possess an electroception sense; for example, the electric eel uses low voltage pulses of electricity for navigation and prey location. Wikipedia:Electroreception electroception sense electroceptive sense biological_process GO:0050956 electroception The series of events required for an organism to receive an electrical stimulus, convert it to a molecular signal, and recognize and characterize the signal. Many fish possess an electroception sense; for example, the electric eel uses low voltage pulses of electricity for navigation and prey location. GOC:ai PMID:10210663 Wikipedia:Electroreception The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light. sensory detection of light stimulus sensory detection of light stimulus during sensory perception sensory perception, sensory detection of light stimulus sensory perception, sensory transduction of light stimulus sensory transduction of light stimulus sensory transduction of light stimulus during sensory perception biological_process GO:0050962 detection of light stimulus involved in sensory perception The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light. GOC:ai GOC:dos The series of events in which an electrical stimulus is received by a cell and converted into a molecular signal as part of sensory perception. sensory detection of electrical stimulus sensory detection of electrical stimulus during sensory perception sensory perception, sensory detection of electrical stimulus sensory perception, sensory transduction of electrical stimulus sensory transduction of electrical stimulus sensory transduction of electrical stimulus during sensory perception biological_process GO:0050963 detection of electrical stimulus involved in sensory perception The series of events in which an electrical stimulus is received by a cell and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events that contribute to electroception in which an electrical stimulus is received and converted into a molecular signal. electroception, detection of electrical stimulus electroception, sensory detection of electrical stimulus electroception, sensory transduction electroception, sensory transduction of electrical stimulus biological_process detection of electrical stimulus during electroreception sensory detection of electrical stimulus during electroception sensory transduction of electrical stimulus during electroception GO:0050964 detection of electrical stimulus involved in electroception The series of events that contribute to electroception in which an electrical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos detection of electrical stimulus during electroreception GOC:dph GOC:tb The series of events that contribute to the perception of pain in which an electrical stimulus is received and converted into a molecular signal. perception of pain, detection of electrical stimulus perception of pain, sensory detection of electrical stimulus perception of pain, sensory transduction of electrical stimulus biological_process detection of electrical stimulus during sensory perception of pain sensory detection of electrical stimulus during perception of pain sensory transduction of electrical stimulus during perception of pain GO:0050967 detection of electrical stimulus involved in sensory perception of pain The series of events that contribute to the perception of pain in which an electrical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos GOC:dph GOC:tb detection of electrical stimulus during sensory perception of pain GOC:dph GOC:tb The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal. perception of pain, detection of chemical stimulus perception of pain, sensory detection of chemical stimulus perception of pain, sensory transduction of chemical stimulus sensory detection of chemical stimulus during perception of pain sensory transduction of chemical stimulus during perception of pain biological_process chemical nociception GO:0050968 detection of chemical stimulus involved in sensory perception of pain The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal. GOC:ai chemical nociception GOC:pr The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach). Wikipedia:Touch perception of touch tactile sense taction tactition biological_process GO:0050975 sensory perception of touch The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach). GOC:ai The series of events by which an electrical stimulus is received and converted into a molecular signal. biological_process GO:0050981 detection of electrical stimulus The series of events by which an electrical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids. regulation of lipid breakdown regulation of lipid catabolism regulation of lipid degradation biological_process GO:0050994 regulation of lipid catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. down regulation of lipid catabolic process down-regulation of lipid catabolic process downregulation of lipid catabolic process negative regulation of lipid breakdown negative regulation of lipid catabolism negative regulation of lipid degradation inhibition of lipid catabolic process biological_process GO:0050995 negative regulation of lipid catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. positive regulation of lipid breakdown positive regulation of lipid catabolism positive regulation of lipid degradation up regulation of lipid catabolic process up-regulation of lipid catabolic process upregulation of lipid catabolic process activation of lipid catabolic process stimulation of lipid catabolic process biological_process GO:0050996 positive regulation of lipid catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids. GOC:ai The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GO:0045011 biological_process actin bundling activity actin cable assembly actin cable formation GO:0051017 actin filament bundle assembly The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GOC:ai actin cable assembly GOC:mah actin cable formation GOC:mah The directed movement of RNA, deoxyribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051027 DNA transport The directed movement of RNA, deoxyribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Enables the transfer of nucleic acids from one side of a membrane to the other. Nucleic acids are single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information. molecular_function GO:0051032 nucleic acid transmembrane transporter activity Enables the transfer of nucleic acids from one side of a membrane to the other. Nucleic acids are single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information. GOC:ai Enables the transfer of RNA, ribonucleic acid, from one side of a membrane to the other. Reactome:R-HSA-203906 molecular_function GO:0051033 RNA transmembrane transporter activity Enables the transfer of RNA, ribonucleic acid, from one side of a membrane to the other. GOC:ai Reactome:R-HSA-203906 Exportin complex translocates pre-miRNA to cytosol Enables the transfer of DNA, deoxyribonucleic acid, from one side of a membrane to the other. molecular_function GO:0051035 DNA transmembrane transporter activity Enables the transfer of DNA, deoxyribonucleic acid, from one side of a membrane to the other. GOC:ai Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. biological_process GO:0051046 regulation of secretion Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. up regulation of secretion up-regulation of secretion upregulation of secretion activation of secretion stimulation of secretion biological_process GO:0051047 positive regulation of secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. down regulation of secretion down-regulation of secretion downregulation of secretion inhibition of secretion biological_process GO:0051048 negative regulation of secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051049 regulation of transport Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of transport up-regulation of transport upregulation of transport activation of transport stimulation of transport biological_process GO:0051050 positive regulation of transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process GO:0051051 negative regulation of transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. regulation of DNA metabolism biological_process GO:0051052 regulation of DNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. down regulation of DNA metabolic process down-regulation of DNA metabolic process downregulation of DNA metabolic process negative regulation of DNA metabolism inhibition of DNA metabolic process biological_process GO:0051053 negative regulation of DNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. positive regulation of DNA metabolism up regulation of DNA metabolic process up-regulation of DNA metabolic process upregulation of DNA metabolic process activation of DNA metabolic process stimulation of DNA metabolic process biological_process GO:0051054 positive regulation of DNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. down regulation of lipid biosynthetic process down-regulation of lipid biosynthetic process downregulation of lipid biosynthetic process negative regulation of lipid anabolism negative regulation of lipid biosynthesis negative regulation of lipid formation negative regulation of lipid synthesis negative regulation of lipogenesis inhibition of lipid biosynthetic process biological_process GO:0051055 negative regulation of lipid biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai negative regulation of lipogenesis GOC:sl The cell cycle process in which the controlled breakdown of the nuclear membranes during meiotic cell division occurs. biological_process meiotic nuclear envelope breakdown meiotic nuclear envelope catabolism meiotic nuclear envelope degradation meiotic nuclear envelope disassembly GO:0051078 meiotic nuclear membrane disassembly The cell cycle process in which the controlled breakdown of the nuclear membranes during meiotic cell division occurs. GOC:bf The controlled breakdown of the nuclear membranes, for example during cellular division. biological_process nuclear envelope breakdown nuclear envelope catabolism nuclear envelope degradation nuclear envelope disassembly GO:0051081 nuclear membrane disassembly The controlled breakdown of the nuclear membranes, for example during cellular division. GOC:ai Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). down regulation of developmental process down-regulation of developmental process downregulation of developmental process inhibition of developmental process biological_process GO:0051093 negative regulation of developmental process Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:ai Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). up regulation of developmental process up-regulation of developmental process upregulation of developmental process activation of developmental process stimulation of developmental process biological_process GO:0051094 positive regulation of developmental process Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:ai Enables the transfer of a sugar from one side of a membrane to the other. A sugar is any member of a class of sweet, water-soluble, crystallizable carbohydrates, which are the monosaccharides and smaller oligosaccharides. Reactome:R-HSA-428779 Reactome:R-HSA-8875902 Reactome:R-HSA-8876319 sugar/polyol channel activity molecular_function GO:0051119 sugar transmembrane transporter activity Enables the transfer of a sugar from one side of a membrane to the other. A sugar is any member of a class of sweet, water-soluble, crystallizable carbohydrates, which are the monosaccharides and smaller oligosaccharides. GOC:ai GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-428779 GLUT7 and GLUT11 transport glucose and fructose Reactome:R-HSA-8875902 SLC45A3 transports Glc from extracellular region to cytosol Reactome:R-HSA-8876319 SLC50A1 transports Glc from cytosol to extracellular region Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. regulation of cellular component organisation biological_process regulation of cell organisation regulation of cell organization regulation of cellular component organization and biogenesis GO:0051128 regulation of cellular component organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai regulation of cell organisation GOC:mah regulation of cell organization GOC:mah regulation of cellular component organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. down regulation of cell organization down-regulation of cell organization downregulation of cell organization inhibition of cell organization biological_process negative regulation of cell organisation negative regulation of cellular component organization and biogenesis GO:0051129 negative regulation of cellular component organization Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai negative regulation of cell organisation GOC:mah negative regulation of cellular component organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. positive regulation of cell organisation up regulation of cell organization up-regulation of cell organization upregulation of cell organization activation of cell organization stimulation of cell organization biological_process positive regulation of cellular component organization and biogenesis GO:0051130 positive regulation of cellular component organization Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai positive regulation of cellular component organization and biogenesis GOC:mah The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary. nonstriated muscle cell differentiation biological_process GO:0051145 smooth muscle cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary. CL:0000192 GOC:ai The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle. voluntary muscle cell differentiation biological_process GO:0051146 striated muscle cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle. CL:0000737 GOC:ai Any process that modulates the frequency, rate or extent of muscle cell differentiation. biological_process GO:0051147 regulation of muscle cell differentiation Any process that modulates the frequency, rate or extent of muscle cell differentiation. CL:0000187 GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of muscle cell differentiation. down regulation of muscle cell differentiation down-regulation of muscle cell differentiation downregulation of muscle cell differentiation inhibition of muscle cell differentiation biological_process GO:0051148 negative regulation of muscle cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of muscle cell differentiation. CL:0000187 GOC:ai Any process that activates or increases the frequency, rate or extent of muscle cell differentiation. up regulation of muscle cell differentiation up-regulation of muscle cell differentiation upregulation of muscle cell differentiation activation of muscle cell differentiation stimulation of muscle cell differentiation biological_process GO:0051149 positive regulation of muscle cell differentiation Any process that activates or increases the frequency, rate or extent of muscle cell differentiation. CL:0000187 GOC:ai Any process that modulates the frequency, rate or extent of smooth muscle cell differentiation. biological_process GO:0051150 regulation of smooth muscle cell differentiation Any process that modulates the frequency, rate or extent of smooth muscle cell differentiation. CL:0000192 GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell differentiation. down regulation of smooth muscle cell differentiation down-regulation of smooth muscle cell differentiation downregulation of smooth muscle cell differentiation inhibition of smooth muscle cell differentiation biological_process GO:0051151 negative regulation of smooth muscle cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell differentiation. CL:0000192 GOC:ai Any process that activates or increases the frequency, rate or extent of smooth muscle cell differentiation. up regulation of smooth muscle cell differentiation up-regulation of smooth muscle cell differentiation upregulation of smooth muscle cell differentiation activation of smooth muscle cell differentiation stimulation of smooth muscle cell differentiation biological_process GO:0051152 positive regulation of smooth muscle cell differentiation Any process that activates or increases the frequency, rate or extent of smooth muscle cell differentiation. CL:0000192 GOC:ai Any process that modulates the frequency, rate or extent of striated muscle cell differentiation. biological_process GO:0051153 regulation of striated muscle cell differentiation Any process that modulates the frequency, rate or extent of striated muscle cell differentiation. CL:0000737 GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle cell differentiation. down regulation of striated muscle cell differentiation down-regulation of striated muscle cell differentiation downregulation of striated muscle cell differentiation inhibition of striated muscle cell differentiation biological_process GO:0051154 negative regulation of striated muscle cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle cell differentiation. CL:0000737 GOC:ai Any process that activates or increases the frequency, rate or extent of striated muscle cell differentiation. up regulation of striated muscle cell differentiation up-regulation of striated muscle cell differentiation upregulation of striated muscle cell differentiation activation of striated muscle cell differentiation stimulation of striated muscle cell differentiation biological_process GO:0051155 positive regulation of striated muscle cell differentiation Any process that activates or increases the frequency, rate or extent of striated muscle cell differentiation. CL:0000737 GOC:ai The directed movement of substances into, out of, or within the nucleus. Wikipedia:Nuclear_transport nucleus transport biological_process GO:0051169 nuclear transport The directed movement of substances into, out of, or within the nucleus. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen metabolic process regulation of nitrogen metabolism biological_process GO:0051171 regulation of nitrogen compound metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb regulation of nitrogen metabolic process GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. down regulation of nitrogen metabolic process down-regulation of nitrogen metabolic process downregulation of nitrogen metabolic process negative regulation of nitrogen metabolic process negative regulation of nitrogen metabolism inhibition of nitrogen metabolic process biological_process GO:0051172 negative regulation of nitrogen compound metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb negative regulation of nitrogen metabolic process GOC:tb Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. positive regulation of nitrogen metabolic process positive regulation of nitrogen metabolism up regulation of nitrogen metabolic process up-regulation of nitrogen metabolic process upregulation of nitrogen metabolic process activation of nitrogen metabolic process stimulation of nitrogen metabolic process biological_process GO:0051173 positive regulation of nitrogen compound metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb positive regulation of nitrogen metabolic process GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. regulation of phosphorus metabolism biological_process GO:0051174 regulation of phosphorus metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. down regulation of sulfur metabolic process down-regulation of sulfur metabolic process downregulation of sulfur metabolic process negative regulation of sulfur metabolism negative regulation of sulphur metabolic process negative regulation of sulphur metabolism inhibition of sulfur metabolic process biological_process GO:0051175 negative regulation of sulfur metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. positive regulation of sulfur metabolism positive regulation of sulphur metabolic process positive regulation of sulphur metabolism up regulation of sulfur metabolic process up-regulation of sulfur metabolic process upregulation of sulfur metabolic process activation of sulfur metabolic process stimulation of sulfur metabolic process biological_process GO:0051176 positive regulation of sulfur metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. GOC:ai Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. jl 2013-12-18T13:51:04Z GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process single organism localization single-organism localization GO:0051179 localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GOC:ai GOC:dos localisation GOC:mah single organism localization GOC:TermGenie The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. Wikipedia:Chondrogenesis cartilage biogenesis cartilage biosynthesis cartilage element development cartilage formation cartilage organ development chondrogenesis biological_process GO:0051216 cartilage development The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. GOC:cjm PMID:23251424 Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of protein transport up-regulation of protein transport upregulation of protein transport activation of protein transport stimulation of protein transport biological_process GO:0051222 positive regulation of protein transport Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051223 regulation of protein transport Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of protein transport down-regulation of protein transport downregulation of protein transport inhibition of protein transport biological_process GO:0051224 negative regulation of protein transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. https://github.com/geneontology/go-ontology/issues/24200 establishment of localisation biological_process GO:0051234 establishment of localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos establishment of localisation GOC:mah The directed movement of RNA to a specific location. RNA positioning RNA recruitment establishment of RNA localisation biological_process GO:0051236 establishment of RNA localization The directed movement of RNA to a specific location. GOC:ai establishment of RNA localisation GOC:mah Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. biological_process GO:0051239 regulation of multicellular organismal process Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. up regulation of multicellular organismal process up-regulation of multicellular organismal process upregulation of multicellular organismal process activation of multicellular organismal process stimulation of multicellular organismal process biological_process GO:0051240 positive regulation of multicellular organismal process Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. down regulation of multicellular organismal process down-regulation of multicellular organismal process downregulation of multicellular organismal process inhibition of multicellular organismal process biological_process GO:0051241 negative regulation of multicellular organismal process Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032268 regulation of protein metabolism biological_process regulation of cellular protein metabolic process regulation of cellular protein metabolism GO:0051246 regulation of protein metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032270 positive regulation of cellular protein metabolic process positive regulation of cellular protein metabolism positive regulation of protein metabolism up regulation of cellular protein metabolic process up regulation of protein metabolic process up-regulation of cellular protein metabolic process up-regulation of protein metabolic process upregulation of cellular protein metabolic process upregulation of protein metabolic process activation of cellular protein metabolic process activation of protein metabolic process stimulation of cellular protein metabolic process stimulation of protein metabolic process biological_process GO:0051247 positive regulation of protein metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032269 down regulation of cellular protein metabolic process down regulation of protein metabolic process down-regulation of cellular protein metabolic process down-regulation of protein metabolic process downregulation of cellular protein metabolic process downregulation of protein metabolic process negative regulation of cellular protein metabolic process negative regulation of cellular protein metabolism negative regulation of protein metabolism inhibition of cellular protein metabolic process inhibition of protein metabolic process biological_process GO:0051248 negative regulation of protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. regulation of RNA metabolism biological_process GO:0051252 regulation of RNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. down regulation of RNA metabolic process down-regulation of RNA metabolic process downregulation of RNA metabolic process negative regulation of RNA metabolism inhibition of RNA metabolic process biological_process GO:0051253 negative regulation of RNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. positive regulation of RNA metabolism up regulation of RNA metabolic process up-regulation of RNA metabolic process upregulation of RNA metabolic process activation of RNA metabolic process stimulation of RNA metabolic process biological_process GO:0051254 positive regulation of RNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein. protein polymer biosynthesis protein polymer biosynthetic process protein polymer formation biological_process GO:0051258 protein polymerization The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein. GOC:ai The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein. protein polymer breakdown protein polymer catabolic process protein polymer catabolism protein polymer degradation biological_process GO:0051261 protein depolymerization The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein. GOC:ai A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 GO:0006323 GO:0007001 GO:0051277 DNA condensation chromosome organisation DNA packaging biological_process chromosome organization and biogenesis maintenance of genome integrity nuclear genome maintenance GO:0051276 chromosome organization A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. GOC:ai GOC:dph GOC:jl GOC:mah chromosome organization and biogenesis GOC:mah The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GOC:di GOC:go_curators GOC:pr Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells. biological_process GO:0051302 regulation of cell division Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells. GOC:go_curators The directed movement of a chromosome to a specific location. chromosome positioning establishment of chromosome localisation biological_process GO:0051303 establishment of chromosome localization The directed movement of a chromosome to a specific location. GOC:ai establishment of chromosome localisation GOC:mah Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. https://github.com/geneontology/go-ontology/issues/24599 GO:0007126 Wikipedia:Meiosis biological_process meiosis GO:0051321 Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. meiotic cell cycle Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. GOC:ai Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. hydrolase regulator biological_process GO:0051336 regulation of hydrolase activity Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3. GOC:ai Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. transferase regulator biological_process GO:0051338 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. GOC:ai Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds. hydrolase activator up regulation of hydrolase activity up-regulation of hydrolase activity upregulation of hydrolase activity activation of hydrolase activity stimulation of hydrolase activity biological_process GO:0051345 positive regulation of hydrolase activity Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds. GOC:ai Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds. down regulation of hydrolase activity down-regulation of hydrolase activity downregulation of hydrolase activity hydrolase inhibitor inhibition of hydrolase activity biological_process GO:0051346 negative regulation of hydrolase activity Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds. GOC:ai Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. transferase activator up regulation of transferase activity up-regulation of transferase activity upregulation of transferase activity activation of transferase activity stimulation of transferase activity biological_process GO:0051347 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. down regulation of transferase activity down-regulation of transferase activity downregulation of transferase activity transferase inhibitor inhibition of transferase activity biological_process GO:0051348 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. apoptosis of neuronal cells apoptosis of neurons neuron programmed cell death by apoptosis neuronal cell apoptosis neuronal cell programmed cell death by apoptosis programmed cell death of neuronal cells by apoptosis programmed cell death of neurons by apoptosis programmed cell death, neuronal cells programmed cell death, neurons neuron apoptosis biological_process GO:0051402 neuron apoptotic process Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. CL:0000540 GOC:mtg_apoptosis Any process that reduces or removes the toxicity of nitrogenous compounds which are dangerous or toxic. This includes the aerobic conversion of toxic compounds to harmless substances. detoxification of nitrogenous compound nitric oxide (NO) detoxification biological_process GO:0051410 detoxification of nitrogen compound Any process that reduces or removes the toxicity of nitrogenous compounds which are dangerous or toxic. This includes the aerobic conversion of toxic compounds to harmless substances. GOC:ai Any process that modulates the rate or extent of progression through the meiotic cell cycle. meiotic cell cycle modulation meiotic cell cycle regulation modulation of meiotic cell cycle progression regulation of meiotic cell cycle progression regulation of progression through meiotic cell cycle biological_process meiotic cell cycle regulator GO:0051445 regulation of meiotic cell cycle Any process that modulates the rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb regulation of progression through meiotic cell cycle GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle. positive regulation of meiotic cell cycle progression positive regulation of progression through meiotic cell cycle up regulation of progression through meiotic cell cycle up-regulation of progression through meiotic cell cycle upregulation of progression through meiotic cell cycle activation of progression through meiotic cell cycle stimulation of progression through meiotic cell cycle biological_process GO:0051446 positive regulation of meiotic cell cycle Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb positive regulation of progression through meiotic cell cycle GOC:dph GOC:tb Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle. down regulation of progression through meiotic cell cycle down-regulation of progression through meiotic cell cycle downregulation of progression through meiotic cell cycle negative regulation of meiotic cell cycle progression negative regulation of progression through meiotic cell cycle inhibition of progression through meiotic cell cycle biological_process GO:0051447 negative regulation of meiotic cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb negative regulation of progression through meiotic cell cycle GOC:dph GOC:tb The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. biological_process GO:0051450 myoblast proliferation The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers. CL:0000056 GOC:ai GOC:mtg_muscle The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole. GO:0042146 biological_process heterotypic vacuole fusion (non-autophagic) heterotypic vacuole fusion, non-autophagic GO:0051469 vesicle fusion with vacuole The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole. GOC:ai Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. regulation of cytoskeleton organisation biological_process regulation of cytoskeleton organization and biogenesis GO:0051493 regulation of cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai regulation of cytoskeleton organisation GOC:mah regulation of cytoskeleton organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. down regulation of cytoskeleton organization down-regulation of cytoskeleton organization downregulation of cytoskeleton organization negative regulation of cytoskeleton organisation inhibition of cytoskeleton organization biological_process negative regulation of cytoskeleton organization and biogenesis GO:0051494 negative regulation of cytoskeleton organization Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai negative regulation of cytoskeleton organisation GOC:mah negative regulation of cytoskeleton organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. positive regulation of cytoskeleton organisation up regulation of cytoskeleton organization up-regulation of cytoskeleton organization upregulation of cytoskeleton organization activation of cytoskeleton organization stimulation of cytoskeleton organization biological_process positive regulation of cytoskeleton organization and biogenesis GO:0051495 positive regulation of cytoskeleton organization Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai positive regulation of cytoskeleton organisation GOC:mah positive regulation of cytoskeleton organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051588 regulation of neurotransmitter transport Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of neurotransmitter transport down-regulation of neurotransmitter transport downregulation of neurotransmitter transport inhibition of neurotransmitter transport biological_process GO:0051589 negative regulation of neurotransmitter transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of neurotransmitter transport up-regulation of neurotransmitter transport upregulation of neurotransmitter transport activation of neurotransmitter transport stimulation of neurotransmitter transport biological_process GO:0051590 positive regulation of neurotransmitter transport Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus. biological_process response to electricity GO:0051602 response to electrical stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus. GOC:ai The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal. stimulus detection biological_process perception of stimulus stimulus sensing GO:0051606 detection of stimulus The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal. GOC:add GOC:ai GOC:dph GOC:mah The directed movement of norepinephrine into a cell, typically presynaptic neurons or glial cells. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine. levarterenol reuptake levarterenol uptake noradrenaline reuptake noradrenaline uptake norepinephrine import norepinephrine reuptake biological_process GO:0051620 norepinephrine uptake The directed movement of norepinephrine into a cell, typically presynaptic neurons or glial cells. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine. GOC:ai norepinephrine import GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter norepinephrine into a cell. regulation of levarterenol uptake regulation of noradrenaline uptake regulation of norepinephrine import biological_process GO:0051621 regulation of norepinephrine uptake Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter norepinephrine into a cell. GOC:ai regulation of norepinephrine import GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of norepinephrine into a cell. down regulation of norepinephrine uptake down-regulation of norepinephrine uptake downregulation of norepinephrine uptake negative regulation of levarterenol uptake negative regulation of noradrenaline uptake negative regulation of norepinephrine import biological_process GO:0051622 negative regulation of norepinephrine uptake Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of norepinephrine into a cell. GOC:ai negative regulation of norepinephrine import GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of norepinephrine into a cell. positive regulation of levarterenol uptake positive regulation of noradrenaline uptake positive regulation of norepinephrine import up regulation of norepinephrine uptake up-regulation of norepinephrine uptake upregulation of norepinephrine uptake activation of norepinephrine uptake stimulation of norepinephrine uptake biological_process GO:0051623 positive regulation of norepinephrine uptake Any process that activates or increases the frequency, rate or extent of the directed movement of norepinephrine into a cell. GOC:ai positive regulation of norepinephrine import GOC:dph GOC:tb The directed movement of acetylcholine into a cell, typically presynaptic neurons or glial cells. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. acetylcholine import biological_process GO:0051630 acetylcholine uptake The directed movement of acetylcholine into a cell, typically presynaptic neurons or glial cells. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. GOC:ai acetylcholine import GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter acetylcholine into a cell. regulation of acetylcholine import biological_process GO:0051631 regulation of acetylcholine uptake Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter acetylcholine into a cell. GOC:ai regulation of acetylcholine import GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of acetylcholine into a cell. down regulation of acetylcholine uptake down-regulation of acetylcholine uptake downregulation of acetylcholine uptake negative regulation of acetylcholine import biological_process GO:0051632 negative regulation of acetylcholine uptake Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of acetylcholine into a cell. GOC:ai negative regulation of acetylcholine import GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of acetylcholine into a cell. positive regulation of acetylcholine import up regulation of acetylcholine uptake up-regulation of acetylcholine uptake upregulation of acetylcholine uptake activation of acetylcholine uptake stimulation of acetylcholine uptake biological_process GO:0051633 positive regulation of acetylcholine uptake Any process that activates or increases the frequency, rate or extent of the directed movement of acetylcholine into a cell. GOC:ai positive regulation of acetylcholine import GOC:dph GOC:tb Any process in which an organelle is transported to, and/or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/19809 establishment and maintenance of organelle localization organelle localisation biological_process GO:0051640 organelle localization Any process in which an organelle is transported to, and/or maintained in, a specific location. GOC:ai organelle localisation GOC:mah A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. jl 2013-12-18T14:04:32Z GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane single organism cellular localization intracellular localization localization within cell biological_process single-organism cellular localization GO:0051641 cellular localization A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. GOC:tb GOC:vw cellular localisation GOC:mah single organism cellular localization GOC:TermGenie Any process in which the Golgi is transported to, and/or maintained in, a specific location within the cell. Golgi apparatus localization Golgi body localization Golgi localisation establishment and maintenance of Golgi localization biological_process GO:0051645 Golgi localization Any process in which the Golgi is transported to, and/or maintained in, a specific location within the cell. GOC:ai Golgi localisation GOC:mah Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell. cell nucleus localization establishment and maintenance of nucleus localization localization of nucleus nucleus localisation biological_process GO:0051647 nucleus localization Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell. GOC:ai nucleus localisation GOC:mah Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. cytoplasmic vesicle localization establishment and maintenance of vesicle localization vesicle localisation biological_process GO:0051648 vesicle localization Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. GOC:ai vesicle localisation GOC:mah Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell positioning within cell biological_process establishment of cellular localization GO:0051649 establishment of localization in cell Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos GOC:dph GOC:tb establishment of localisation in cell GOC:mah establishment of cellular localization GOC:dph GOC:tb The directed movement of a vesicle to a specific location. establishment of vesicle localisation biological_process GO:0051650 establishment of vesicle localization The directed movement of a vesicle to a specific location. GOC:ai establishment of vesicle localisation GOC:mah The directed movement of an organelle to a specific location. establishment of organelle localisation biological_process GO:0051656 establishment of organelle localization The directed movement of an organelle to a specific location. GOC:ai establishment of organelle localisation GOC:mah Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane. establishment and maintenance of localization in membrane establishment and maintenance of position in membrane localisation within membrane localization to membrane positioning within membrane biological_process GO:0051668 localization within membrane Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane. GOC:ai localisation within membrane GOC:mah Any process in which a cell is transported to, and/or maintained in, a specific location. cell localization establishment and maintenance of cell localization establishment and maintenance of localization of cell localisation of cell biological_process GO:0051674 localization of cell Any process in which a cell is transported to, and/or maintained in, a specific location. GOC:ai localisation of cell GOC:mah The directed movement of the Golgi to a specific location. establishment of Golgi apparatus localization establishment of Golgi body localization establishment of Golgi localisation biological_process GO:0051683 establishment of Golgi localization The directed movement of the Golgi to a specific location. GOC:ai establishment of Golgi localisation GOC:mah Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. GO:0009613 GO:0042828 biological_process GO:0051707 response to other organism Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. GOC:ai Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process GO:0051716 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. GOC:bf GOC:jl Any process that modulates the rate or extent of progression through the cell cycle. GO:0000074 GO:0007050 GO:0071156 GO:0071157 GO:0071158 GO:0071850 cell cycle modulation cell cycle regulation control of cell cycle progression modulation of cell cycle progression regulation of cell cycle progression regulation of progression through cell cycle arrest of mitotic cell cycle progression cell cycle arrest mitotic cell cycle arrest negative regulation of cell cycle arrest positive regulation of cell cycle arrest regulation of cell cycle arrest biological_process cell cycle regulator tumor suppressor GO:0051726 regulation of cell cycle Any process that modulates the rate or extent of progression through the cell cycle. GOC:ai GOC:dph GOC:tb arrest of mitotic cell cycle progression GOC:mah Any process that activates or increases the frequency, rate or extent of cell division. up regulation of cell division up-regulation of cell division upregulation of cell division activation of cell division stimulation of cell division biological_process GO:0051781 positive regulation of cell division Any process that activates or increases the frequency, rate or extent of cell division. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of cell division. down regulation of cell division down-regulation of cell division downregulation of cell division inhibition of cell division biological_process GO:0051782 negative regulation of cell division Any process that stops, prevents, or reduces the frequency, rate or extent of cell division. GOC:ai Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. biological_process GO:0051783 regulation of nuclear division Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. down regulation of nuclear division down-regulation of nuclear division downregulation of nuclear division inhibition of nuclear division biological_process GO:0051784 negative regulation of nuclear division Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. up regulation of nuclear division up-regulation of nuclear division upregulation of nuclear division activation of nuclear division stimulation of nuclear division biological_process GO:0051785 positive regulation of nuclear division Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process in which a pigment granule is transported to, and/or maintained in, a specific location within the cell. pigment granule localisation biological_process GO:0051875 pigment granule localization Any process in which a pigment granule is transported to, and/or maintained in, a specific location within the cell. GOC:ai pigment granule localisation GOC:mah Any process that modulates the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. biological_process GO:0051890 regulation of cardioblast differentiation Any process that modulates the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. GOC:ai Any process that activates or increases the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. up regulation of cardioblast differentiation up-regulation of cardioblast differentiation upregulation of cardioblast differentiation activation of cardioblast differentiation stimulation of cardioblast differentiation biological_process GO:0051891 positive regulation of cardioblast differentiation Any process that activates or increases the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. down regulation of cardioblast differentiation down-regulation of cardioblast differentiation downregulation of cardioblast differentiation inhibition of cardioblast differentiation biological_process GO:0051892 negative regulation of cardioblast differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. GOC:ai The directed movement of pigment granules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. pigment granule translocation biological_process GO:0051904 pigment granule transport The directed movement of pigment granules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of a pigment granule to a specific location. establishment of pigment granule localisation biological_process GO:0051905 establishment of pigment granule localization The directed movement of a pigment granule to a specific location. GOC:ai establishment of pigment granule localisation GOC:mah Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. biological_process GO:0051930 regulation of sensory perception of pain Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. GOC:ai Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. biological_process GO:0051931 regulation of sensory perception Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. GOC:ai The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. biological_process GO:0051937 catecholamine transport The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:ai ISBN:0198506732 Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051952 regulation of amine transport Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of amine transport down-regulation of amine transport downregulation of amine transport inhibition of amine transport biological_process GO:0051953 negative regulation of amine transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of amine transport up-regulation of amine transport upregulation of amine transport activation of amine transport stimulation of amine transport biological_process GO:0051954 positive regulation of amine transport Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051955 regulation of amino acid transport Any process that modulates the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of amino acid transport down-regulation of amino acid transport downregulation of amino acid transport negative regulation of amino acid transmembrane transport inhibition of amino acid transport biological_process GO:0051956 negative regulation of amino acid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai negative regulation of amino acid transmembrane transport GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. positive regulation of amino acid transmembrane transport up regulation of amino acid transport up-regulation of amino acid transport upregulation of amino acid transport activation of amino acid transport stimulation of amino acid transport biological_process GO:0051957 positive regulation of amino acid transport Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai positive regulation of amino acid transmembrane transport GOC:mah Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. biological_process GO:0051960 regulation of nervous system development Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. down regulation of nervous system development down-regulation of nervous system development downregulation of nervous system development inhibition of nervous system development biological_process GO:0051961 negative regulation of nervous system development Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. up regulation of nervous system development up-regulation of nervous system development upregulation of nervous system development activation of nervous system development stimulation of nervous system development biological_process GO:0051962 positive regulation of nervous system development Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. regulation of synapse biogenesis regulation of synaptogenesis biological_process GO:0051963 regulation of synapse assembly Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. GOC:ai GOC:pr Any process that stops, prevents, or reduces the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. down regulation of synapse assembly down-regulation of synapse assembly downregulation of synapse assembly negative regulation of synapse biogenesis negative regulation of synaptogenesis inhibition of synapse assembly biological_process GO:0051964 negative regulation of synapse assembly Any process that stops, prevents, or reduces the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. GOC:ai GOC:pr Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. positive regulation of synapse biogenesis positive regulation of synaptogenesis up regulation of synapse assembly up-regulation of synapse assembly upregulation of synapse assembly activation of synapse assembly stimulation of synapse assembly biological_process GO:0051965 positive regulation of synapse assembly Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse. GOC:ai GOC:pr Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. regulation of conduction of nerve impulse biological_process GO:0051969 regulation of transmission of nerve impulse Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai regulation of conduction of nerve impulse GOC:dph Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. down regulation of transmission of nerve impulse down-regulation of transmission of nerve impulse downregulation of transmission of nerve impulse negative regulation of conduction of nerve impulse inhibition of transmission of nerve impulse biological_process GO:0051970 negative regulation of transmission of nerve impulse Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai negative regulation of conduction of nerve impulse GOC:dph Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. positive regulation of conduction of nerve impulse up regulation of transmission of nerve impulse up-regulation of transmission of nerve impulse upregulation of transmission of nerve impulse activation of transmission of nerve impulse stimulation of transmission of nerve impulse biological_process GO:0051971 positive regulation of transmission of nerve impulse Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai positive regulation of conduction of nerve impulse GOC:dph Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. biological_process GO:0051983 regulation of chromosome segregation Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. up regulation of chromosome segregation up-regulation of chromosome segregation upregulation of chromosome segregation activation of chromosome segregation stimulation of chromosome segregation biological_process GO:0051984 positive regulation of chromosome segregation Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. down regulation of chromosome segregation down-regulation of chromosome segregation downregulation of chromosome segregation inhibition of chromosome segregation biological_process GO:0051985 negative regulation of chromosome segregation Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate. GO:0048747 muscle fiber development muscle fibre development myofiber development myofibre development biological_process GO:0055001 muscle cell development The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate. CL:0000187 GOC:devbiol The process whose specific outcome is the progression of a striated muscle cell over time, from its formation to the mature structure. Striated muscle cells contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. biological_process GO:0055002 striated muscle cell development The process whose specific outcome is the progression of a striated muscle cell over time, from its formation to the mature structure. Striated muscle cells contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. CL:0000737 GOC:devbiol The process whose specific outcome is the progression of the cardiac myofibril over time, from its formation to the mature structure. A cardiac myofibril is a myofibril specific to cardiac muscle cells. cardiac myofibril development cardiac myofibril morphogenesis biological_process heart myofibril assembly GO:0055003 cardiac myofibril assembly The process whose specific outcome is the progression of the cardiac myofibril over time, from its formation to the mature structure. A cardiac myofibril is a myofibril specific to cardiac muscle cells. GOC:devbiol The process whose specific outcome is the progression of a cardiac cell over time, from its formation to the mature state. A cardiac cell is a cell that will form part of the cardiac organ of an individual. cardiocyte development biological_process heart cell development GO:0055006 cardiac cell development The process whose specific outcome is the progression of a cardiac cell over time, from its formation to the mature state. A cardiac cell is a cell that will form part of the cardiac organ of an individual. GOC:devbiol cardiocyte development GOC:dph The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. cardiomyocyte differentiation biological_process heart muscle cell differentiation GO:0055007 cardiac muscle cell differentiation The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. GOC:devbiol GOC:mtg_heart The process in which the anatomical structures of cardiac muscle tissue are generated and organized. myocardium morphogenesis heart muscle morphogenesis biological_process GO:0055008 cardiac muscle tissue morphogenesis The process in which the anatomical structures of cardiac muscle tissue are generated and organized. GOC:devbiol myocardium morphogenesis GOC:mtg_heart The process in which the anatomical structure of cardiac atrium muscle is generated and organized. atrial heart muscle morphogenesis atrial myocardium morphogenesis cardiac atrium muscle morphogenesis biological_process GO:0055009 atrial cardiac muscle tissue morphogenesis The process in which the anatomical structure of cardiac atrium muscle is generated and organized. GOC:devbiol atrial myocardium morphogenesis GOC:mtg_heart The process in which the anatomical structures of cardiac ventricle muscle is generated and organized. cardiac ventricle muscle morphogenesis ventricular heart muscle morphogenesis biological_process GO:0055010 ventricular cardiac muscle tissue morphogenesis The process in which the anatomical structures of cardiac ventricle muscle is generated and organized. GOC:devbiol The process whose specific outcome is the progression of a cardiac muscle cell over time, from its formation to the mature state. GO:0048739 cardiac muscle fiber development cardiac muscle fibre development cardiomyocyte cell development heart muscle cell development biological_process heart muscle fiber development GO:0055013 cardiac muscle cell development The process whose specific outcome is the progression of a cardiac muscle cell over time, from its formation to the mature state. GOC:devbiol GOC:mtg_heart cardiomyocyte cell development GOC:mtg_muscle The increase in size or mass of a cardiac muscle, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. heart muscle growth biological_process GO:0055017 cardiac muscle tissue growth The increase in size or mass of a cardiac muscle, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. GOC:devbiol Any process that modulates the frequency, rate or extent of cardiac muscle fiber development. regulation of cardiac muscle fibre development regulation of heart muscle fiber development biological_process GO:0055018 regulation of cardiac muscle fiber development Any process that modulates the frequency, rate or extent of cardiac muscle fiber development. GOC:vk Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle fiber development. down regulation of cardiac muscle fiber development down-regulation of cardiac muscle fiber development downregulation of cardiac muscle fiber development negative regulation of cardiac muscle fibre development inhibition of cardiac muscle fiber development biological_process negative regulation of heart muscle fiber development GO:0055019 negative regulation of cardiac muscle fiber development Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle fiber development. GOC:vk Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle fiber development. positive regulation of cardiac muscle fibre development positive regulation of heart muscle fiber development up regulation of cardiac muscle fiber development up-regulation of cardiac muscle fiber development upregulation of cardiac muscle fiber development activation of cardiac muscle fiber development stimulation of cardiac muscle fiber development biological_process GO:0055020 positive regulation of cardiac muscle fiber development Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle fiber development. GOC:vk Any process that modulates the frequency, rate or extent of cardiac muscle growth. biological_process GO:0055021 regulation of cardiac muscle tissue growth Any process that modulates the frequency, rate or extent of cardiac muscle growth. GOC:vk Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle growth. down regulation of cardiac muscle growth down-regulation of cardiac muscle growth downregulation of cardiac muscle growth inhibition of cardiac muscle growth biological_process negative regulation of heart muscle growth GO:0055022 negative regulation of cardiac muscle tissue growth Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle growth. GOC:vk Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle growth. positive regulation of heart muscle growth up regulation of cardiac muscle growth up-regulation of cardiac muscle growth upregulation of cardiac muscle growth activation of cardiac muscle growth stimulation of cardiac muscle growth biological_process GO:0055023 positive regulation of cardiac muscle tissue growth Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle growth. GOC:vk Any process that modulates the frequency, rate or extent of cardiac muscle tissue development. regulation of heart muscle development biological_process GO:0055024 regulation of cardiac muscle tissue development Any process that modulates the frequency, rate or extent of cardiac muscle tissue development. GOC:vk Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle tissue development. positive regulation of heart muscle development up regulation of cardiac muscle development up-regulation of cardiac muscle development upregulation of cardiac muscle development activation of cardiac muscle development stimulation of cardiac muscle development biological_process GO:0055025 positive regulation of cardiac muscle tissue development Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle tissue development. GOC:vk Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle tissue development. down regulation of cardiac muscle development down-regulation of cardiac muscle development downregulation of cardiac muscle development negative regulation of heart muscle development inhibition of cardiac muscle development biological_process GO:0055026 negative regulation of cardiac muscle tissue development Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle tissue development. GOC:vk The process resulting in the physical partitioning and separation of a neuroblast into daughter cells. A neuroblast is any cell that will divide and give rise to a neuron. neuroblast cell division biological_process GO:0055057 neuroblast division The process resulting in the physical partitioning and separation of a neuroblast into daughter cells. A neuroblast is any cell that will divide and give rise to a neuron. PMID:11163136 PMID:11250167 The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials. biological_process GO:0055059 asymmetric neuroblast division The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials. GOC:dph The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. tb 2015-10-21T13:22:47Z GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process GO:0055085 Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. transmembrane transport The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GOC:dph GOC:jid The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide. nucleobase, nucleoside and nucleotide metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process GO:0055086 nucleobase-containing small molecule metabolic process The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide. GOC:vw The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bounded particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex. biological_process GO:0055107 Golgi to secretory granule transport The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bounded particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex. GOC:curators The directed movement of proteins from the Golgi to a transport vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis. biological_process GO:0055108 Golgi to transport vesicle transport The directed movement of proteins from the Golgi to a transport vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis. GOC:jid Any process that modulates the frequency, rate or extent of cardiac muscle contraction. biological_process GO:0055117 regulation of cardiac muscle contraction Any process that modulates the frequency, rate or extent of cardiac muscle contraction. GOC:ecd Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction. biological_process GO:0055118 negative regulation of cardiac muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction. GOC:ecd The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0055123 digestive system development The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:jid The biological process whose specific outcome is the progression of the roof of the mouth from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The roof of the mouth is the partition that separates the nasal and oral cavities. palatum development biological_process GO:0060021 roof of mouth development The biological process whose specific outcome is the progression of the roof of the mouth from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The roof of the mouth is the partition that separates the nasal and oral cavities. GOC:dph ISBN:0721662544 palatum development ISBN:0721662544 The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear. biological_process GO:0060037 pharyngeal system development The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear. GOC:dph The expansion of a cardiac muscle cell population by cell division. cardiac myocyte proliferation heart muscle cell proliferation biological_process cardiomyocyte proliferation GO:0060038 cardiac muscle cell proliferation The expansion of a cardiac muscle cell population by cell division. GOC:dph GOC:rph PMID:11161571 cardiomyocyte proliferation GOC:dph PMID:10074473 The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery. biological_process GO:0060039 pericardium development The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery. GOC:dph GOC:rph PMID:15138308 PMID:16376438 The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. GO:0002073 retina development in camera-style eye biological_process retinal development GO:0060041 retina development in camera-type eye The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. GOC:bf GOC:dph ISBN:0815340729 retinal development GOC:dph GOC:tb The process in which the anatomical structure of the retina is generated and organized. retina morphogenesis in camera-style eye retinogenesis biological_process GO:0060042 retina morphogenesis in camera-type eye The process in which the anatomical structure of the retina is generated and organized. GOC:bf GOC:dph GOC:mtg_sensu Any process that modulates the frequency, rate or extent of cardiac muscle cell proliferation. regulation of heart muscle cell proliferation biological_process regulation of cardiomyocyte proliferation GO:0060043 regulation of cardiac muscle cell proliferation Any process that modulates the frequency, rate or extent of cardiac muscle cell proliferation. GOC:dph GOC:rph regulation of cardiomyocyte proliferation GOC:dph Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation. negative regulation of heart muscle cell proliferation biological_process GO:0060044 negative regulation of cardiac muscle cell proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation. GOC:dph GOC:rph Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation. biological_process positive regulation of heart muscle cell proliferation GO:0060045 positive regulation of cardiac muscle cell proliferation Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation. GOC:dph GOC:rph The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. heart beating biological_process cardiac contraction hemolymph circulation GO:0060047 heart contraction The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. GOC:dph Muscle contraction of cardiac muscle tissue. heart muscle contraction biological_process GO:0060048 cardiac muscle contraction Muscle contraction of cardiac muscle tissue. GOC:dph The regulated release of serotonin by a cell, in which released serotonin acts as a neurotransmitter. biological_process serotonin release, neurotransmission GO:0060096 serotonin secretion, neurotransmission The regulated release of serotonin by a cell, in which released serotonin acts as a neurotransmitter. GOC:dph serotonin release, neurotransmission GOC:tb Any process that modulates the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. biological_process GO:0060142 regulation of syncytium formation by plasma membrane fusion Any process that modulates the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. GOC:dph Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. biological_process GO:0060143 positive regulation of syncytium formation by plasma membrane fusion Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. GOC:dph The portion of the plasma membrane surrounding a cilium. GO:0020017 cilial membrane cilium membrane flagellar membrane flagellum membrane cellular_component GO:0060170 Note that cilia and eukaryotic flagella are deemed to be equivalent. ciliary membrane The portion of the plasma membrane surrounding a cilium. GOC:cilia GOC:dph GOC:rph The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin. Wikipedia:Limb_development paired limb/fin development limb bud development biological_process GO:0060173 limb development The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin. GOC:dgh GOC:dph PMID:11487378 limb bud development GOC:dph Formation of the endocardium of the heart. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. biological_process GO:0060214 endocardium formation Formation of the endocardium of the heart. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. GOC:bf GOC:dph PMID:17722983 The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. haematopoietic stem cell differentiation haemopoietic stem cell differentiation hemopoietic stem cell differentiation biological_process GO:0060218 hematopoietic stem cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. GOC:BHF GOC:bf GOC:dph GOC:rl PMID:15378083 The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell in a camera-type eye. biological_process GO:0060219 camera-type eye photoreceptor cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell in a camera-type eye. GOC:ascb_2009 GOC:dph GOC:tb The process in which a relatively unspecialized cell acquires the specialized features of a retinal rod cell. biological_process GO:0060221 retinal rod cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a retinal rod cell. GOC:dph A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell. epithelial cell differentiation from mesenchymal cell mesenchymal-epithelial transition biological_process GO:0060231 mesenchymal to epithelial transition A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell. GOC:ascb_2009 GOC:dph GOC:tb epithelial cell differentiation from mesenchymal cell GOC:BHF GOC:dph GOC:rl mesenchymal-epithelial transition GOC:dph Any process that modulates the frequency, rate or extent of glial cell proliferation. biological_process GO:0060251 regulation of glial cell proliferation Any process that modulates the frequency, rate or extent of glial cell proliferation. GOC:dph GOC:tb Any process that activates or increases the rate or extent of glial cell proliferation. biological_process GO:0060252 positive regulation of glial cell proliferation Any process that activates or increases the rate or extent of glial cell proliferation. GOC:dph GOC:sl GOC:tb Any process that stops or decreases the rate or extent of glial cell proliferation. biological_process GO:0060253 negative regulation of glial cell proliferation Any process that stops or decreases the rate or extent of glial cell proliferation. GOC:dph GOC:sl GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0060255 regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GO:0042384 Reactome:R-HSA-5617833.2 ciliogenesis cilium formation microtubule-based flagellum assembly biological_process cilium biogenesis cilium morphogenesis cilium organization GO:0060271 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium assembly The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:BHF GOC:cilia GOC:dph GOC:kmv GOC:pr GOC:vw ISBN:0198506732 PMID:13978319 PMID:27350441 Reactome:R-HSA-5617833.2 cilium biogenesis GOC:mah cilium organization GOC:dph Any process that modulates the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. biological_process GO:0060281 regulation of oocyte development Any process that modulates the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. GOC:dph GOC:tb PMID:2394318 Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. biological_process GO:0060282 positive regulation of oocyte development Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. GOC:dph GOC:tb Any process that decreases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. biological_process GO:0060283 negative regulation of oocyte development Any process that decreases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0060284 regulation of cell development Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. regulation of sarcomere organisation biological_process GO:0060297 regulation of sarcomere organization Any process that modulates the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. GOC:BHF GOC:dph GOC:tb regulation of sarcomere organisation GOC:mah Any process that increases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. positive regulation of sarcomere organisation biological_process GO:0060298 positive regulation of sarcomere organization Any process that increases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. GOC:BHF GOC:dph GOC:tb positive regulation of sarcomere organisation GOC:mah Any process that decreases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. negative regulation of sarcomere organisation biological_process GO:0060299 negative regulation of sarcomere organization Any process that decreases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. GOC:BHF GOC:dph GOC:tb negative regulation of sarcomere organisation GOC:mah The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body. biological_process GO:0060322 head development The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body. GOC:dph The process in which the anatomical structures of the head are generated and organized. The head is the anterior-most division of the body. biological_process GO:0060323 head morphogenesis The process in which the anatomical structures of the head are generated and organized. The head is the anterior-most division of the body. GOC:dph The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head. biological_process GO:0060324 face development The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head. GOC:dph The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head. biological_process GO:0060325 face morphogenesis The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head. GOC:dph Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. regulation of cellular localisation biological_process GO:0060341 regulation of cellular localization Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. GOC:dph GOC:tb regulation of cellular localisation GOC:mah The process of creating a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue. trabeculation biological_process trabecula biogenesis GO:0060343 trabecula formation The process of creating a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue. GOC:dph trabeculation GOC:dph trabecula biogenesis GOC:dph The process of creating a trabecula in the liver. A trabecula is a tissue element in the form of a small beam, strut or rod. liver trabeculation biological_process liver trabecula biogenesis GO:0060344 liver trabecula formation The process of creating a trabecula in the liver. A trabecula is a tissue element in the form of a small beam, strut or rod. GOC:dph liver trabeculation GOC:dph The process of creating a trabecula in the spleen. A trabecula is a tissue element in the form of a small beam, strut or rod. spleen trabeculation biological_process spleen trabecula biogenesis GO:0060345 spleen trabecula formation The process of creating a trabecula in the spleen. A trabecula is a tissue element in the form of a small beam, strut or rod. GOC:dph spleen trabeculation GOC:dph spleen trabecula biogenesis GOC:dph The process of creating a trabecula in the heart. A trabecula is a tissue element in the form of a small beam, strut or rod. cardiac trabecula formation cardiac trabeculation heart trabeculation biological_process heart trabecula biogenesis GO:0060347 heart trabecula formation The process of creating a trabecula in the heart. A trabecula is a tissue element in the form of a small beam, strut or rod. GOC:dph cardiac trabecula formation GOC:dph cardiac trabeculation GOC:dph heart trabeculation GOC:dph heart trabecula biogenesis GOC:dph The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. biological_process GO:0060348 bone development The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. GOC:dph The process in which bones are generated and organized. biological_process GO:0060349 bone morphogenesis The process in which bones are generated and organized. GOC:dph The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone. biological_process GO:0060350 endochondral bone morphogenesis The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone. GOC:dph PMID:11680679 The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones. biological_process GO:0060351 cartilage development involved in endochondral bone morphogenesis The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones. GOC:dph Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium stimulus. GO:1903717 response to ammonia biological_process GO:0060359 response to ammonium ion Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium stimulus. GOC:TermGenie GO_REF:0000071 PMID:23509267 The process in which a relatively unspecialized cell acquires specialized features of a cardiac myoblast. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life. myocardial precursor cell differentiation biological_process cardiac myoblast differentiation GO:0060379 cardiac muscle cell myoblast differentiation The process in which a relatively unspecialized cell acquires specialized features of a cardiac myoblast. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life. GOC:dph GOC:tb myocardial precursor cell differentiation GOC:mtg_heart cardiac myoblast differentiation GOC:dph GOC:tb The removal of tubulin heterodimers from one or both ends of an axonemal microtubule. An axonemal microtubule is a microtubule in the axoneme of a cilium or flagellum; an axoneme contains nine modified doublet microtubules surrounding a pair of single microtubules. biological_process GO:0060404 axonemal microtubule depolymerization The removal of tubulin heterodimers from one or both ends of an axonemal microtubule. An axonemal microtubule is a microtubule in the axoneme of a cilium or flagellum; an axoneme contains nine modified doublet microtubules surrounding a pair of single microtubules. GOC:cilia GOC:dph GOC:krc GOC:tb Any process that modulates the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. biological_process GO:0060408 regulation of acetylcholine metabolic process Any process that modulates the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. biological_process GO:0060409 positive regulation of acetylcholine metabolic process Any process that increases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. biological_process GO:0060410 negative regulation of acetylcholine metabolic process Any process that decreases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues. GOC:dph GOC:tb The process in which the anatomical structure of a cardiac septum is generated and organized. A cardiac septum is a partition that separates parts of the heart. GO:0003280 heart septum morphogenesis biological_process GO:0060411 cardiac septum morphogenesis The process in which the anatomical structure of a cardiac septum is generated and organized. A cardiac septum is a partition that separates parts of the heart. GOC:dph GOC:mtg_heart The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another. interventricular septum morphogenesis biological_process GO:0060412 ventricular septum morphogenesis The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another. GOC:dph interventricular septum morphogenesis GOC:dph The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another. GO:0003287 interatrial septum morphogenesis biological_process GO:0060413 atrial septum morphogenesis The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another. GOC:dph GOC:mtg_heart interatrial septum morphogenesis GOC:dph The process in which the structure of the smooth muscle tissue surrounding the aorta is generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body. biological_process GO:0060414 aorta smooth muscle tissue morphogenesis The process in which the structure of the smooth muscle tissue surrounding the aorta is generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body. GOC:bf GOC:dgh GOC:dph Wikipedia:Aorta The process in which the anatomical structures of muscle tissue are generated and organized. Muscle tissue consists of a set of cells that are part of an organ and carry out a contractive function. biological_process GO:0060415 muscle tissue morphogenesis The process in which the anatomical structures of muscle tissue are generated and organized. Muscle tissue consists of a set of cells that are part of an organ and carry out a contractive function. GOC:dph The increase in size or mass of the heart. biological_process GO:0060419 heart growth The increase in size or mass of the heart. GOC:dph GOC:tb Any process that modulates the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart. biological_process GO:0060420 regulation of heart growth Any process that modulates the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart. GOC:dph GOC:tb Any process that increases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart. biological_process GO:0060421 positive regulation of heart growth Any process that increases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart. GOC:BHF GOC:dph GOC:tb The process in which the anatomical structures of the lung are generated and organized. biological_process GO:0060425 lung morphogenesis The process in which the anatomical structures of the lung are generated and organized. GOC:dph The biological process whose specific outcome is the progression of a lung vasculature from an initial condition to its mature state. This process begins with the formation of the lung vasculature and ends with the mature structure. The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs. pulmonary vasculature development biological_process GO:0060426 lung vasculature development The biological process whose specific outcome is the progression of a lung vasculature from an initial condition to its mature state. This process begins with the formation of the lung vasculature and ends with the mature structure. The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs. GOC:dph GOC:mtg_lung pulmonary vasculature development GOC:dph GOC:mtg_lung The biological process whose specific outcome is the progression of lung connective tissue from an initial condition to its mature state. This process begins with the formation of lung connective tissue and ends with the mature structure. The lung connective tissue is a material made up of fibers forming a framework and support structure for the lungs. pulmonary connective tissue development biological_process GO:0060427 lung connective tissue development The biological process whose specific outcome is the progression of lung connective tissue from an initial condition to its mature state. This process begins with the formation of lung connective tissue and ends with the mature structure. The lung connective tissue is a material made up of fibers forming a framework and support structure for the lungs. GOC:dph GOC:mtg_lung The biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung. pulmonary epithelium development biological_process GO:0060428 lung epithelium development The biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung. GOC:dph GOC:mtg_lung pulmonary epithelium development GOC:dph GOC:mtg_lung The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. biological_process GO:0060429 epithelium development The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. GOC:dph GOC:mtg_lung The morphogenetic process in which the foregut region specified to become the lung forms the initial left and right buds. lung formation biological_process GO:0060431 primary lung bud formation The morphogenetic process in which the foregut region specified to become the lung forms the initial left and right buds. GOC:dph GOC:mtg_lung lung formation GOC:dph The increase in size or mass of a lung. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. biological_process GO:0060437 lung growth The increase in size or mass of a lung. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax. GOC:dph The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches. biological_process GO:0060438 trachea development The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches. GOC:dph The process in which a trachea is generated and organized. The trachea is the portion of the airway that attaches to the bronchi as it branches. biological_process GO:0060439 trachea morphogenesis The process in which a trachea is generated and organized. The trachea is the portion of the airway that attaches to the bronchi as it branches. GOC:dph The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches. biological_process GO:0060440 trachea formation The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches. GOC:dph The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. lung branching morphogenesis biological_process GO:0060441 epithelial tube branching involved in lung morphogenesis The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. GOC:dph GOC:mtg_lung lung branching morphogenesis GOC:dph Any process that increases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. biological_process GO:0060450 positive regulation of hindgut contraction Any process that increases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. biological_process GO:0060451 negative regulation of hindgut contraction Any process that decreases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cardiac muscle contraction. biological_process GO:0060452 positive regulation of cardiac muscle contraction Any process that increases the frequency, rate or extent of cardiac muscle contraction. GOC:dph GOC:tb Any process that modulates the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. biological_process GO:0060453 regulation of gastric acid secretion Any process that modulates the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. GOC:dph GOC:tb Any process that increases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. biological_process GO:0060454 positive regulation of gastric acid secretion Any process that increases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. GOC:dph GOC:tb Any process that decreases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. biological_process GO:0060455 negative regulation of gastric acid secretion Any process that decreases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0060456 positive regulation of digestive system process Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0060457 negative regulation of digestive system process Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:dph GOC:tb The biological process whose specific outcome is the progression of a right lung from an initial condition to its mature state. This process begins with the formation of the right lung and ends with the mature structure. The right lung is the lung which is on the right side of the anterior posterior axis looking from a dorsal to ventral aspect. right pulmonary development biological_process GO:0060458 right lung development The biological process whose specific outcome is the progression of a right lung from an initial condition to its mature state. This process begins with the formation of the right lung and ends with the mature structure. The right lung is the lung which is on the right side of the anterior posterior axis looking from a dorsal to ventral aspect. GOC:dph GOC:mtg_lung right pulmonary development GOC:dph GOC:mtg_lung The biological process whose specific outcome is the progression of a left lung from an initial condition to its mature state. This process begins with the formation of the left lung and ends with the mature structure. The left lung is the lung which is on the left side of the anterior posterior axis looking from a dorsal to ventral aspect. left pulmonary development biological_process GO:0060459 left lung development The biological process whose specific outcome is the progression of a left lung from an initial condition to its mature state. This process begins with the formation of the left lung and ends with the mature structure. The left lung is the lung which is on the left side of the anterior posterior axis looking from a dorsal to ventral aspect. GOC:dph GOC:mtg_lung left pulmonary development GOC:dph The process in which anatomical structures of the left lung are generated and organized. biological_process GO:0060460 left lung morphogenesis The process in which anatomical structures of the left lung are generated and organized. GOC:dph The process in which anatomical structures of the right lung are generated and organized. biological_process GO:0060461 right lung morphogenesis The process in which anatomical structures of the right lung are generated and organized. GOC:dph GOC:mtg_lung The biological process whose specific outcome is the progression of a lung lobe from an initial condition to its mature state. This process begins with the formation of a lung lobe by branching morphogenesis and ends with the mature structure. A lung lobe is one of the rounded projections that compose the lung. biological_process GO:0060462 lung lobe development The biological process whose specific outcome is the progression of a lung lobe from an initial condition to its mature state. This process begins with the formation of a lung lobe by branching morphogenesis and ends with the mature structure. A lung lobe is one of the rounded projections that compose the lung. GOC:dph The process in which the anatomical structures of a lung lobe are generated and organized. A lung lobe is a projection that extends from the lung. biological_process GO:0060463 lung lobe morphogenesis The process in which the anatomical structures of a lung lobe are generated and organized. A lung lobe is a projection that extends from the lung. GOC:dph The developmental process pertaining to the initial formation of a lung lobe from unspecified parts. This process begins with the specific processes that contribute to the appearance of the lobe and ends when the structural rudiment is recognizable. A lung lobe is a projection that extends from the lung. biological_process GO:0060464 lung lobe formation The developmental process pertaining to the initial formation of a lung lobe from unspecified parts. This process begins with the specific processes that contribute to the appearance of the lobe and ends when the structural rudiment is recognizable. A lung lobe is a projection that extends from the lung. GOC:dph The biological process whose specific outcome is the progression of a pharynx from an initial condition to its mature state. The pharynx is the part of the digestive system immediately posterior to the mouth. biological_process pharyngeal development GO:0060465 pharynx development The biological process whose specific outcome is the progression of a pharynx from an initial condition to its mature state. The pharynx is the part of the digestive system immediately posterior to the mouth. GOC:dph GOC:rk Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). biological_process GO:0060467 negative regulation of fertilization Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:dph The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features of a mature cell found in the lung. Differentiation includes the processes involved in commitment of a cell to a specific fate. pulmonary cell differentiation biological_process GO:0060479 lung cell differentiation The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features of a mature cell found in the lung. Differentiation includes the processes involved in commitment of a cell to a specific fate. GOC:dph GOC:mtg_lung pulmonary cell differentiation GOC:dph The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells. mesenchymal development biological_process GO:0060485 mesenchyme development The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells. GOC:dph mesenchymal development GOC:dph The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell that contributes to the epithelium of the lung. biological_process pulmonary epithelial cell differentiation GO:0060487 lung epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell that contributes to the epithelium of the lung. GOC:dph pulmonary epithelial cell differentiation GOC:dph Any process that modulates the rate, frequency, or extent of cell projection assembly. biological_process regulation of cell projection formation GO:0060491 regulation of cell projection assembly Any process that modulates the rate, frequency, or extent of cell projection assembly. GOC:dph GOC:tb regulation of cell projection formation GOC:dph GOC:tb Any process that mediates the transfer of information from one cell to another and contributes to the progression of the lung, from its initial state to the mature structure. cell-cell signalling involved in lung development biological_process GO:0060495 cell-cell signaling involved in lung development Any process that mediates the transfer of information from one cell to another and contributes to the progression of the lung, from its initial state to the mature structure. GOC:dph GOC:mtg_lung cell-cell signalling involved in lung development GOC:mah Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell and contributes to the development of the lung. mesenchymal-epithelial cell signalling involved in lung development biological_process GO:0060496 mesenchymal-epithelial cell signaling involved in lung development Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell and contributes to the development of the lung. GOC:dph GOC:mtg_lung mesenchymal-epithelial cell signalling involved in lung development GOC:mah Any process that mediates the transfer of information between a mesenchymal cell and an endodermal cell. mesenchymal-endodermal cell signalling biological_process GO:0060497 mesenchymal-endodermal cell signaling Any process that mediates the transfer of information between a mesenchymal cell and an endodermal cell. GOC:dph mesenchymal-endodermal cell signalling GOC:mah Any process that increases the rate or frequency of epithelial cell proliferation that results in the lung attaining its shape. biological_process GO:0060501 positive regulation of epithelial cell proliferation involved in lung morphogenesis Any process that increases the rate or frequency of epithelial cell proliferation that results in the lung attaining its shape. GOC:dph The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the lung. biological_process GO:0060502 epithelial cell proliferation involved in lung morphogenesis The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the lung. GOC:dph The process in which the anatomical structures of cartilage are generated and organized. dph 2009-04-10T09:13:27Z biological_process GO:0060536 cartilage morphogenesis The process in which the anatomical structures of cartilage are generated and organized. GOC:dph The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers. dph 2009-04-10T08:05:37Z biological_process GO:0060537 muscle tissue development The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers. GOC:dph The progression of a skeletal muscle organ over time from its initial formation to its mature state. A skeletal muscle organ includes the skeletal muscle tissue and its associated connective tissue. dph 2009-04-10T08:25:12Z biological_process GO:0060538 skeletal muscle organ development The progression of a skeletal muscle organ over time from its initial formation to its mature state. A skeletal muscle organ includes the skeletal muscle tissue and its associated connective tissue. GOC:dph The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs. dph 2009-04-10T08:44:56Z biological_process GO:0060539 diaphragm development The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs. GOC:dph The process in which the anatomical structures of the diaphragm are generated and organized. dph 2009-04-10T08:47:51Z biological_process GO:0060540 diaphragm morphogenesis The process in which the anatomical structures of the diaphragm are generated and organized. GOC:dph The progression of the respiratory system over time from its formation to its mature structure. The respiratory system carries out respiratory gaseous exchange. dph 2009-04-10T08:55:42Z biological_process GO:0060541 respiratory system development The progression of the respiratory system over time from its formation to its mature structure. The respiratory system carries out respiratory gaseous exchange. GOC:dph The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape. dph 2009-04-28T08:42:53Z differential growth biological_process GO:0060560 developmental growth involved in morphogenesis The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape. GOC:dph differential growth GOC:dph Any apoptotic process that contributes to the shaping of an anatomical structure. dph 2009-04-28T09:17:27Z apoptosis involved in morphogenesis biological_process apoptosis involved in development morphogenetic apoptosis GO:0060561 apoptotic process involved in morphogenesis Any apoptotic process that contributes to the shaping of an anatomical structure. GOC:dph GOC:mtg_apoptosis morphogenetic apoptosis GOC:dph The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. dph 2009-04-28T09:33:36Z biological_process GO:0060562 epithelial tube morphogenesis The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GOC:dph The process in which epiblast cells acquire specialized features of neuroepithelial cells. dph 2009-04-29T01:50:05Z biological_process GO:0060563 neuroepithelial cell differentiation The process in which epiblast cells acquire specialized features of neuroepithelial cells. GOC:dph GOC:tb The morphogenetic process in which an epithelial sheet bends along a linear axis. dph 2009-04-30T09:27:17Z epithelial folding biological_process folding of an epithelial sheet GO:0060571 morphogenesis of an epithelial fold The morphogenetic process in which an epithelial sheet bends along a linear axis. GOC:dph epithelial folding GOC:dph folding of an epithelial sheet GOC:dph The morphogenetic process in which a bud forms from an epithelial sheet. A bud is a protrusion that forms form the sheet by localized folding. dph 2009-04-30T09:38:35Z biological_process GO:0060572 morphogenesis of an epithelial bud The morphogenetic process in which a bud forms from an epithelial sheet. A bud is a protrusion that forms form the sheet by localized folding. GOC:dph The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell of the intestine to attain its fully functional state. A columnar/cuboidal epithelial cell of the intestine mature as they migrate from the intestinal crypt to the villus. dph 2009-05-06T08:10:41Z biological_process GO:0060574 intestinal epithelial cell maturation The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell of the intestine to attain its fully functional state. A columnar/cuboidal epithelial cell of the intestine mature as they migrate from the intestinal crypt to the villus. GOC:dph PMID:18824147 The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell of the intestine. dph 2009-05-06T08:17:56Z biological_process GO:0060575 intestinal epithelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell of the intestine. GOC:dph The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure. dph 2009-05-06T08:20:24Z biological_process GO:0060576 intestinal epithelial cell development The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure. GOC:dph The process in which the anatomical structure of the pulmonary venous blood vessels are generated and organized. Pulmonary veins are blood vessels that transport blood from the lungs to the heart. dph 2009-05-06T08:44:04Z biological_process pulmonary venous blood vessel morphogenesis GO:0060577 pulmonary vein morphogenesis The process in which the anatomical structure of the pulmonary venous blood vessels are generated and organized. Pulmonary veins are blood vessels that transport blood from the lungs to the heart. GOC:dph pulmonary venous blood vessel morphogenesis GOC:dph The process in which the anatomical structure of superior vena cava generated and organized. The superior vena cava is a blood vessel that transports blood from the upper body to the heart. dph 2009-05-06T08:47:21Z biological_process GO:0060578 superior vena cava morphogenesis The process in which the anatomical structure of superior vena cava generated and organized. The superior vena cava is a blood vessel that transports blood from the upper body to the heart. GOC:dph The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells within a field of cells that will exhibit a certain pattern of differentiation. Positional information is established through protein signals that emanate from a localized source within a developmental field resulting in specification of a cell type. Those signals are then interpreted in a cell-autonomous manner resulting in the determination of the cell type. dph 2009-05-07T12:40:55Z biological_process GO:0060581 cell fate commitment involved in pattern specification The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells within a field of cells that will exhibit a certain pattern of differentiation. Positional information is established through protein signals that emanate from a localized source within a developmental field resulting in specification of a cell type. Those signals are then interpreted in a cell-autonomous manner resulting in the determination of the cell type. GOC:dph The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes. dph 2009-05-11T07:47:36Z biological_process chondrocyte progenitor cell differentiation GO:0060591 chondroblast differentiation The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes. GOC:dph chondrocyte progenitor cell differentiation GOC:dph The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat. dph 2009-05-15T12:36:28Z biological_process adipogenesis GO:0060612 adipose tissue development The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat. GOC:dph adipogenesis GOC:mah GOC:sl Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. dph 2009-05-18T02:12:13Z biological_process GO:0060623 regulation of chromosome condensation Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. dph 2009-05-18T02:29:43Z biological_process GO:0060627 regulation of vesicle-mediated transport Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins. dph 2009-05-18T03:07:02Z biological_process GO:0060632 regulation of microtubule-based movement Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins. GOC:dph GOC:tb Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted. dph 2009-05-19T03:59:05Z mesenchymal-epithelial cell signalling biological_process GO:0060638 mesenchymal-epithelial cell signaling Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted. GOC:dph mesenchymal-epithelial cell signalling GOC:mah Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell where it is interpreted. dph 2009-06-03T06:36:46Z epithelial-mesenchymal cell signalling biological_process GO:0060684 epithelial-mesenchymal cell signaling Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell where it is interpreted. GOC:dph epithelial-mesenchymal cell signalling GOC:mah Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized. dph 2009-06-05T12:41:44Z biological_process GO:0060688 regulation of morphogenesis of a branching structure Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized. GOC:dph The developmental process in which an ectodermal placode forms. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm. dph 2009-08-04T12:15:57Z biological_process GO:0060788 ectodermal placode formation The developmental process in which an ectodermal placode forms. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm. GOC:dph GOC:sdb_2009 GOC:tb The commitment of cells to specific cell fates of the endoderm, ectoderm, or mesoderm as a part of gastrulation. dph 2009-08-04T03:11:22Z biological_process GO:0060795 cell fate commitment involved in formation of primary germ layer The commitment of cells to specific cell fates of the endoderm, ectoderm, or mesoderm as a part of gastrulation. GOC:dph GOC:sdb_2009 GOC:tb The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell, a thin flattened cell that lines the inside surfaces of blood vessels. dph 2009-08-11T03:47:36Z biological_process GO:0060837 blood vessel endothelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell, a thin flattened cell that lines the inside surfaces of blood vessels. GOC:dph GOC:sdb_2009 GOC:tb The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed. dph 2009-08-12T10:10:51Z biological_process GO:0060840 artery development The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed. GOC:dph GOC:sdb_2009 GOC:tb The progression of the venous blood vessel over time from its initial formation to the mature structure. Venous blood vessels carry blood back to the heart after the capillary bed. dph 2009-08-12T10:14:07Z biological_process GO:0060841 venous blood vessel development The progression of the venous blood vessel over time from its initial formation to the mature structure. Venous blood vessels carry blood back to the heart after the capillary bed. GOC:dph GOC:sdb_2009 GOC:tb The process in which a relatively unspecialized endothelial cell acquires specialized features of an arterial endothelial cell, a thin flattened cell that lines the inside surfaces of arteries. dph 2009-08-12T10:41:34Z biological_process GO:0060842 arterial endothelial cell differentiation The process in which a relatively unspecialized endothelial cell acquires specialized features of an arterial endothelial cell, a thin flattened cell that lines the inside surfaces of arteries. GOC:dph GOC:sdb_2009 GOC:tb The process in which a relatively unspecialized endothelial cell acquires specialized features of a venous endothelial cell, a thin flattened cell that lines the inside surfaces of veins. dph 2009-08-12T10:43:40Z biological_process GO:0060843 venous endothelial cell differentiation The process in which a relatively unspecialized endothelial cell acquires specialized features of a venous endothelial cell, a thin flattened cell that lines the inside surfaces of veins. GOC:dph GOC:sdb_2009 GOC:tb The developmental process that results in the creation of defined areas or spaces within the neural plate to which cells respond and eventually are instructed to differentiate. dph 2009-08-13T02:06:27Z biological_process GO:0060896 neural plate pattern specification The developmental process that results in the creation of defined areas or spaces within the neural plate to which cells respond and eventually are instructed to differentiate. GOC:dph GOC:sdb_2009 GOC:tb The pattern specification process that results in the subdivision of an axis or axes of the neural plate in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment. dph 2009-08-13T02:09:04Z biological_process GO:0060897 neural plate regionalization The pattern specification process that results in the subdivision of an axis or axes of the neural plate in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment. GOC:dph GOC:sdb_2009 GOC:tb The developmental process pertaining to the initial formation of a camera-type eye from unspecified neurectoderm. This process begins with the differentiation of cells that form the optic field and ends when the optic cup has attained its shape. dph 2009-08-13T02:26:54Z biological_process GO:0060900 embryonic camera-type eye formation The developmental process pertaining to the initial formation of a camera-type eye from unspecified neurectoderm. This process begins with the differentiation of cells that form the optic field and ends when the optic cup has attained its shape. GOC:dph GOC:sdb_2009 GOC:tb The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable. dph 2009-09-17T09:02:13Z biological_process cardiogenesis GO:0060914 heart formation The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable. GOC:mtg_heart cardiogenesis GOC:mtg_heart The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell of the lung. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types. dph 2009-09-18T11:45:33Z biological_process GO:0060915 mesenchymal cell differentiation involved in lung development The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell of the lung. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types. GOC:dph The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population that contributes to the progression of the lung over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. dph 2009-09-18T11:50:17Z biological_process GO:0060916 mesenchymal cell proliferation involved in lung development The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population that contributes to the progression of the lung over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a pacemaker cell. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions. dph 2009-09-29T11:01:31Z pacemaker cell differentiation biological_process GO:0060920 cardiac pacemaker cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a pacemaker cell. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions. GOC:mtg_cardiac_conduct_nov11 GOC:mtg_heart The process in which a relatively unspecialized cell acquires specialized features of a sinoatrial (SA) node cell. SA node cells are pacemaker cells that are found in the sinoatrial node. dph 2009-09-29T11:03:30Z SA node cell differentiation SAN cell differentiation sinus node cell differentiation biological_process GO:0060921 sinoatrial node cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a sinoatrial (SA) node cell. SA node cells are pacemaker cells that are found in the sinoatrial node. GOC:mtg_heart SA node cell differentiation GOC:mtg_heart SAN cell differentiation GOC:BHF GOC:mtg_cardiac_conduct_nov11 sinus node cell differentiation GOC:BHF GOC:mtg_cardiac_conduct_nov11 The process in which a relatively unspecialized cell acquires specialized features of an atrioventricular (AV) node cell. AV node cells are pacemaker cells that are found in the atrioventricular node. dph 2009-09-29T11:07:06Z biological_process AV node cell differentiation GO:0060922 atrioventricular node cell differentiation The process in which a relatively unspecialized cell acquires specialized features of an atrioventricular (AV) node cell. AV node cells are pacemaker cells that are found in the atrioventricular node. GOC:mtg_heart AV node cell differentiation GOC:mtg_heart The process whose specific outcome is the progression of a pacemaker cell over time, from its formation to the mature state. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions. dph 2009-09-29T11:51:55Z pacemaker cell development biological_process GO:0060926 cardiac pacemaker cell development The process whose specific outcome is the progression of a pacemaker cell over time, from its formation to the mature state. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions. GOC:mtg_cardiac_conduct_nov11 GOC:mtg_heart The process whose specific outcome is the progression of an atrioventricular (AV) node cell over time, from its formation to the mature state. dph 2009-09-29T11:59:26Z AV node cell development biological_process GO:0060928 atrioventricular node cell development The process whose specific outcome is the progression of an atrioventricular (AV) node cell over time, from its formation to the mature state. GOC:mtg_heart AV node cell development GOC:mtg_heart The process whose specific outcome is the progression of a sinoatrial (SA) node cell over time, from its formation to the mature state. SA node cells are pacemaker cells that are found in the sinoatrial node. dph 2009-09-29T12:05:47Z SA node cell development SAN cell development sinus node cell development biological_process GO:0060931 sinoatrial node cell development The process whose specific outcome is the progression of a sinoatrial (SA) node cell over time, from its formation to the mature state. SA node cells are pacemaker cells that are found in the sinoatrial node. GOC:mtg_heart SA node cell development GOC:mtg_heart SAN cell development GOC:BHF GOC:mtg_cardiac_conduct_nov11 sinus node cell development GOC:BHF GOC:mtg_cardiac_conduct_nov11 The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the His-Purkinje system. These cells form the fibers regulate cardiac muscle contraction in the ventricles. dph 2009-09-29T01:10:32Z biological_process GO:0060932 His-Purkinje system cell differentiation The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the His-Purkinje system. These cells form the fibers regulate cardiac muscle contraction in the ventricles. GOC:mtg_heart The process whose specific outcome is the progression of a His-Purkinje cell over time, from its formation to the mature state. These cells form the fibers that regulate cardiac muscle contraction in the ventricles. dph 2009-09-29T01:15:02Z biological_process GO:0060933 His-Purkinje system cell development The process whose specific outcome is the progression of a His-Purkinje cell over time, from its formation to the mature state. These cells form the fibers that regulate cardiac muscle contraction in the ventricles. GOC:mtg_heart The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac fibroblast. A cardiac fibroblast is a connective tissue cell in the heart which secretes an extracellular matrix rich in collagen and other macromolecules. dph 2009-09-29T01:20:04Z biological_process GO:0060935 cardiac fibroblast cell differentiation The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac fibroblast. A cardiac fibroblast is a connective tissue cell in the heart which secretes an extracellular matrix rich in collagen and other macromolecules. GOC:mtg_heart The process whose specific outcome is the progression of a cardiac fibroblast over time, from its formation to the mature state. A cardiac fibroblast is a connective tissue cell of the heart which secretes an extracellular matrix rich in collagen and other macromolecules. dph 2009-09-29T01:23:03Z biological_process GO:0060936 cardiac fibroblast cell development The process whose specific outcome is the progression of a cardiac fibroblast over time, from its formation to the mature state. A cardiac fibroblast is a connective tissue cell of the heart which secretes an extracellular matrix rich in collagen and other macromolecules. GOC:mtg_heart The process in which a relatively unspecialized cell acquires specialized features of a neuron of the heart. dph 2009-09-29T02:45:33Z heart neuron differentiation biological_process GO:0060945 cardiac neuron differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuron of the heart. GOC:mtg_heart heart neuron differentiation GOC:mtg_heart The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell of the heart. Blood vessel endothelial cells are thin flattened cells that line the inside surfaces of blood vessels. dph 2009-09-29T02:48:55Z biological_process GO:0060946 cardiac blood vessel endothelial cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell of the heart. Blood vessel endothelial cells are thin flattened cells that line the inside surfaces of blood vessels. GOC:mtg_heart The process in which a relatively unspecialized cell acquires the specialized features of a glial cell of the heart. dph 2009-09-29T03:06:37Z biological_process GO:0060950 cardiac glial cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a glial cell of the heart. GOC:mtg_heart The process aimed at the progression of a cardiac glial cell over time, from its formation to the fully functional mature cell. dph 2009-09-29T03:09:24Z biological_process GO:0060952 cardiac glial cell development The process aimed at the progression of a cardiac glial cell over time, from its formation to the fully functional mature cell. GOC:mtg_heart The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers. dph 2009-09-29T03:20:39Z biological_process GO:0060956 endocardial cell differentiation The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers. GOC:mtg_heart The progression of an endocardial cell over time, from its formation to the mature cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. dph 2009-09-29T03:26:59Z biological_process GO:0060958 endocardial cell development The progression of an endocardial cell over time, from its formation to the mature cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. GOC:mtg_heart The process whose specific outcome is the progression of a cardiac neuron over time, from its formation to the mature state. dph 2009-09-30T10:14:56Z heart neuron development biological_process GO:0060959 cardiac neuron development The process whose specific outcome is the progression of a cardiac neuron over time, from its formation to the mature state. GOC:mtg_heart heart neuron development GOC:mtg_heart The orderly movement of a cell from one site to another that will contribute to the progression of the heart over time, from its initial formation, to the mature organ. dph 2009-10-06T10:53:49Z biological_process GO:0060973 cell migration involved in heart development The orderly movement of a cell from one site to another that will contribute to the progression of the heart over time, from its initial formation, to the mature organ. GOC:mtg_heart The orderly movement of a cell from one site to another that contribute to the formation of the heart. The initial heart structure is made up of mesoderm-derived heart progenitor cells and neural crest-derived cells. dph 2009-10-06T10:56:33Z biological_process GO:0060974 cell migration involved in heart formation The orderly movement of a cell from one site to another that contribute to the formation of the heart. The initial heart structure is made up of mesoderm-derived heart progenitor cells and neural crest-derived cells. GOC:mtg_heart The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure. dph 2009-10-06T12:15:23Z cardiac blood vessel development cardiac vasculature development coronary blood vessel development heart blood vessel development heart vasculature development biological_process GO:0060976 coronary vasculature development The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure. GOC:mtg_heart cardiac blood vessel development GOC:mtg_heart cardiac vasculature development GOC:mtg_heart coronary blood vessel development GOC:mtg_heart heart blood vessel development GOC:mtg_heart heart vasculature development GOC:mtg_heart The process in which the anatomical structures of blood vessels of the heart are generated and organized. The blood vessel is the vasculature carrying blood. dph 2009-10-06T12:28:23Z cardiac blood vessel morphogenesis cardiac vasculature morphogenesis coronary blood vessel morphogenesis heart blood vessel morphogenesis heart vasculature morphogenesis biological_process GO:0060977 coronary vasculature morphogenesis The process in which the anatomical structures of blood vessels of the heart are generated and organized. The blood vessel is the vasculature carrying blood. GOC:mtg_heart cardiac blood vessel morphogenesis GOC:mtg_heart cardiac vasculature morphogenesis GOC:mtg_heart coronary blood vessel morphogenesis GOC:mtg_heart heart blood vessel morphogenesis GOC:mtg_heart heart vasculature morphogenesis GOC:mtg_heart Blood vessel formation in the heart when new vessels emerge from the proliferation of pre-existing blood vessels. dph 2009-10-06T02:02:12Z angiogenesis involved in cardiac vascular morphogenesis angiogenesis involved in heart vascular morphogenesis coronary blood vessel angiogenesis coronary vasculature angiogenesis biological_process GO:0060978 angiogenesis involved in coronary vascular morphogenesis Blood vessel formation in the heart when new vessels emerge from the proliferation of pre-existing blood vessels. GOC:mtg_heart angiogenesis involved in cardiac vascular morphogenesis GOC:mtg_heart angiogenesis involved in heart vascular morphogenesis GOC:mtg_heart coronary blood vessel angiogenesis GOC:mtg_heart coronary vasculature angiogenesis GOC:mtg_heart The differentiation of endothelial cells from progenitor cells that contributes to blood vessel development in the heart, and the de novo formation of blood vessels and tubes. dph 2009-10-06T02:19:42Z coronary vasculogenesis vasculogenesis involved in coronary blood vessel morphogenesis biological_process GO:0060979 vasculogenesis involved in coronary vascular morphogenesis The differentiation of endothelial cells from progenitor cells that contributes to blood vessel development in the heart, and the de novo formation of blood vessels and tubes. GOC:mtg_heart coronary vasculogenesis GOC:mtg_heart vasculogenesis involved in coronary blood vessel morphogenesis GOC:mtg_heart The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form the blood vessels of the heart. dph 2009-10-06T02:33:06Z biological_process GO:0060980 cell migration involved in coronary vasculogenesis The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form the blood vessels of the heart. GOC:mtg_heart The orderly movement of a cell from one site to another that will contribute to the formation of new blood vessels in the heart from pre-existing blood vessels. dph 2009-10-06T02:49:12Z biological_process GO:0060981 cell migration involved in coronary angiogenesis The orderly movement of a cell from one site to another that will contribute to the formation of new blood vessels in the heart from pre-existing blood vessels. GOC:mtg_heart The regulated release of a hormone into the circulatory system. dph 2010-01-11T09:03:48Z biological_process GO:0060986 endocrine hormone secretion The regulated release of a hormone into the circulatory system. GOC:dph An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. dph 2010-01-22T09:09:10Z hepatobiliary system process biological_process GO:0061007 hepaticobiliary system process An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. GOC:dph hepatobiliary system process GOC:dph The progression of the hepaticobiliary system over time, from its formation to the mature structure. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. dph 2010-01-22T09:11:59Z hepatobiliary system development biological_process GO:0061008 hepaticobiliary system development The progression of the hepaticobiliary system over time, from its formation to the mature structure. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. GOC:dph hepatobiliary system development GOC:dph The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gallbladder. The common bile duct transports bile from the liver and gallbladder to the intestine. dph 2010-01-22T09:17:13Z EHBD development extrahepatic bile duct development CBD development bile duct development biological_process GO:0061009 common bile duct development The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gallbladder. The common bile duct transports bile from the liver and gallbladder to the intestine. PMID:20614624 EHBD development PMID:20614624 extrahepatic bile duct development PMID:20614624 CBD development PMID:20614624 bile duct development GOC:dph The progression of the gallbladder over time, from its initial formation to the mature structure. The gallbladder is a cavitated organ that stores bile. dph 2010-01-22T09:38:44Z biological_process GO:0061010 gallbladder development The progression of the gallbladder over time, from its initial formation to the mature structure. The gallbladder is a cavitated organ that stores bile. GOC:dph The progression of the hepatic duct over time, from its formation to the mature structure. The hepatic duct is the duct that leads from the liver to the common bile duct. dph 2010-01-22T09:44:39Z biological_process GO:0061011 hepatic duct development The progression of the hepatic duct over time, from its formation to the mature structure. The hepatic duct is the duct that leads from the liver to the common bile duct. GOC:dph PMID:20614624 The process in which a relatively unspecialized cell acquires specialized features of a hepatoblast. A hepatoblast is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into hepatocytes and cholangiocytes. dph 2010-02-02T09:08:03Z biological_process GO:0061017 hepatoblast differentiation The process in which a relatively unspecialized cell acquires specialized features of a hepatoblast. A hepatoblast is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into hepatocytes and cholangiocytes. GOC:dph PMID:15226394 A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. jl 2010-02-08T02:43:11Z GO:0016044 GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation biological_process membrane organization and biogenesis single-organism membrane organization GO:0061024 membrane organization A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GOC:dph GOC:tb membrane organisation GOC:mah membrane organization and biogenesis GOC:mah The membrane organization process that joins two lipid bilayers to form a single membrane. jl 2010-02-08T02:48:06Z GO:0006944 GO:0044801 Wikipedia:Lipid_bilayer_fusion cellular membrane fusion biological_process single-organism membrane fusion GO:0061025 membrane fusion The membrane organization process that joins two lipid bilayers to form a single membrane. GOC:dph GOC:tb The progression of the visceral serous pericardium from its formation to the mature structure. The visceral serous pericardium is the inner layer of the pericardium. dph 2010-02-09T09:52:49Z epicardium development biological_process GO:0061032 visceral serous pericardium development The progression of the visceral serous pericardium from its formation to the mature structure. The visceral serous pericardium is the inner layer of the pericardium. GOC:dph GOC:yaf epicardium development GOC:dph Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. dph 2010-02-09T03:41:35Z biological_process GO:0061035 regulation of cartilage development Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. GOC:dph Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. dph 2010-02-09T03:41:35Z biological_process GO:0061036 positive regulation of cartilage development Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. GOC:dph Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. dph 2010-02-09T03:41:35Z biological_process GO:0061037 negative regulation of cartilage development Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. GOC:dph The process in which a female gonad is generated and organized. dph 2010-02-22T11:29:28Z biological_process ovary morphogenesis GO:0061040 female gonad morphogenesis The process in which a female gonad is generated and organized. GOC:BHF GOC:dph ovary morphogenesis GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. dph 2010-02-25T10:41:38Z biological_process GO:0061046 regulation of branching involved in lung morphogenesis Any process that modulates the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. GOC:dph GOC:yaf Any process that increases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. dph 2010-02-25T10:50:01Z biological_process GO:0061047 positive regulation of branching involved in lung morphogenesis Any process that increases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. GOC:dph GOC:yaf Any process that decreases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. dph 2010-02-25T10:51:31Z biological_process GO:0061048 negative regulation of branching involved in lung morphogenesis Any process that decreases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units. GOC:dph GOC:yaf The growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state. dph 2010-02-25T12:56:07Z biological_process cardiac muscle cell hypertrophy cardiomyocyte growth heart muscle cell growth GO:0061049 cell growth involved in cardiac muscle cell development The growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state. GOC:dph cardiac muscle cell hypertrophy GOC:dph cardiomyocyte growth GOC:dph heart muscle cell growth GOC:dph Any process that modulates the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state. dph 2010-02-25T01:05:16Z biological_process GO:0061050 regulation of cell growth involved in cardiac muscle cell development Any process that modulates the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state. GOC:dph Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state. dph 2010-02-25T01:08:08Z biological_process GO:0061051 positive regulation of cell growth involved in cardiac muscle cell development Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state. GOC:dph Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state. dph 2010-02-25T01:11:30Z biological_process GO:0061052 negative regulation of cell growth involved in cardiac muscle cell development Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state. GOC:dph The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo. dph 2010-03-02T12:05:13Z biological_process GO:0061053 somite development The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo. GOC:dph The progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin. dph 2010-03-02T12:07:37Z biological_process GO:0061054 dermatome development The progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin. GOC:dph The progression of the myotome over time, from its formation to the mature structure. The myotome is the portion of the somite that will give rise to muscle. dph 2010-03-02T12:11:01Z biological_process GO:0061055 myotome development The progression of the myotome over time, from its formation to the mature structure. The myotome is the portion of the somite that will give rise to muscle. GOC:dph The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra. dph 2010-03-02T12:12:40Z biological_process GO:0061056 sclerotome development The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra. GOC:dph The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms. dph 2010-03-09T08:55:14Z biological_process GO:0061061 muscle structure development The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms. GOC:dph Any process that modulates the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. dph 2010-03-11T12:59:21Z biological_process GO:0061062 regulation of nematode larval development Any process that modulates the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. GOC:dph GOC:kmv Any process that increases the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. dph 2010-03-11T01:03:34Z biological_process GO:0061063 positive regulation of nematode larval development Any process that increases the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. GOC:dph GOC:kmv Any process that decreases the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. dph 2010-03-11T01:04:39Z biological_process GO:0061064 negative regulation of nematode larval development Any process that decreases the rate, frequency, or extent of nematode larval development, the process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. GOC:dph GOC:kmv The process in which the iris is generated and organized. The iris is an anatomical structure in the eye whose opening forms the pupil. The iris is responsible for controlling the diameter and size of the pupil and the amount of light reaching the retina. dph 2010-03-16T10:48:42Z biological_process GO:0061072 iris morphogenesis The process in which the iris is generated and organized. The iris is an anatomical structure in the eye whose opening forms the pupil. The iris is responsible for controlling the diameter and size of the pupil and the amount of light reaching the retina. GOC:dph The process in which the ciliary body generated and organized. The ciliary body is the circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes. dph 2010-03-16T10:55:19Z biological_process GO:0061073 ciliary body morphogenesis The process in which the ciliary body generated and organized. The ciliary body is the circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes. GOC:dph Any process that modulates the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells. dph 2010-03-16T11:47:05Z biological_process GO:0061074 regulation of neural retina development Any process that modulates the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells. GOC:dph Any process that increases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells. dph 2010-03-16T11:59:48Z biological_process GO:0061075 positive regulation of neural retina development Any process that increases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells. GOC:dph Any process that decreases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells. dph 2010-03-16T12:46:11Z biological_process GO:0061076 negative regulation of neural retina development Any process that decreases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells. GOC:dph The progression of the right horn of the sinus venosus from its formation to the mature structure. dph 2010-04-08T02:45:10Z biological_process GO:0061080 right horn of sinus venosus development The progression of the right horn of the sinus venosus from its formation to the mature structure. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the lung epithelium. dph 2010-04-27T03:28:46Z biological_process GO:0061100 lung neuroendocrine cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the lung epithelium. GOC:dph PMID:9126746 The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a neuroendocrine cell. A neuroendocrine cell is a cell that receives input form a neuron which controls the secretion of an endocrine substance. dph 2010-04-28T09:42:20Z biological_process GO:0061101 neuroendocrine cell differentiation The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a neuroendocrine cell. A neuroendocrine cell is a cell that receives input form a neuron which controls the secretion of an endocrine substance. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the stomach epithelium. dph 2010-04-28T09:47:07Z biological_process gastric neuroendocrine cell differentiation GO:0061102 stomach neuroendocrine cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the stomach epithelium. GOC:dph PMID:18173746 gastric neuroendocrine cell differentiation GOC:dph Any process that modulates the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach. dph 2010-04-29T12:19:37Z biological_process GO:0061105 regulation of stomach neuroendocrine cell differentiation Any process that modulates the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach. GOC:dph Any process that decreases the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach. dph 2010-04-29T12:23:05Z biological_process GO:0061106 negative regulation of stomach neuroendocrine cell differentiation Any process that decreases the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach. GOC:dph A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a dense core granule. A dense core granule is a secretory organelle found in endocrine cells. dph 2010-05-01T09:34:37Z dense core granule organisation biological_process GO:0061109 dense core granule organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a dense core granule. A dense core granule is a secretory organelle found in endocrine cells. GOC:dph dense core granule organisation GOC:mah Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell and contributes to the progression of the lung over time from its initial formation to the mature organ. dph 2010-05-05T11:14:38Z epithelial-mesenchymal cell signalling involved in lung development biological_process GO:0061111 epithelial-mesenchymal cell signaling involved in lung development Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell and contributes to the progression of the lung over time from its initial formation to the mature organ. GOC:dph epithelial-mesenchymal cell signalling involved in lung development GOC:mah Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized. dph 2010-05-05T11:55:30Z biological_process GO:0061113 pancreas morphogenesis Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized. GOC:dph The process in which the branches of the pancreas are generated and organized. dph 2010-05-05T12:03:04Z biological_process GO:0061114 branching involved in pancreas morphogenesis The process in which the branches of the pancreas are generated and organized. GOC:dph Any process that decreases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart. dph 2010-05-17T07:31:28Z biological_process GO:0061117 negative regulation of heart growth Any process that decreases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart. GOC:dph GOC:hjd The morphogenetic process in which the foregut region specified to become the pancreas forms a bud. dph 2010-05-17T09:33:40Z biological_process GO:0061130 pancreatic bud formation The morphogenetic process in which the foregut region specified to become the pancreas forms a bud. GOC:dph The process in which the anatomical structures of a branched epithelium are generated and organized. dph 2010-05-25T09:05:34Z biological_process GO:0061138 morphogenesis of a branching epithelium The process in which the anatomical structures of a branched epithelium are generated and organized. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a lung secretory cell. A lung secretory cell is a specialized epithelial cell of the lung that contains large secretory granules in its apical part. dph 2010-05-25T09:28:53Z biological_process GO:0061140 lung secretory cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a lung secretory cell. A lung secretory cell is a specialized epithelial cell of the lung that contains large secretory granules in its apical part. GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a lung ciliated cell. A lung ciliated cell is a specialized lung epithelial cell that contains cilia for moving substances released from lung secretory cells. dph 2010-05-25T09:31:14Z biological_process GO:0061141 lung ciliated cell differentiation The process in which a relatively unspecialized cell acquires specialized features of a lung ciliated cell. A lung ciliated cell is a specialized lung epithelial cell that contains cilia for moving substances released from lung secretory cells. GOC:cilia GOC:dph GOC:krc The progression of the endocardial endothelium over time, from its initial formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. dph 2010-06-03T09:15:31Z biological_process GO:0061147 endocardial endothelium development The progression of the endocardial endothelium over time, from its initial formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. GOC:dph A process which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix of the endocardium. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. dph 2010-06-03T09:18:02Z extracellular matrix organisation involved in endocardium development biological_process GO:0061148 extracellular matrix organization involved in endocardium development A process which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix of the endocardium. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers. GOC:dph extracellular matrix organisation involved in endocardium development GOC:mah The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells. dph 2010-06-15T09:05:00Z biological_process GO:0061154 endothelial tube morphogenesis The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells. GOC:dph GOC:yaf The process in which the anatomical structures of a tube are generated and organized from the pulmonary artery endothelium. An pulmonary artery endothelium is an epithelium that lines the pulmonary artery. dph 2010-06-15T09:09:04Z biological_process GO:0061155 pulmonary artery endothelial tube morphogenesis The process in which the anatomical structures of a tube are generated and organized from the pulmonary artery endothelium. An pulmonary artery endothelium is an epithelium that lines the pulmonary artery. GOC:dph GOC:yaf The process in which the anatomical structures of the pulmonary artery are generated and organized. The pulmonary artery is the artery that carries blood from the heart to the lungs. dph 2010-06-15T09:13:47Z biological_process GO:0061156 pulmonary artery morphogenesis The process in which the anatomical structures of the pulmonary artery are generated and organized. The pulmonary artery is the artery that carries blood from the heart to the lungs. GOC:dph GOC:yaf Any process that modulates the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate. dph 2010-07-14T08:28:52Z biological_process GO:0061181 regulation of chondrocyte development Any process that modulates the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate. GOC:BHF GOC:dph Any process that decreases the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate. dph 2010-07-14T08:33:05Z biological_process GO:0061182 negative regulation of chondrocyte development Any process that decreases the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate. GOC:BHF GOC:dph Any process that modulates the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin. dph 2010-07-14T08:40:26Z biological_process GO:0061183 regulation of dermatome development Any process that modulates the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin. GOC:BHF GOC:dph Any process that increases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin. dph 2010-07-14T08:42:03Z biological_process GO:0061184 positive regulation of dermatome development Any process that increases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin. GOC:BHF GOC:dph Any process that decreases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin. dph 2010-07-14T08:43:08Z biological_process GO:0061185 negative regulation of dermatome development Any process that decreases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin. GOC:BHF GOC:dph Any process that increases the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra. dph 2010-07-14T09:17:23Z biological_process GO:0061189 positive regulation of sclerotome development Any process that increases the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra. GOC:BHF GOC:dph Any process that modulates the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra. dph 2010-07-14T09:19:47Z biological_process GO:0061190 regulation of sclerotome development Any process that modulates the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra. GOC:dph The process whose specific outcome is the progression of the vasculature of the retina over time, from its formation to the mature structure. dph 2010-09-06T03:27:06Z retinal vasculature development biological_process GO:0061298 retina vasculature development in camera-type eye The process whose specific outcome is the progression of the vasculature of the retina over time, from its formation to the mature structure. GOC:BHF GOC:dph retinal vasculature development GOC:dph The process in which the vasculature of the retina is generated and organized. dph 2010-09-06T03:28:25Z retinal vasculature morphogenesis biological_process GO:0061299 retina vasculature morphogenesis in camera-type eye The process in which the vasculature of the retina is generated and organized. GOC:BHF GOC:dph retinal vasculature morphogenesis GOC:dph The progression of the cornea over time, from its formation to the mature structure. The cornea is the transparent structure that covers the anterior of the eye. dph 2010-09-14T02:09:08Z biological_process GO:0061303 cornea development in camera-type eye The progression of the cornea over time, from its formation to the mature structure. The cornea is the transparent structure that covers the anterior of the eye. GOC:dph The process whose specific outcome is the progression of a blood vessel of the retina over time, from its formation to the mature structure. dph 2010-09-16T09:02:59Z biological_process GO:0061304 retinal blood vessel morphogenesis The process whose specific outcome is the progression of a blood vessel of the retina over time, from its formation to the mature structure. GOC:BHF GOC:dph The process in which a relatively unspecialized cell acquires specialized features of a cardiac neural crest cell that will migrate to the heart and contribute to its development. Cardiac neural crest cells are specialized cells that migrate toward the heart from the third, fourth and sixth pharyngeal arches. dph 2010-09-23T08:50:56Z biological_process GO:0061307 cardiac neural crest cell differentiation involved in heart development The process in which a relatively unspecialized cell acquires specialized features of a cardiac neural crest cell that will migrate to the heart and contribute to its development. Cardiac neural crest cells are specialized cells that migrate toward the heart from the third, fourth and sixth pharyngeal arches. GOC:dph GOC:mtg_heart PMID:19705442 The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the development of the heart. dph 2010-09-23T09:01:49Z biological_process GO:0061308 cardiac neural crest cell development involved in heart development The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the development of the heart. GOC:dph GOC:mtg_heart The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the shaping of the outflow tract. dph 2010-09-23T09:08:37Z biological_process GO:0061309 cardiac neural crest cell development involved in outflow tract morphogenesis The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the shaping of the outflow tract. GOC:dph GOC:mtg_heart The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the heart. dph 2010-09-28T09:05:26Z biological_process GO:0061323 cell proliferation involved in heart morphogenesis The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the heart. GOC:dph GOC:mtg_heart The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the outflow tract. dph 2010-09-28T09:29:30Z biological_process GO:0061325 cell proliferation involved in outflow tract morphogenesis The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the outflow tract. GOC:dph GOC:mtg_heart Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles. dph 2010-09-29T08:46:05Z biological_process GO:0061337 cardiac conduction Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles. GOC:dph The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell. dph 2010-10-01T11:06:04Z biological_process GO:0061351 neural precursor cell proliferation The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell. GOC:dph GOC:yaf The process of shaping a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue. dph 2010-12-02T08:51:45Z biological_process GO:0061383 trabecula morphogenesis The process of shaping a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue. GOC:dph The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue. dph 2010-12-02T08:54:20Z biological_process GO:0061384 heart trabecula morphogenesis The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue. GOC:dph The multiplication or reproduction of fibroblasts, resulting in the expansion of a fibroblast population that contributes to the shaping of the heart. dph 2011-02-10T01:41:59Z biological_process GO:0061385 fibroblast proliferation involved in heart morphogenesis The multiplication or reproduction of fibroblasts, resulting in the expansion of a fibroblast population that contributes to the shaping of the heart. GOC:dph The progression of a connective tissue over time, from its formation to the mature structure. dph 2012-03-22T12:53:41Z biological_process GO:0061448 connective tissue development The progression of a connective tissue over time, from its formation to the mature structure. GOC:BHF The process in which a relatively unspecialized cell acquires specialized features of an interstitial cell of Cajal. An interstitial cell of Cajal is an intestinal neuroepithelial cell that serves as a pacemaker to trigger gut contraction. dph 2012-07-20T08:20:50Z biological_process ICC differentiation GO:0061453 interstitial cell of Cajal differentiation The process in which a relatively unspecialized cell acquires specialized features of an interstitial cell of Cajal. An interstitial cell of Cajal is an intestinal neuroepithelial cell that serves as a pacemaker to trigger gut contraction. GOC:dph ICC differentiation GOC:dph The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction. dph 2012-08-22T17:47:53Z biological_process GO:0061458 reproductive system development The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction. GOC:dph Any process that modulates the frequency, rate or extent of type B pancreatic cell proliferation. dph 2012-11-01T13:16:23Z biological_process GO:0061469 regulation of type B pancreatic cell proliferation Any process that modulates the frequency, rate or extent of type B pancreatic cell proliferation. GOC:dph Any biological process involved in the maintenance of the steady-state number of hematopoietic stem cells within a population of cells. dph 2012-12-04T09:41:02Z biological_process GO:0061484 hematopoietic stem cell homeostasis Any biological process involved in the maintenance of the steady-state number of hematopoietic stem cells within a population of cells. GOC:dph PMID:21508411 A process in which a protein is transported to, or maintained in, a location within a cilium. dph 2013-03-22T15:41:44Z biological_process GO:0061512 protein localization to cilium A process in which a protein is transported to, or maintained in, a location within a cilium. GOC:dph The process whose specific outcome is the progression of a myeloid cell over time, from its formation to the mature structure. dph 2013-04-18T13:03:16Z biological_process GO:0061515 myeloid cell development The process whose specific outcome is the progression of a myeloid cell over time, from its formation to the mature structure. GOC:dph A cellular process that results in the breakdown of a cilium. dph 2013-04-18T14:59:59Z cilium resorption biological_process GO:0061523 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium disassembly A cellular process that results in the breakdown of a cilium. GOC:cilia GOC:dph PMID:17604723 PMID:27350441 cilium resorption GOC:dph The process whose specific outcome is the progression of the hindgut over time, from its formation to the mature structure. The hindgut is part of the alimentary canal that lies posterior to the midgut. dph 2013-06-14T11:22:21Z biological_process GO:0061525 hindgut development The process whose specific outcome is the progression of the hindgut over time, from its formation to the mature structure. The hindgut is part of the alimentary canal that lies posterior to the midgut. GOC:dph The regulated release of acetylcholine by a cell. dph 2013-06-21T15:40:39Z biological_process GO:0061526 acetylcholine secretion The regulated release of acetylcholine by a cell. GOC:dph The regulated release of norepinephrine by a cell, in which the norepinephrine acts as a neurotransmitter. dph 2013-06-21T16:05:08Z noradrenaline secretion, neurotransmission biological_process GO:0061533 norepinephrine secretion, neurotransmission The regulated release of norepinephrine by a cell, in which the norepinephrine acts as a neurotransmitter. GOC:dph noradrenaline secretion, neurotransmission GOC:dph The process whose specific outcome is the progression of a ganglion over time, from its formation to the mature structure. dph 2013-07-10T08:36:12Z gangliogenesis biological_process ganglia development GO:0061548 ganglion development The process whose specific outcome is the progression of a ganglion over time, from its formation to the mature structure. GOC:dph gangliogenesis GOC:BHF GOC:rl ganglia development GOC:dph The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure. dph 2013-07-10T08:38:01Z biological_process sympathetic ganglia development GO:0061549 sympathetic ganglion development The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure. GOC:BHF GOC:rl sympathetic ganglia development GOC:dph The process whose specific outcome is the progression of a cranial ganglion over time, from its formation to the mature structure. dph 2013-07-10T08:40:14Z biological_process cranial ganglia development GO:0061550 cranial ganglion development The process whose specific outcome is the progression of a cranial ganglion over time, from its formation to the mature structure. GOC:dph cranial ganglia development GOC:dph The process whose specific outcome is the progression of a trigeminal ganglion over time, from its formation to the mature structure. dph 2013-07-10T08:42:19Z biological_process trigeminal ganglia development GO:0061551 trigeminal ganglion development The process whose specific outcome is the progression of a trigeminal ganglion over time, from its formation to the mature structure. GOC:dph trigeminal ganglia development GOC:dph The process in which the anatomical structures of ganglion are generated and organized. dph 2013-07-10T08:44:57Z biological_process ganglia morphogenesis GO:0061552 ganglion morphogenesis The process in which the anatomical structures of ganglion are generated and organized. GOC:dph ganglia morphogenesis GOC:dph A developmental process, independent of morphogenetic (shape) change, that is required for ganglion to attain its fully functional state. dph 2013-07-10T08:45:59Z biological_process ganglia maturation GO:0061553 ganglion maturation A developmental process, independent of morphogenetic (shape) change, that is required for ganglion to attain its fully functional state. GOC:dph ganglia maturation GOC:dph The process that gives rise to ganglion. This process pertains to the initial formation of a structure from unspecified parts. dph 2013-07-10T08:51:50Z biological_process ganglia formation GO:0061554 ganglion formation The process that gives rise to ganglion. This process pertains to the initial formation of a structure from unspecified parts. GOC:dph ganglia formation GOC:dph The process in which the anatomical structure of a trigeminal ganglion is generated and organized. dph 2013-07-10T08:57:12Z biological_process trigeminal ganglia morphogenesis GO:0061556 trigeminal ganglion morphogenesis The process in which the anatomical structure of a trigeminal ganglion is generated and organized. GOC:dph trigeminal ganglia morphogenesis GOC:dph A developmental process, independent of morphogenetic (shape) change, that is required for a trigeminal ganglion to attain its fully functional state. dph 2013-07-10T08:58:24Z biological_process trigeminal ganglia maturation GO:0061557 trigeminal ganglion maturation A developmental process, independent of morphogenetic (shape) change, that is required for a trigeminal ganglion to attain its fully functional state. GOC:dph trigeminal ganglia maturation GOC:dph A developmental process, independent of morphogenetic (shape) change, that is required for a cranial ganglion to attain its fully functional state. dph 2013-07-10T08:59:52Z biological_process cranial ganglia maturation GO:0061558 cranial ganglion maturation A developmental process, independent of morphogenetic (shape) change, that is required for a cranial ganglion to attain its fully functional state. GOC:dph cranial ganglia maturation GOC:dph The process in which the anatomical structure of a cranial ganglion is generated and organized. dph 2013-07-10T09:02:15Z biological_process cranial ganglia morphogenesis GO:0061559 cranial ganglion morphogenesis The process in which the anatomical structure of a cranial ganglion is generated and organized. GOC:dph cranial ganglia morphogenesis GOC:dph The process that gives rise to a cranial ganglion. This process pertains to the initial formation of a structure from unspecified parts. dph 2013-07-10T09:07:27Z biological_process cranial ganglia formation GO:0061560 cranial ganglion formation The process that gives rise to a cranial ganglion. This process pertains to the initial formation of a structure from unspecified parts. GOC:dph cranial ganglia formation GOC:dph The process that gives rise to the trigeminal ganglion. This process pertains to the initial formation of a structure from unspecified parts. dph 2013-07-10T09:08:13Z biological_process trigeminal ganglia formation GO:0061561 trigeminal ganglion formation The process that gives rise to the trigeminal ganglion. This process pertains to the initial formation of a structure from unspecified parts. GOC:dph trigeminal ganglia formation GOC:dph A process that results in the assembly, arrangement of constituent parts, or disassembly of an actin filament bundle. dph 2013-08-02T11:24:11Z biological_process actin filament cable organization GO:0061572 actin filament bundle organization A process that results in the assembly, arrangement of constituent parts, or disassembly of an actin filament bundle. GOC:dph actin filament cable organization GOC:dph The process in which the anatomical structures of a pharyngeal arch artery is generated and organized. The pharyngeal arch arteries are a series of six paired embryological vascular structures, the development of which give rise to several major arteries, such as the stapedial artery, the middle meningeal artery, the internal carotid artery and the pulmonary artery. dph 2014-05-09T15:34:06Z aortic arch artery morphogenesis biological_process GO:0061626 pharyngeal arch artery morphogenesis The process in which the anatomical structures of a pharyngeal arch artery is generated and organized. The pharyngeal arch arteries are a series of six paired embryological vascular structures, the development of which give rise to several major arteries, such as the stapedial artery, the middle meningeal artery, the internal carotid artery and the pulmonary artery. GOC:BHF GOC:dph PMID:20122914 aortic arch artery morphogenesis GOC:dph Any process that reduces or removes the toxicity of inorganic compounds. These include transport of such compounds away from sensitive areas and to compartments or complexes whose purpose is sequestration of inorganic compounds. dph 2015-03-09T09:16:23Z biological_process GO:0061687 detoxification of inorganic compound Any process that reduces or removes the toxicity of inorganic compounds. These include transport of such compounds away from sensitive areas and to compartments or complexes whose purpose is sequestration of inorganic compounds. GOC:vw A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). dph 2015-05-06T11:22:38Z cellular_component GO:0061695 transferase complex, transferring phosphorus-containing groups A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:bhm GOC:dph Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodeling. dph 2016-09-09T13:24:34Z biological_process GO:0061792 secretory granule maturation Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodeling. GOC:PARL GOC:bf GOC:dph PMID:16618809 A process in which a protein is transported to or maintained in a location within the somatodendritic compartment. dph 2017-09-08T13:22:26Z somatodendritic protein localization biological_process GO:0061938 protein localization to somatodendritic compartment A process in which a protein is transported to or maintained in a location within the somatodendritic compartment. PMID:18341993 The directed movement of a protein to a specific location in a plasma membrane. dph 2017-10-26T12:55:15Z biological_process GO:0061951 establishment of protein localization to plasma membrane The directed movement of a protein to a specific location in a plasma membrane. GOC:dph GOC:vw The process in which bones are generated and organized as a result of the conversion of another structural tissue into bone. dph 2018-02-12T18:10:59Z biological_process GO:0061971 replacement bone morphogenesis The process in which bones are generated and organized as a result of the conversion of another structural tissue into bone. PMID:29852585 The process in which bone which forms superficially in the organism are generated and organized. dph 2018-02-12T18:16:21Z biological_process GO:0061972 dermal bone morphogenesis The process in which bone which forms superficially in the organism are generated and organized. PMID:12588850 PMID:15003632 The process in which bone which forms deep in the organism are generated and organized. dph 2018-02-12T18:21:09Z biological_process GO:0061973 membrane bone morphogenesis The process in which bone which forms deep in the organism are generated and organized. PMID:14579374 Any process that modulates the rate, frequency or extent of a small molecule metabolic process. dph 2018-03-19T14:11:54Z regulation of small molecule metabolism biological_process GO:0062012 regulation of small molecule metabolic process Any process that modulates the rate, frequency or extent of a small molecule metabolic process. GOC:vw Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process. dph 2018-03-19T14:25:10Z positive regulation of small molecule metabolism biological_process GO:0062013 positive regulation of small molecule metabolic process Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process. GOC:vw Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process. dph 2018-03-19T14:27:23Z negative regulation of small molecule metabolism biological_process GO:0062014 negative regulation of small molecule metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process. GOC:vw An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. dph 2018-04-13T12:47:21Z cellular_component GO:0062023 collagen-containing extracellular matrix An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. GOC:BHF GOC:rph PMID:21123617 Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis. dph 2018-04-23T14:32:23Z biological_process GO:0062033 positive regulation of mitotic sister chromatid segregation Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis. PMID:12773390 The process whose specific outcome is the progression of the stomach over time, from its formation to the mature structure. The stomach is an expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. dph 2018-11-20T18:15:45Z biological_process GO:0062094 stomach development The process whose specific outcome is the progression of the stomach over time, from its formation to the mature structure. The stomach is an expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. PMID:11967278 The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal. dph 2019-09-13T13:48:47Z biological_process GO:0062149 detection of stimulus involved in sensory perception of pain The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal. PMID:19837031 Any process in which a protein is transported to, and/or maintained at the postsynapse, the part of a synapse that is part of the post-synaptic cell. dph 2020-04-20T13:58:43Z biological_process GO:0062237 protein localization to postsynapse Any process in which a protein is transported to, and/or maintained at the postsynapse, the part of a synapse that is part of the post-synaptic cell. PMID:31189538 The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore. intracellular membrane translocation of a protein intracellular protein membrane transport intracellular protein transport across a membrane biological_process GO:0065002 Note that this term is not intended for use in annotating lateral movement within membranes. intracellular protein transmembrane transport The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore. GOC:isa_complete The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 GO:0006461 GO:0034622 GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly cellular protein-containing complex assembly chaperone activity macromolecular complex assembly macromolecule complex assembly protein complex assembly protein complex formation GO:0065003 protein-containing complex assembly The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. GOC:jl The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex. DNA-protein complex assembly biological_process GO:0065004 protein-DNA complex assembly The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex. GOC:jl DNA-protein complex assembly GOC:mah Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. regulation of a molecular function biological_process GO:0065009 regulation of molecular function Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GOC:isa_complete Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell. extracellular membrane-enclosed organelle cellular_component GO:0065010 extracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell. GOC:isa_complete An organelle lumen that is part of an intracellular organelle. cellular_component GO:0070013 intracellular organelle lumen An organelle lumen that is part of an intracellular organelle. GOC:mah The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state. https://github.com/geneontology/go-ontology/issues/24218 neuron maintenance biological_process GO:0070050 neuron cellular homeostasis The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state. GOC:BHF GOC:mah A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. exosome extracellular vesicular exosome cellular_component GO:0070062 extracellular exosome A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm. GOC:BHF GOC:mah GOC:vesicles PMID:15908444 PMID:17641064 PMID:19442504 PMID:19498381 PMID:22418571 PMID:24009894 exosome GOC:pr extracellular vesicular exosome GOC:vesicles The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). biological_process GO:0070091 glucagon secretion The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). GOC:BHF GOC:rl Any process that modulates the frequency, rate or extent of the regulated release of glucagon. biological_process GO:0070092 regulation of glucagon secretion Any process that modulates the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon. down regulation of glucagon secretion down-regulation of glucagon secretion downregulation of glucagon secretion inhibition of glucagon secretion biological_process GO:0070093 negative regulation of glucagon secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon. up regulation of glucagon secretion up-regulation of glucagon secretion upregulation of glucagon secretion activation of glucagon secretion stimulation of glucagon secretion biological_process GO:0070094 positive regulation of glucagon secretion Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix. anchoring cell junction cellular_component GO:0070161 anchoring junction A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix. ISBN:0815332181 anchoring cell junction GOC:mah A process of chromosome organization that is involved in a meiotic cell cycle. chromosome organisation involved in meiosis meiotic chromosome organization biological_process GO:0070192 chromosome organization involved in meiotic cell cycle A process of chromosome organization that is involved in a meiotic cell cycle. GOC:mah chromosome organisation involved in meiosis GOC:mah meiotic chromosome organization GOC:mah The directed movement of a protein to a specific location on a chromosome. establishment of protein localisation to chromosome biological_process GO:0070199 establishment of protein localization to chromosome The directed movement of a protein to a specific location on a chromosome. GOC:BHF GOC:mah establishment of protein localisation to chromosome GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. regulation of establishment of protein localisation biological_process GO:0070201 regulation of establishment of protein localization Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. GOC:BHF GOC:mah regulation of establishment of protein localisation GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome. regulation of establishment of protein localisation to chromosome biological_process GO:0070202 regulation of establishment of protein localization to chromosome Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome. GOC:BHF GOC:mah regulation of establishment of protein localisation to chromosome GOC:mah The regulated release of somatostatin from secretory granules in the D cells of the pancreas. biological_process GO:0070253 somatostatin secretion The regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:mah The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function. mucus production biological_process GO:0070254 mucus secretion The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function. GOC:add ISBN:068340007X ISBN:0721662544 mucus production GOC:add Any process that modulates the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. regulation of mucus production biological_process GO:0070255 regulation of mucus secretion Any process that modulates the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add regulation of mucus production GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. negative regulation of mucus production biological_process GO:0070256 negative regulation of mucus secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add negative regulation of mucus production GOC:add Any process that activates or increases the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. positive regulation of mucus production biological_process GO:0070257 positive regulation of mucus secretion Any process that activates or increases the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add positive regulation of mucus production GOC:add The process whose specific outcome is the progression of a pigment cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a pigment cell fate. biological_process GO:0070285 pigment cell development The process whose specific outcome is the progression of a pigment cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a pigment cell fate. GOC:cvs The multiplication or reproduction of fat cells by cell division, resulting in the expansion of their population. A fat cell is an animal connective tissue cell specialized for the synthesis and storage of fat. adipocyte proliferation adipose cell proliferation biological_process GO:0070341 fat cell proliferation The multiplication or reproduction of fat cells by cell division, resulting in the expansion of their population. A fat cell is an animal connective tissue cell specialized for the synthesis and storage of fat. GOC:mah GOC:sl adipocyte proliferation GOC:sl adipose cell proliferation GOC:sl Any process that modulates the frequency, rate or extent of fat cell proliferation. regulation of adipocyte proliferation regulation of adipose cell proliferation biological_process GO:0070344 regulation of fat cell proliferation Any process that modulates the frequency, rate or extent of fat cell proliferation. GOC:mah GOC:sl regulation of adipocyte proliferation GOC:sl regulation of adipose cell proliferation GOC:sl Any process that stops or decreases the rate or extent of fat cell proliferation. down regulation of fat cell proliferation down-regulation of fat cell proliferation downregulation of fat cell proliferation negative regulation of adipocyte proliferation negative regulation of adipose cell proliferation inhibition of fat cell proliferation biological_process GO:0070345 negative regulation of fat cell proliferation Any process that stops or decreases the rate or extent of fat cell proliferation. GOC:mah GOC:sl down regulation of fat cell proliferation GOC:mah down-regulation of fat cell proliferation GOC:mah downregulation of fat cell proliferation GOC:mah negative regulation of adipocyte proliferation GOC:sl negative regulation of adipose cell proliferation GOC:sl inhibition of fat cell proliferation GOC:mah Any process that activates or increases the rate or extent of fat cell proliferation. positive regulation of adipocyte proliferation positive regulation of adipose cell proliferation up regulation of fat cell proliferation up-regulation of fat cell proliferation upregulation of fat cell proliferation activation of fat cell proliferation stimulation of fat cell proliferation biological_process GO:0070346 positive regulation of fat cell proliferation Any process that activates or increases the rate or extent of fat cell proliferation. GOC:mah GOC:sl positive regulation of adipocyte proliferation GOC:sl positive regulation of adipose cell proliferation GOC:sl up regulation of fat cell proliferation GOC:mah up-regulation of fat cell proliferation GOC:mah upregulation of fat cell proliferation GOC:mah activation of fat cell proliferation GOC:mah stimulation of fat cell proliferation GOC:mah The process in which a relatively unspecialized cell acquires the specialized features of a hepatocyte. A hepatocyte is specialized epithelial cell that is organized into interconnected plates called lobules, and is the main structural component of the liver. liver cell differentiation biological_process GO:0070365 hepatocyte differentiation The process in which a relatively unspecialized cell acquires the specialized features of a hepatocyte. A hepatocyte is specialized epithelial cell that is organized into interconnected plates called lobules, and is the main structural component of the liver. CL:0000182 PMID:7588884 liver cell differentiation GOC:mah Any process that modulates the frequency, rate or extent of hepatocyte differentiation. regulation of liver cell differentiation biological_process GO:0070366 regulation of hepatocyte differentiation Any process that modulates the frequency, rate or extent of hepatocyte differentiation. GOC:mah GOC:sl regulation of liver cell differentiation GOC:sl Any process that stops or decreases the rate or extent of hepatocyte differentiation. down regulation of hepatocyte differentiation down-regulation of hepatocyte differentiation downregulation of hepatocyte differentiation negative regulation of liver cell differentiation inhibition of hepatocyte differentiation biological_process GO:0070367 negative regulation of hepatocyte differentiation Any process that stops or decreases the rate or extent of hepatocyte differentiation. GOC:mah GOC:sl down regulation of hepatocyte differentiation GOC:mah down-regulation of hepatocyte differentiation GOC:mah downregulation of hepatocyte differentiation GOC:mah negative regulation of liver cell differentiation GOC:sl inhibition of hepatocyte differentiation GOC:mah Any process that activates or increases the rate or extent of hepatocyte differentiation. positive regulation of liver cell differentiation up regulation of hepatocyte differentiation up-regulation of hepatocyte differentiation upregulation of hepatocyte differentiation activation of hepatocyte differentiation stimulation of hepatocyte differentiation biological_process GO:0070368 positive regulation of hepatocyte differentiation Any process that activates or increases the rate or extent of hepatocyte differentiation. GOC:mah GOC:sl positive regulation of liver cell differentiation GOC:sl up regulation of hepatocyte differentiation GOC:mah up-regulation of hepatocyte differentiation GOC:mah upregulation of hepatocyte differentiation GOC:mah activation of hepatocyte differentiation GOC:mah stimulation of hepatocyte differentiation GOC:mah A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis. exocytic constitutive secretory pathway transport vesicle exocytotic vesicle cellular_component GO:0070382 exocytic vesicle A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis. GOC:kad GOC:mah exocytotic vesicle GOC:kad Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen. biological_process GO:0070482 response to oxygen levels Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen. GOC:BHF GOC:mah The series of events in which a stimulus indicating lowered oxygen tension is received by a cell and converted into a molecular signal. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. detection of reduced oxygen levels biological_process GO:0070483 detection of hypoxia The series of events in which a stimulus indicating lowered oxygen tension is received by a cell and converted into a molecular signal. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. GOC:BHF GOC:mah detection of reduced oxygen levels GOC:vk Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. regulation of microtubule cytoskeleton organisation regulation of microtubule dynamics biological_process GO:0070507 regulation of microtubule cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah regulation of microtubule cytoskeleton organisation GOC:mah regulation of microtubule dynamics GOC:dph GOC:tb The directed movement of a substance from one side of an epithelium to the other. mah 2009-05-06T03:31:02Z biological_process GO:0070633 transepithelial transport The directed movement of a substance from one side of an epithelium to the other. GOC:mah GOC:yaf ISBN:0716731363 The directed movement of ammonium ions from one side of an epithelium to the other. mah 2009-05-06T03:34:43Z biological_process GO:0070634 transepithelial ammonium transport The directed movement of ammonium ions from one side of an epithelium to the other. GOC:mah GOC:yaf The expansion of a leukocyte population by cell division. mah 2009-05-28T05:25:28Z biological_process GO:0070661 leukocyte proliferation The expansion of a leukocyte population by cell division. GOC:add Any process that modulates the frequency, rate or extent of leukocyte proliferation. mah 2009-05-28T05:30:39Z biological_process GO:0070663 regulation of leukocyte proliferation Any process that modulates the frequency, rate or extent of leukocyte proliferation. GOC:add GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation. mah 2009-05-28T05:34:50Z down regulation of leukocyte proliferation down-regulation of leukocyte proliferation downregulation of leukocyte proliferation inhibition of leukocyte proliferation biological_process GO:0070664 negative regulation of leukocyte proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation. GOC:add GOC:mah down regulation of leukocyte proliferation GOC:mah down-regulation of leukocyte proliferation GOC:mah downregulation of leukocyte proliferation GOC:mah inhibition of leukocyte proliferation GOC:mah Any process that activates or increases the frequency, rate or extent of leukocyte proliferation. mah 2009-05-28T05:36:46Z up regulation of leukocyte proliferation up-regulation of leukocyte proliferation upregulation of leukocyte proliferation activation of leukocyte proliferation stimulation of leukocyte proliferation biological_process GO:0070665 positive regulation of leukocyte proliferation Any process that activates or increases the frequency, rate or extent of leukocyte proliferation. GOC:add GOC:mah up regulation of leukocyte proliferation GOC:mah up-regulation of leukocyte proliferation GOC:mah upregulation of leukocyte proliferation GOC:mah activation of leukocyte proliferation GOC:mah stimulation of leukocyte proliferation GOC:mah Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. mah 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process GO:0070727 cellular macromolecule localization Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular macromolecule localisation GOC:mah The aggregation, arrangement and bonding together of a set of components to form a basement membrane, a part of the extracellular region that consists of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. mah 2009-07-23T05:01:51Z biological_process GO:0070831 Note that this term has no relationship to 'membrane assembly ; GO:0071709' because the basement membrane is not a lipid bilayer. basement membrane assembly The aggregation, arrangement and bonding together of a set of components to form a basement membrane, a part of the extracellular region that consists of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. mah 2009-08-14T03:09:02Z regulation of bile acid anabolism regulation of bile acid biosynthesis regulation of bile acid formation regulation of bile acid synthesis biological_process GO:0070857 regulation of bile acid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. GOC:BHF GOC:mah regulation of bile acid anabolism GOC:mah regulation of bile acid biosynthesis GOC:mah regulation of bile acid formation GOC:mah regulation of bile acid synthesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. mah 2009-08-14T03:16:40Z down regulation of bile acid biosynthetic process down-regulation of bile acid biosynthetic process downregulation of bile acid biosynthetic process negative regulation of bile acid anabolism negative regulation of bile acid biosynthesis negative regulation of bile acid formation negative regulation of bile acid synthesis inhibition of bile acid biosynthetic process biological_process GO:0070858 negative regulation of bile acid biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. GOC:BHF GOC:mah down regulation of bile acid biosynthetic process GOC:mah down-regulation of bile acid biosynthetic process GOC:mah downregulation of bile acid biosynthetic process GOC:mah negative regulation of bile acid anabolism GOC:mah negative regulation of bile acid biosynthesis GOC:mah negative regulation of bile acid formation GOC:mah negative regulation of bile acid synthesis GOC:mah inhibition of bile acid biosynthetic process GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. mah 2009-08-14T03:22:58Z positive regulation of bile acid anabolism positive regulation of bile acid biosynthesis positive regulation of bile acid formation positive regulation of bile acid synthesis up regulation of bile acid biosynthetic process up-regulation of bile acid biosynthetic process upregulation of bile acid biosynthetic process activation of bile acid biosynthetic process stimulation of bile acid biosynthetic process biological_process GO:0070859 positive regulation of bile acid biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. GOC:BHF GOC:mah positive regulation of bile acid anabolism GOC:mah positive regulation of bile acid biosynthesis GOC:mah positive regulation of bile acid formation GOC:mah positive regulation of bile acid synthesis GOC:mah up regulation of bile acid biosynthetic process GOC:mah up-regulation of bile acid biosynthetic process GOC:mah upregulation of bile acid biosynthetic process GOC:mah activation of bile acid biosynthetic process GOC:mah stimulation of bile acid biosynthetic process GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen. mah 2009-08-20T02:44:53Z regulation of glycogen metabolism biological_process GO:0070873 regulation of glycogen metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen. GOC:mah regulation of glycogen metabolism GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen. mah 2009-08-20T02:50:41Z negative regulation of glycogen metabolism biological_process GO:0070874 negative regulation of glycogen metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen. GOC:mah negative regulation of glycogen metabolism GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen. mah 2009-08-20T02:53:55Z positive regulation of glycogen metabolism biological_process GO:0070875 positive regulation of glycogen metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen. GOC:mah positive regulation of glycogen metabolism GOC:mah The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. mah 2009-09-15T03:00:51Z biological_process GO:0070925 organelle assembly The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah A developmental process, independent of morphogenetic (shape) change, that is required for bone to attain its fully functional state. mah 2009-10-05T04:35:31Z biological_process GO:0070977 bone maturation A developmental process, independent of morphogenetic (shape) change, that is required for bone to attain its fully functional state. GOC:dph GOC:mah Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin. mah 2009-11-20T11:51:20Z protein localisation to chromatin biological_process GO:0071168 protein localization to chromatin Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin. GOC:mah protein localisation to chromatin GOC:mah The directed movement of a protein to a part of a chromosome that is organized into chromatin. mah 2009-11-20T11:52:43Z establishment of protein localisation to chromatin biological_process GO:0071169 establishment of protein localization to chromatin The directed movement of a protein to a part of a chromosome that is organized into chromatin. GOC:mah establishment of protein localisation to chromatin GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus. mah 2009-12-03T01:02:11Z cellular response to abiotic stress biological_process GO:0071214 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to abiotic stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus. GOC:mah cellular response to abiotic stress GOC:mah The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop. mah 2009-12-16T10:22:52Z hemopoietic stem cell proliferation biological_process GO:0071425 hematopoietic stem cell proliferation The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop. CL:0000037 GOC:BHF GOC:add GOC:mah GOC:rl Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. mah 2009-12-18T01:59:37Z cellular response to electromagnetic radiation stimulus cellular response to radiation stimulus biological_process GO:0071478 Note that 'radiation' refers to electromagnetic radiation of any wavelength. cellular response to radiation Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. GOC:mah cellular response to electromagnetic radiation stimulus GOC:mah cellular response to radiation stimulus GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. mah 2009-12-18T02:00:31Z cellular response to ionising radiation cellular response to ionizing radiation stimulus biological_process GO:0071479 cellular response to ionizing radiation Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. GOC:mah cellular response to ionising radiation GOC:mah cellular response to ionizing radiation stimulus GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum. mah 2009-12-18T02:00:50Z biological_process cellular response to gamma ray cellular response to gamma-ray photon GO:0071480 cellular response to gamma radiation Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum. GOC:mah cellular response to gamma ray GOC:mah cellular response to gamma-ray photon GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz). mah 2009-12-18T02:00:59Z cellular response to X-ray radiation stimulus biological_process GO:0071481 cellular response to X-ray Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz). GOC:mah cellular response to X-ray radiation stimulus GOC:mah The process of biting and mashing food with the teeth prior to swallowing. mah 2010-02-10T11:19:48Z chewing biological_process GO:0071626 mastication The process of biting and mashing food with the teeth prior to swallowing. GOC:gvg chewing GOC:mah Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. mah 2010-02-25T04:00:13Z protein localisation in extracellular region protein localization in extracellular region biological_process GO:0071692 protein localization to extracellular region Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. GOC:mah protein localisation in extracellular region GOC:mah A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state. mah 2010-03-02T11:43:38Z biological_process GO:0071695 anatomical structure maturation A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state. GOC:mah The progression of an ectodermal placode over time from its initial formation until its mature state. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm. mah 2010-03-02T11:48:01Z biological_process GO:0071696 ectodermal placode development The progression of an ectodermal placode over time from its initial formation until its mature state. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm. GOC:mah The process in which the anatomical structures of an ectodermal placode are generated and organized. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm. mah 2010-03-02T11:49:51Z biological_process GO:0071697 ectodermal placode morphogenesis The process in which the anatomical structures of an ectodermal placode are generated and organized. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm. GOC:mah The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. mah 2010-03-08T02:15:14Z biological_process GO:0071702 organic substance transport The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. GOC:mah The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. https://github.com/geneontology/go-ontology/issues/26424 mah 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process GO:0071704 organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. GOC:mah The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. mah 2010-03-08T03:56:28Z biological_process GO:0071705 nitrogen compound transport The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The aggregation, arrangement and bonding together of a set of components to form a membrane. mah 2010-03-10T11:19:17Z biological_process GO:0071709 membrane assembly The aggregation, arrangement and bonding together of a set of components to form a membrane. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane. mah 2010-03-10T11:57:10Z basement membrane organisation biological_process GO:0071711 Note that this term has no relationship to 'membrane organization ; GO:0061024' because the basement membrane is not a lipid bilayer. basement membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane. GOC:mah basement membrane organisation GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane. mah 2010-03-29T03:59:35Z nuclear membrane organisation biological_process nuclear membrane organization and biogenesis GO:0071763 nuclear membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane. GOC:mah nuclear membrane organisation GOC:mah nuclear membrane organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear outer membrane. mah 2010-03-29T04:03:37Z nuclear outer membrane organisation biological_process nuclear outer membrane organization and biogenesis GO:0071764 nuclear outer membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear outer membrane. GOC:mah nuclear outer membrane organisation GOC:mah nuclear outer membrane organization and biogenesis GOC:mah The process in which a protein is transported across a membrane. mah 2010-09-03T02:54:26Z protein membrane transport biological_process GO:0071806 Note that this term is not intended for use in annotating lateral movement within membranes. protein transmembrane transport The process in which a protein is transported across a membrane. GOC:mah GOC:vw Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex. mah 2010-09-08T10:03:26Z DNA-protein complex subunit organization protein-DNA complex subunit organisation protein-DNA complex subunit organization biological_process GO:0071824 protein-DNA complex organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex. GOC:mah DNA-protein complex subunit organization GOC:mah protein-DNA complex subunit organisation GOC:mah Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization ribonucleoprotein complex subunit organisation ribonucleoprotein complex subunit organization biological_process GO:0071826 protein-RNA complex organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. GOC:mah RNA-protein complex subunit organization GOC:mah protein-RNA complex subunit organization GOC:mah ribonucleoprotein complex subunit organisation GOC:mah A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. mah 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monoamine stimulus. A monoamine is any of a group of molecular messengers that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan. mah 2010-09-13T02:36:37Z response to monoamine stimulus biological_process GO:0071867 response to monoamine Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monoamine stimulus. A monoamine is any of a group of molecular messengers that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan. GOC:mah response to monoamine stimulus GOC:dos Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a catecholamine stimulus. A catecholamine is any of a group of biogenic amines that includes 4-(2-aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution. mah 2010-09-13T02:51:13Z response to catecholamine stimulus biological_process GO:0071869 response to catecholamine Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a catecholamine stimulus. A catecholamine is any of a group of biogenic amines that includes 4-(2-aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution. GOC:BHF GOC:mah response to catecholamine stimulus GOC:dos Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a norepinephrine stimulus. Norepinephrine is a catecholamine that has the formula C8H11NO3; it acts as a hormone, and as a neurotransmitter in most of the sympathetic nervous system. mah 2010-09-13T03:31:53Z response to noradrenaline stimulus response to norepinephrine stimulus biological_process GO:0071873 Note that epinephrine and norepinephrine are ligands for the same receptors, and there are multiple adrenergic receptors. response to norepinephrine Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a norepinephrine stimulus. Norepinephrine is a catecholamine that has the formula C8H11NO3; it acts as a hormone, and as a neurotransmitter in most of the sympathetic nervous system. GOC:BHF GOC:mah response to noradrenaline stimulus GOC:mah response to norepinephrine stimulus GOC:dos Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. mah 2010-09-14T12:44:09Z leukocyte apoptosis biological_process GO:0071887 Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). leukocyte apoptotic process Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. CL:0000738 GOC:BHF GOC:mah GOC:mtg_apoptosis The biosynthetic process resulting in the formation of DNA. mah 2010-09-15T02:14:33Z DNA anabolism DNA biosynthesis DNA formation DNA synthesis biological_process GO:0071897 DNA biosynthetic process The biosynthetic process resulting in the formation of DNA. GOC:mah DNA anabolism GOC:mah DNA biosynthesis GOC:mah DNA formation GOC:mah DNA synthesis GOC:mah The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. mah 2010-10-04T01:51:47Z cellular_component GO:0071944 cell periphery The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. GOC:pdt An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain. mah 2010-10-11T11:44:57Z elastic fibre elastin fiber cellular_component GO:0071953 elastic fiber An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain. GOC:BHF GOC:mah PMID:20236620 elastic fibre GOC:mah elastin fiber GOC:BHF The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process GO:0071971 extracellular exosome assembly The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. GOC:mah GOC:tfm PMID:19442504 PMID:27462458 extracellular vesicular exosome assembly GOC:vesicles The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels. mah 2010-01-25T10:31:00Z urinary system development urinary tract development biological_process GO:0072001 renal system development The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels. GOC:mtg_kidney_jan10 GOC:yaf http://en.wikibooks.org/wiki/Human_Physiology/The_Urinary_System urinary system development GOC:yaf urinary tract development GOC:yaf PMID:17881463 The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. mah 2010-02-08T02:03:36Z biological_process GO:0072089 stem cell proliferation The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. GOC:mtg_kidney_jan10 Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. mah 2010-02-08T02:09:03Z biological_process GO:0072091 regulation of stem cell proliferation Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. GOC:mtg_kidney_jan10 The process in which the anatomical structures of a mesenchymal tissue are generated and organized. A mesenchymal tissue is made up of loosely packed stellate cells. mah 2010-02-22T02:17:15Z biological_process GO:0072132 mesenchyme morphogenesis The process in which the anatomical structures of a mesenchymal tissue are generated and organized. A mesenchymal tissue is made up of loosely packed stellate cells. GOC:mtg_kidney_jan10 The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 mah 2010-02-26T02:15:40Z biological_process GO:0072175 epithelial tube formation The developmental process pertaining to the initial formation of an epithelial tube. GOC:mtg_kidney_jan10 Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. mah 2010-03-01T03:43:29Z biological_process GO:0072201 negative regulation of mesenchymal cell proliferation Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. GOC:mtg_kidney_jan10 The chemical reactions and pathways resulting in the breakdown of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. mah 2010-11-02T04:41:55Z biological_process GO:0072329 monocarboxylic acid catabolic process The chemical reactions and pathways resulting in the breakdown of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. GOC:mah The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. mah 2010-11-02T04:51:32Z monocarboxylic acid anabolism monocarboxylic acid biosynthesis monocarboxylic acid formation monocarboxylic acid synthesis biological_process GO:0072330 monocarboxylic acid biosynthetic process The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. GOC:mah monocarboxylic acid anabolism GOC:mah monocarboxylic acid biosynthesis GOC:mah monocarboxylic acid formation GOC:mah monocarboxylic acid synthesis GOC:mah The directed movement of compounds that contain sulfur, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. mah 2010-11-11T11:43:56Z sulfur-containing compound transport biological_process GO:0072348 sulfur compound transport The directed movement of compounds that contain sulfur, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah sulfur-containing compound transport GOC:mah The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. mah 2010-11-16T11:27:39Z GO:0072358 cardiovascular system development biological_process GO:0072359 circulatory system development The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. GOC:mah UBERON:0001009 The progression of the vascular cord over time from its initial formation until its mature state. The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis. mah 2010-11-16T11:46:55Z biological_process GO:0072360 vascular cord development The progression of the vascular cord over time from its initial formation until its mature state. The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis. GOC:mah PMID:7084422 ZFA:0005077 The directed movement of an organelle along a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination. mah 2010-12-01T04:59:11Z microtubule-based organelle localization biological_process GO:0072384 organelle transport along microtubule The directed movement of an organelle along a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination. GOC:mah microtubule-based organelle localization GOC:rl The process in which ammonium is transported across a membrane. Ammonium is the cation NH4+. https://github.com/geneontology/go-ontology/issues/22228 mah 2010-12-10T10:29:57Z GO:0015696 ammonia transport ammonium transport ammonium membrane transport biological_process GO:0072488 Note that this term is not intended for use in annotating lateral movement within membranes. ammonium transmembrane transport The process in which ammonium is transported across a membrane. Ammonium is the cation NH4+. GOC:mah A developmental process, independent of morphogenetic (shape) change, that is required for a type B pancreatic cell to attain its fully functional state. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin. mah 2011-01-27T01:57:14Z pancreatic B cell maturation pancreatic beta cell maturation biological_process GO:0072560 These processes continue to 60 DPA in Gossypium spp. type B pancreatic cell maturation A developmental process, independent of morphogenetic (shape) change, that is required for a type B pancreatic cell to attain its fully functional state. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin. CL:0000169 GOC:BHF pancreatic B cell maturation CL:0000169 GOC:mah pancreatic beta cell maturation CL:0000169 GOC:mah The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the liver. mah 2011-02-02T03:37:50Z biological_process GO:0072575 epithelial cell proliferation involved in liver morphogenesis The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the liver. GOC:BHF GOC:mah The process in which the anatomical structures of the liver are generated and organized. mah 2011-02-02T03:41:30Z biological_process GO:0072576 liver morphogenesis The process in which the anatomical structures of the liver are generated and organized. GOC:mah Any apoptotic process in an endothelial cell. An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. mah 2011-02-02T03:56:24Z apoptosis of endothelial cells endothelial cell programmed cell death by apoptosis killing of endothelial cells programmed cell death of endothelial cells by apoptosis programmed cell death, endothelial cells endothelial cell apoptosis biological_process GO:0072577 endothelial cell apoptotic process Any apoptotic process in an endothelial cell. An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. CL:0000115 GOC:BHF GOC:mah GOC:mtg_apoptosis apoptosis of endothelial cells GOC:mah endothelial cell programmed cell death by apoptosis GOC:mah killing of endothelial cells GOC:mah programmed cell death of endothelial cells by apoptosis GOC:mah programmed cell death, endothelial cells GOC:mah The chemical reactions and pathways involving diatomic oxygen (O2). mah 2011-02-11T10:46:51Z diatomic oxygen metabolic process oxygen metabolism biological_process GO:0072592 oxygen metabolic process The chemical reactions and pathways involving diatomic oxygen (O2). GOC:mah diatomic oxygen metabolic process CHEBI:33263 oxygen metabolism GOC:mah The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle. mah 2011-02-14T01:56:51Z establishment of protein localisation to organelle biological_process GO:0072594 establishment of protein localization to organelle The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle. GOC:mah establishment of protein localisation to organelle GOC:mah A process in which a protein is transported to, or maintained in, a specific location in a membrane. mah 2011-02-14T02:35:18Z protein localisation in membrane protein localization in membrane biological_process GO:0072657 protein localization to membrane A process in which a protein is transported to, or maintained in, a specific location in a membrane. GOC:mah protein localisation in membrane GOC:mah A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane. tb 2009-07-10T10:29:23Z GO:0072661 GO:0090002 biological_process protein localisation in plasma membrane protein localization in plasma membrane protein targeting to plasma membrane protein-plasma membrane targeting GO:0072659 protein localization to plasma membrane A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane. GOC:mah protein localisation in plasma membrane GOC:mah protein-plasma membrane targeting GOC:mah A process in which a protein is transported to, or maintained at, a location in a vacuole. mah 2011-02-14T02:55:35Z protein localisation to vacuole biological_process GO:0072665 protein localization to vacuole A process in which a protein is transported to, or maintained at, a location in a vacuole. GOC:ecd protein localisation to vacuole GOC:mah The directed movement of a protein to a specific location in a vacuole. mah 2011-02-14T02:56:29Z establishment of protein localisation to vacuole biological_process GO:0072666 establishment of protein localization to vacuole The directed movement of a protein to a specific location in a vacuole. GOC:mah establishment of protein localisation to vacuole GOC:mah A process in which a protein is transported to, or maintained in, the cell cortex. mah 2012-04-11T01:16:33Z protein localisation to cell cortex biological_process GO:0072697 protein localization to cell cortex A process in which a protein is transported to, or maintained in, the cell cortex. GOC:mah protein localisation to cell cortex GOC:mah A cellular protein localization process in which a protein is transported to, or maintained at, a location within the microtubule cytoskeleton. mah 2012-04-11T01:19:35Z protein localisation to microtubule cytoskeleton biological_process GO:0072698 protein localization to microtubule cytoskeleton A cellular protein localization process in which a protein is transported to, or maintained at, a location within the microtubule cytoskeleton. GOC:mah protein localisation to microtubule cytoskeleton GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. dhl 2009-04-22T04:30:52Z biological_process GO:0080090 regulation of primary metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. PMID:19211694 Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). dhl 2009-05-06T04:51:28Z biological_process GO:0080134 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to stress Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:dhl Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). dhl 2009-05-06T05:02:52Z biological_process GO:0080135 regulation of cellular response to stress Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:dhl Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). dhl 2010-09-01T03:44:27Z biological_process GO:0080154 regulation of fertilization Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:DHL PMID:20478994 The aggregation, arrangement and bonding together of the extracellular matrix. jl 2010-07-14T12:52:49Z biological_process GO:0085029 extracellular matrix assembly The aggregation, arrangement and bonding together of the extracellular matrix. GOC:jl An action potential that occurs in a cardiac muscle cell. tb 2011-11-10T07:45:11Z biological_process GO:0086001 cardiac muscle cell action potential An action potential that occurs in a cardiac muscle cell. GOC:BHF GOC:mtg_cardiac_conduct_nov11 An action potential that occurs in a sinoatrial node cardiac muscle cell. tb 2011-11-10T08:50:15Z SA node cardiac muscle cell action potential SAN cardiac muscle cell action potential sinoatrial node cardiac muscle cell action potential sinus node cardiac muscle cell action potential biological_process GO:0086015 SA node cell action potential An action potential that occurs in a sinoatrial node cardiac muscle cell. GOC:BHF GOC:mtg_cardiac_conduct_nov11 An action potential that occurs in an atrioventricular node cardiac muscle cell. tb 2011-11-10T08:58:56Z AV node cardiac muscle cell action potential atrioventricular node cardiac muscle cell action potential biological_process GO:0086016 AV node cell action potential An action potential that occurs in an atrioventricular node cardiac muscle cell. GOC:BHF GOC:mtg_cardiac_conduct_nov11 An action potential that occurs in a Purkinje myocyte. tb 2011-11-10T08:58:56Z biological_process GO:0086017 Purkinje myocyte action potential An action potential that occurs in a Purkinje myocyte. GOC:BHF GOC:mtg_cardiac_conduct_nov11 Any process that mediates the transfer of information from an SA node cardiomyocyte to an atrial cardiomyocyte. tb 2011-11-10T09:15:01Z SA node cardiac muscle cell to atrial cardiac muscle cell signalling SA node cardiomyocyte to atrial cardiomyocyte signalling SAN cardiomyocyte to atrial cardiomyocyte signalling sinoatrial node cardiomyocyte to atrial cardiomyocyte signalling sinus node cardiomyocyte to atrial cardiomyocyte signalling biological_process GO:0086018 SA node cell to atrial cardiac muscle cell signaling Any process that mediates the transfer of information from an SA node cardiomyocyte to an atrial cardiomyocyte. GOC:BHF GOC:mtg_cardiac_conduct_nov11 Any process that mediates the transfer of information from one cell to another and contributes to the heart process that regulates cardiac muscle contraction; beginning with the generation of an action potential in the sinoatrial node and ending with regulation of contraction of the myocardium. dph 2011-11-16T03:43:52Z cell-cell signalling involved in cardiac conduction biological_process GO:0086019 cell-cell signaling involved in cardiac conduction Any process that mediates the transfer of information from one cell to another and contributes to the heart process that regulates cardiac muscle contraction; beginning with the generation of an action potential in the sinoatrial node and ending with regulation of contraction of the myocardium. GOC:BHF GOC:mtg_cardiac_conduct_nov11 cell-cell signalling involved in cardiac conduction GOC:mah Any process that mediates the transfer of information from an AV node cardiac muscle cell to a bundle of His cardiomyocyte. tb 2011-11-11T02:02:14Z AV node cell to bundle of His cell signalling atrioventricular node to bundle of His cell signaling biological_process GO:0086027 AV node cell to bundle of His cell signaling Any process that mediates the transfer of information from an AV node cardiac muscle cell to a bundle of His cardiomyocyte. GOC:BHF GOC:mtg_cardiac_conduct_nov11 AV node cell to bundle of His cell signalling GOC:mah Any process that mediates the transfer of information from a Purkinje myocyte to a ventricular cardiac muscle cell. tb 2011-11-11T02:02:14Z Purkinje myocyte to ventricular cardiac muscle cell signalling biological_process GO:0086029 Purkinje myocyte to ventricular cardiac muscle cell signaling Any process that mediates the transfer of information from a Purkinje myocyte to a ventricular cardiac muscle cell. GOC:BHF GOC:mtg_cardiac_conduct_nov11 Purkinje myocyte to ventricular cardiac muscle cell signalling GOC:mah Any process that mediates interactions between a cell and its surroundings that contributes to the process of cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. dph 2011-11-22T08:57:02Z biological_process GO:0086065 cell communication involved in cardiac conduction Any process that mediates interactions between a cell and its surroundings that contributes to the process of cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:BHF GOC:mtg_cardiac_conduct_nov11 The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. dph 2011-11-22T09:11:44Z atrioventricular node cell to bundle of His cell communication biological_process GO:0086067 AV node cell to bundle of His cell communication The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:BHF GOC:mtg_cardiac_conduct_nov11 The process that mediates interactions between a Purkinje myocyte and its surroundings that contributes to the process of the Purkinje myocyte communicating with a ventricular cardiac muscle cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. dph 2011-11-22T09:14:49Z biological_process GO:0086068 Purkinje myocyte to ventricular cardiac muscle cell communication The process that mediates interactions between a Purkinje myocyte and its surroundings that contributes to the process of the Purkinje myocyte communicating with a ventricular cardiac muscle cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:BHF GOC:mtg_cardiac_conduct_nov11 The process that mediates interactions between an SA node cardiomyocyte and its surroundings that contributes to the process of the SA node cardiomyocyte communicating with an atrial cardiomyocyte in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. dph 2011-11-22T09:32:45Z SA node cardiac muscle cell to atrial cardiac muscle cell communication SA node cardiomyocyte to atrial cardiomyocyte communication SAN cardiomyocyte to atrial cardiomyocyte communication sinoatrial node cardiomyocyte to atrial cardiomyocyte communication sinus node cardiomyocyte to atrial cardiomyocyte communication biological_process GO:0086070 SA node cell to atrial cardiac muscle cell communication The process that mediates interactions between an SA node cardiomyocyte and its surroundings that contributes to the process of the SA node cardiomyocyte communicating with an atrial cardiomyocyte in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:BHF GOC:mtg_cardiac_conduct_nov11 Any process that increases the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell. tb 2009-08-12T11:33:09Z biological_process GO:0090063 positive regulation of microtubule nucleation Any process that increases the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tb 2009-09-09T11:39:52Z biological_process GO:0090068 positive regulation of cell cycle process Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits. tb 2009-09-11T10:32:17Z biological_process GO:0090069 regulation of ribosome biogenesis Any process that modulates the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits. tb 2009-09-11T10:32:17Z biological_process GO:0090070 positive regulation of ribosome biogenesis Any process that increases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits. tb 2009-09-11T10:32:17Z biological_process GO:0090071 negative regulation of ribosome biogenesis Any process that decreases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. tb 2009-10-23T11:21:38Z biological_process GO:0090087 regulation of peptide transport Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. tb 2009-11-04T10:03:25Z biological_process GO:0090091 positive regulation of extracellular matrix disassembly Any process that increases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix. GOC:dph GOC:tb The directed movement of a protein to a specific location in a membrane. tb 2009-12-08T03:18:51Z establishment of protein localisation in membrane establishment of protein localization in membrane biological_process GO:0090150 establishment of protein localization to membrane The directed movement of a protein to a specific location in a membrane. GOC:ascb_2009 GOC:dph GOC:tb establishment of protein localisation in membrane GOC:mah The specification and formation of anisotropic intracellular organization of an epithelial cell. tb 2009-12-08T08:58:27Z biological_process GO:0090162 establishment of epithelial cell polarity The specification and formation of anisotropic intracellular organization of an epithelial cell. GOC:ascb_2009 GOC:dph GOC:tb A cellular process that results in the breakdown of a Golgi apparatus that contributes to Golgi inheritance. tb 2009-12-08T09:15:11Z Golgi apparatus disassembly biological_process GO:0090166 Golgi disassembly A cellular process that results in the breakdown of a Golgi apparatus that contributes to Golgi inheritance. GOC:ascb_2009 GOC:dph GOC:tb The reformation of the Golgi following its breakdown and partitioning contributing to Golgi inheritance. tb 2009-12-08T09:15:11Z Golgi apparatus reassembly biological_process GO:0090168 Golgi reassembly The reformation of the Golgi following its breakdown and partitioning contributing to Golgi inheritance. GOC:ascb_2009 GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division. tb 2009-12-11T10:21:59Z biological_process GO:0090170 regulation of Golgi inheritance Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division. GOC:ascb_2009 GOC:dph GOC:tb The process in which the structures of a chondrocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a chondrocyte. tb 2009-12-11T10:36:02Z biological_process GO:0090171 chondrocyte morphogenesis The process in which the structures of a chondrocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a chondrocyte. GOC:ascb_2009 GOC:dph GOC:tb The joining of two lipid bilayers to form a single organelle membrane. tb 2009-12-11T11:44:58Z biological_process GO:0090174 organelle membrane fusion The joining of two lipid bilayers to form a single organelle membrane. GOC:ascb_2009 GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system. tb 2010-02-03T11:48:13Z biological_process GO:0090257 regulation of muscle system process Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system. GOC:dph GOC:tb Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090273 regulation of somatostatin secretion Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090274 positive regulation of somatostatin secretion Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090275 negative regulation of somatostatin secretion Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090276 regulation of peptide hormone secretion Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090277 positive regulation of peptide hormone secretion Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090278 negative regulation of peptide hormone secretion Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that modulates the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds. tb 2010-03-12T04:08:26Z biological_process GO:0090299 regulation of neural crest formation Any process that modulates the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds. GOC:tb Any process that increases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes. tb 2010-03-12T04:08:26Z biological_process GO:0090300 positive regulation of neural crest formation Any process that increases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes. GOC:tb Any process that decreases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes. tb 2010-03-12T04:08:26Z biological_process GO:0090301 negative regulation of neural crest formation Any process that decreases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes. GOC:tb Any cellular metabolic process involving nucleic acids. https://github.com/geneontology/go-ontology/issues/26133 tb 2010-04-07T10:18:47Z biological_process GO:0090304 nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. tb 2010-04-16T03:45:07Z biological_process GO:0090316 positive regulation of intracellular protein transport Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. tb 2010-04-16T03:45:07Z biological_process GO:0090317 negative regulation of intracellular protein transport Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. tb 2010-05-14T10:24:29Z biological_process GO:0090325 regulation of locomotion involved in locomotory behavior Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. GOC:dph GOC:kmv GOC:tb Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. tb 2010-05-14T10:26:58Z biological_process GO:0090326 positive regulation of locomotion involved in locomotory behavior Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. GOC:dph GOC:kmv GOC:tb Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. tb 2010-05-14T10:26:58Z biological_process GO:0090327 negative regulation of locomotion involved in locomotory behavior Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. GOC:dph GOC:kmv GOC:tb The epithelial cell differentiation process in which a relatively unspecialized cell acquires specialized features of an acinar cell, a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini. tb 2012-05-04T09:24:48Z biological_process GO:0090425 acinar cell differentiation The epithelial cell differentiation process in which a relatively unspecialized cell acquires specialized features of an acinar cell, a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini. GOC:dph GOC:tb A process in which a protein is transported to, or maintained at, a location within a nuclear envelope. tb 2012-07-30T01:50:41Z protein localization in nuclear envelope biological_process GO:0090435 protein localization to nuclear envelope A process in which a protein is transported to, or maintained at, a location within a nuclear envelope. GOC:tb The directed movement of catecholamine into a cell. tb 2012-10-17T11:06:17Z biological_process GO:0090493 catecholamine uptake The directed movement of catecholamine into a cell. GOC:dph GOC:tb Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. tb 2014-08-22T13:23:20Z biological_process GO:0090596 sensory organ morphogenesis Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:kmv ISBN:978-0199210893 A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus. tb 2016-07-19T17:00:49Z RNA localisation to nucleus biological_process GO:0090685 RNA localization to nucleus A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus. GOC:mah PMID:26305931 RNA localisation to nucleus GOC:mah A region of a chromosome at which DNA damage has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. tb 2017-02-03T17:24:08Z Wikipedia:DNA_repair cellular_component GO:0090734 site of DNA damage A region of a chromosome at which DNA damage has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. GOC:pg Any membrane that is part of a pigment granule. tb 2017-05-16T22:33:39Z cellular_component GO:0090741 pigment granule membrane Any membrane that is part of a pigment granule. PMID:11294610 All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. pr 2011-03-23T01:52:31Z cilium plasm microtubule-based flagellar matrix microtubule-based flagellum matrix cellular_component cilial cytoplasm ciliary cytoplasm cilium cytoplasm microtubule-based flagellar cytoplasm microtubule-based flagellum cytoplasm GO:0097014 Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm". ciliary plasm All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. GOC:BHF GOC:cilia GOC:dos PMID:17895364 Any apoptotic process in a motor neuron, an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement. pr 2011-05-04T02:21:43Z motoneuron apoptosis motor neuron apoptosis biological_process GO:0097049 motor neuron apoptotic process Any apoptotic process in a motor neuron, an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement. CL:0000100 GOC:BHF GOC:mtg_apoptosis PMID:14523086 Any apoptotic process in a type B pancreatic cell, a cell located towards center of the islets of Langerhans that secretes insulin. pr 2011-05-04T02:24:38Z pancreatic B cell apoptosis pancreatic beta cell apoptosis type B pancreatic cell apoptosis biological_process GO:0097050 type B pancreatic cell apoptotic process Any apoptotic process in a type B pancreatic cell, a cell located towards center of the islets of Langerhans that secretes insulin. CL:0000169 GOC:BHF GOC:mtg_apoptosis PMID:16087305 A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. pr 2011-06-07T11:22:09Z cellular_component GO:0097060 synaptic membrane A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. GOC:BHF PMID:20410104 The process aimed at the progression of a vascular smooth muscle cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels. pr 2011-06-20T04:03:08Z vascular smooth muscle cell development biological_process GO:0097084 vascular associated smooth muscle cell development The process aimed at the progression of a vascular smooth muscle cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels. GOC:BHF Any apoptotic process in a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types. pr 2011-09-06T02:31:59Z mesenchymal cell apoptosis biological_process GO:0097152 mesenchymal cell apoptotic process Any apoptotic process in a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types. CL:0000134 GOC:mtg_apoptosis GOC:yaf PMID:18231833 The chemical reactions and pathways involving the ammonium ion. pr 2011-09-28T04:21:30Z ammonium ion metabolism biological_process ammonium metabolic process GO:0097164 ammonium ion metabolic process The chemical reactions and pathways involving the ammonium ion. GOC:dhl GOC:tb PMID:14671018 The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. pr 2011-11-23T09:30:23Z GO:0008624 apoptotic signalling pathway induction of apoptosis by extracellular signals biological_process GO:0097190 This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. apoptotic signaling pathway The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. GOC:mtg_apoptosis apoptotic signalling pathway GOC:mah A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis biological_process GO:0097194 execution phase of apoptosis A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:mtg_apoptosis PMID:21760595 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. pr 2012-02-02T12:23:31Z biological_process GO:0097237 cellular response to toxic substance Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. GOC:pr The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs. https://github.com/geneontology/go-ontology/issues/22368 pr 2012-03-05T02:03:58Z biological_process GO:0097254 renal tubular secretion The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs. GOC:rph PMID:25287933 Wikipedia:Renal_secretion#Secretion Any apoptotic process in a hepatocyte, the main structural component of the liver. pr 2012-03-29T10:23:21Z hepatocyte apoptosis biological_process GO:0097284 hepatocyte apoptotic process Any apoptotic process in a hepatocyte, the main structural component of the liver. CL:0000182 GOC:jc GOC:mtg_apoptosis PMID:15856020 Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin. pr 2012-07-03T03:19:07Z protein localisation to heterochromatin biological_process GO:0097355 protein localization to heterochromatin Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin. GOC:mah protein localisation to heterochromatin GOC:mah A prolongation or process extending from a glial cell. pr 2012-10-22T13:55:54Z cellular_component glial process glial projection GO:0097386 glial cell projection A prolongation or process extending from a glial cell. GOC:mc An arrangement of closely apposed microtubules running parallel to each other. pr 2012-11-07T15:01:27Z NIF_Subcellular:sao1872343973 microtubule fascicle cellular_component GO:0097427 microtubule bundle An arrangement of closely apposed microtubules running parallel to each other. NIF_Subcellular:sao1872343973 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. pr 2012-11-27T15:46:25Z GO:0043206 extracellular fibril organisation extracellular fibril organization extracellular fibril organization and biogenesis biological_process fibril organisation fibril organization GO:0097435 supramolecular fiber organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GOC:pr extracellular fibril organization and biogenesis GOC:mah Any apoptotic process in a retinal rod cell, one of the two photoreceptor cell types of the vertebrate retina. pr 2013-03-21T09:44:45Z rod photoreceptor apoptotic process biological_process GO:0097473 retinal rod cell apoptotic process Any apoptotic process in a retinal rod cell, one of the two photoreceptor cell types of the vertebrate retina. CL:0000604 GOC:jc PMID:17202487 Any apoptotic process in a retinal cone cell, one of the two photoreceptor cell types of the vertebrate retina. pr 2013-03-21T09:46:22Z cone photoreceptor apoptotic process biological_process GO:0097474 retinal cone cell apoptotic process Any apoptotic process in a retinal cone cell, one of the two photoreceptor cell types of the vertebrate retina. CL:0000573 GOC:jc A cardiac myofibril is a myofibril specific to cardiac muscle cells. pr 2013-10-16T13:04:58Z cellular_component GO:0097512 cardiac myofibril A cardiac myofibril is a myofibril specific to cardiac muscle cells. GOC:cjm GOC:devbiol Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole. pr 2014-02-28T09:49:31Z biological_process GO:0097576 vacuole fusion Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole. GOC:pr GOC:vw Wikipedia:Vacuole Any vesicle that is part of the intracellular region. pr 2016-03-29T17:39:45Z cellular_component GO:0097708 intracellular vesicle Any vesicle that is part of the intracellular region. GOC:vesicles The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane. pr 2016-08-05T16:12:33Z Reactome:R-HSA-5620912.1 ciliary basal body docking biological_process anchoring of the basal body to the plasma membrane GO:0097711 Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella. ciliary basal body-plasma membrane docking The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane. GOC:cilia PMID:13978319 PMID:23348840 PMID:23530209 PMID:25686250 PMID:26981235 Reactome:R-HSA-5620912.1 The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. pr 2016-08-05T16:16:28Z biological_process GO:0097712 vesicle targeting, trans-Golgi to periciliary membrane compartment The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. GOC:cilia PMID:20106869 PMID:23351793 PMID:24814148 PMID:26485645 Reactome:R-HSA-5620920.1 The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis exosome production biological_process ILV assembly intraluminal vesicle assembly GO:0097734 extracellular exosome biogenesis The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. GOC:PARL GOC:bf PMID:19442504 PMID:25392495 A neuromuscular junction in which the target muscle cell is a myotube. dos 2013-10-14T12:05:12Z cellular_component GO:0098523 In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting the myotubes of skeletal muscle (AKA skeletal muscle fibers). Neuromuscular junctions targeting other muscle cell types exist in invertebrates such as the mononucleate somatic muscles of nematodes. neuromuscular junction of myotube A neuromuscular junction in which the target muscle cell is a myotube. GOC:dos The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle fiber cell. Skeletal muscle fiber differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual skeletal muscle fibers fuse to form bigger myotubes and start to contract. dos 2013-10-15T14:00:34Z biological_process GO:0098528 skeletal muscle fiber differentiation The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle fiber cell. Skeletal muscle fiber differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual skeletal muscle fibers fuse to form bigger myotubes and start to contract. GOC:dos The lipid bilayer that forms the outer-most layer of an organelle. dos 2014-02-26T13:41:31Z cellular_component GO:0098588 Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. bounding membrane of organelle The lipid bilayer that forms the outer-most layer of an organelle. GOC:dos A membrane that is a (regional) part of the plasma membrane. dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component GO:0098590 Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. plasma membrane region A membrane that is a (regional) part of the plasma membrane. GOC:dos A collagen trimer that forms networks. cellular_component GO:0098642 network-forming collagen trimer A collagen trimer that forms networks. PMID:21421911 A supramolecular assembly of fibrillar collagen complexes in the form of a long fiber (fibril) with transverse striations (bands). cellular_component GO:0098643 banded collagen fibril A supramolecular assembly of fibrillar collagen complexes in the form of a long fiber (fibril) with transverse striations (bands). GOC:dos PMID:21421911 A complex of collagen trimers such as a fibril or collagen network. Supramolecular aggregate of collagen Supramolecular collagen assembly cellular_component GO:0098644 complex of collagen trimers A complex of collagen trimers such as a fibril or collagen network. GOC:dos Supramolecular aggregate of collagen PMID:19693541 Supramolecular collagen assembly PMID:21421911 A supramolecular complex that consists of collagen triple helices associated to form a network. cellular_component GO:0098645 collagen network A supramolecular complex that consists of collagen triple helices associated to form a network. GOC:dos PMID:21421911 Any collagen timer that is part of a basement membrane. cellular_component GO:0098651 basement membrane collagen trimer Any collagen timer that is part of a basement membrane. GOC:dos PMID:21421911 The process in which a monoatomic cation is transported across a membrane. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom. GO:0099132 cation transmembrane transport ATP hydrolysis coupled cation transmembrane transport biological_process GO:0098655 monoatomic cation transmembrane transport The process in which a monoatomic cation is transported across a membrane. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom. GOC:dos GOC:vw The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. uptake biological_process GO:0098657 import into cell The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. GOC:dos The process in which an inorganic ion is transported across a membrane. inorganic ion membrane transport transmembrane inorganic ion transport biological_process GO:0098660 Note that this term is not intended for use in annotating lateral movement within membranes. inorganic ion transmembrane transport The process in which an inorganic ion is transported across a membrane. GOC:mah transmembrane inorganic ion transport GOC:dph GOC:tb The process in which an inorganic anion is transported across a membrane. inorganic anion membrane transport transmembrane inorganic anion transport biological_process GO:0098661 Note that this term is not intended for use in annotating lateral movement within membranes. inorganic anion transmembrane transport The process in which an inorganic anion is transported across a membrane. GOC:mah transmembrane inorganic anion transport GOC:dph GOC:tb A process in which an inorganic cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. GO:0015672 GO:0072511 inorganic cation membrane transport transmembrane inorganic cation transport divalent inorganic cation transport monovalent inorganic cation transport biological_process GO:0098662 Note that this term is not intended for use in annotating lateral movement within membranes. inorganic cation transmembrane transport A process in which an inorganic cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. GOC:mah transmembrane inorganic cation transport GOC:dph GOC:tb Division of a stem cell during which it retains its identity and buds off a daughter cell with a new identity. biological_process GO:0098722 asymmetric stem cell division Division of a stem cell during which it retains its identity and buds off a daughter cell with a new identity. GOC:dos PMID:18513950 A myofibril of a skeletal muscle fiber. cellular_component GO:0098723 skeletal muscle myofibril A myofibril of a skeletal muscle fiber. GOC:dos The self-renewing division of a germline stem cell, to produce a daughter stem cell and a daughter germ cell which will divide to form one or more gametes. biological_process GO:0098728 germline stem cell asymmetric division The self-renewing division of a germline stem cell, to produce a daughter stem cell and a daughter germ cell which will divide to form one or more gametes. GOC:dos The process whose specific outcome is the progression of a bone cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. biological_process GO:0098751 Not to be used for manual annotation. Please choose a more specific cell development term or if not possible, bone or bone tissue development. bone cell development The process whose specific outcome is the progression of a bone cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. GOC:dos Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. biological_process GO:0098754 detoxification Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. GOC:dos The process whose specific outcome is the progression of the skin epidermis over time, from its formation to the mature structure. biological_process GO:0098773 skin epidermis development The process whose specific outcome is the progression of the skin epidermis over time, from its formation to the mature structure. GOC:dos The part of a synapse that is part of the presynaptic cell. presynaptic terminal cellular_component GO:0098793 presynapse The part of a synapse that is part of the presynaptic cell. GOC:dos The part of a synapse that is part of the post-synaptic cell. cellular_component GO:0098794 postsynapse The part of a synapse that is part of the post-synaptic cell. GOC:dos Any protein complex that is part of a membrane. cellular_component GO:0098796 membrane protein complex Any protein complex that is part of a membrane. GOC:dos Any protein complex that is part of the plasma membrane. cellular_component GO:0098797 plasma membrane protein complex Any protein complex that is part of the plasma membrane. GOC:dos Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system. biological_process GO:0098801 regulation of renal system process Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system. GOC:dos The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. biological_process GO:0098813 nuclear chromosome segregation The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:dos The directed movement of a protein along a microtubule, mediated by motor proteins. microtubule-based protein transport biological_process GO:0098840 protein transport along microtubule The directed movement of a protein along a microtubule, mediated by motor proteins. PMID:25987607 A cell projection supported by an assembly of actin filaments, and which lacks microtubules. cellular_component GO:0098858 actin-based cell projection A cell projection supported by an assembly of actin filaments, and which lacks microtubules. PMID:15661519 The increase in size or mass of an intramembranous bone that contributes to the shaping of the bone. biological_process GO:0098867 intramembranous bone growth The increase in size or mass of an intramembranous bone that contributes to the shaping of the bone. PMID:26399686 The increase in size or mass of a bone that contributes to the shaping of that bone. biological_process GO:0098868 bone growth The increase in size or mass of a bone that contributes to the shaping of that bone. GOC:dos The actin cytoskeleton that is part of a postsynapse. cellular_component GO:0098871 postsynaptic actin cytoskeleton The actin cytoskeleton that is part of a postsynapse. GOC:dos The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis. biological_process GO:0098876 vesicle-mediated transport to the plasma membrane The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis. GOC:dos A cellular process that results in the controlled breakdown of synapse. After it starts the process is continuous until the synapse has disappeared. synapse clearance synapse disassembly synapse elimination synapse removal biological_process GO:0098883 synapse pruning A cellular process that results in the controlled breakdown of synapse. After it starts the process is continuous until the synapse has disappeared. GOC:dos PMID:12062020 PMID:18083105 PMID:22632716 PMID:29844190 synapse clearance GOC:aruk GOC:bc PMID:22632716 synapse disassembly PMID:12062020 synapse elimination GOC:aruk GOC:bc PMID:18083105 PMID:29844190 synapse removal GOC:aruk GOC:bc PMID:22632716 Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. biological_process GO:0098900 The ion channels through which current flows during an action potential should be annotated to the process 'action potential'. Gene products involved in modulating the characteristics of an action potential via changing the expression levels or the activity of these channels (e.g. modulating their kinetics or voltage sensitivity) should be annotated to this regulation term. regulation of action potential Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:dos GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. biological_process GO:0098901 regulation of cardiac muscle cell action potential Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:dos GOC:mtg_cardiac_conduct_nov11 Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrioventricular node myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. tb 2011-11-10T08:58:56Z regulation of AV node cardiac muscle cell action potential regulation of atrioventricular node cardiac muscle cell action potential biological_process GO:0098904 regulation of AV node cell action potential Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrioventricular node myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:BHF GOC:mtg_cardiac_conduct_nov11 Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a Purkinje myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. tb 2011-11-10T08:58:56Z biological_process GO:0098906 regulation of Purkinje myocyte action potential Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a Purkinje myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:BHF GOC:mtg_cardiac_conduct_nov11 Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an SA node cardiac myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. tb 2011-11-10T08:50:15Z regulation of SA node cardiac muscle cell action potential regulation of SAN cardiac muscle cell action potential regulation of sinoatrial node cardiac muscle cell action potential regulation of sinus node cardiac muscle cell action potential biological_process GO:0098907 regulation of SA node cell action potential Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an SA node cardiac myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:BHF GOC:mtg_cardiac_conduct_nov11 Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a neuron. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. biological_process generation of action potential GO:0098908 regulation of neuronal action potential Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a neuron. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:dph GOC:isa_complete GOC:tb generation of action potential GOC:dph GOC:tb Cell-cell signaling from pre to post-synapse, across the synaptic cleft. biological_process GO:0098916 anterograde trans-synaptic signaling Cell-cell signaling from pre to post-synapse, across the synaptic cleft. GOC:dos Cell-cell signaling from post to pre-synapse, across the synaptic cleft. biological_process GO:0098917 retrograde trans-synaptic signaling Cell-cell signaling from post to pre-synapse, across the synaptic cleft. GOC:dos Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a lipid ligand. biological_process GO:0098920 retrograde trans-synaptic signaling by lipid Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a lipid ligand. GOC:dos Signal transduction in which the initial step occurs in a postsynapse. postsynaptic signaling pathway biological_process GO:0098926 postsynaptic signal transduction Signal transduction in which the initial step occurs in a postsynapse. GOC:dos postsynaptic signaling pathway Signal transduction in which the initial step occurs in a presynapse. presynaptic signaling pathway biological_process GO:0098928 presynaptic signal transduction Signal transduction in which the initial step occurs in a presynapse. GOC:dos presynaptic signaling pathway A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the postsynaptic actin cytoskeleton. biological_process GO:0098974 postsynaptic actin cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the postsynaptic actin cytoskeleton. GOC:dos The postsynapse of a neuromuscular junction. In vertebrate muscles this includes the motor end-plate, consisting of postjunctional folds of the sarcolemma. cellular_component GO:0098975 postsynapse of neuromuscular junction The postsynapse of a neuromuscular junction. In vertebrate muscles this includes the motor end-plate, consisting of postjunctional folds of the sarcolemma. GOC:dos Wikipedia:Neuromuscular_junction&oldid=723623502 A synapse that uses acetylcholine as a neurotransmitter. cellular_component GO:0098981 cholinergic synapse A synapse that uses acetylcholine as a neurotransmitter. GOC:dos A dense core vesicle (granule) that is part of a neuron. These vesicles typically contain neuropeptides. They can be found in all parts of neurons, including the soma, dendrites, axonal swellings (varicosities) and synaptic terminals. cellular_component GO:0098992 neuronal dense core vesicle A dense core vesicle (granule) that is part of a neuron. These vesicles typically contain neuropeptides. They can be found in all parts of neurons, including the soma, dendrites, axonal swellings (varicosities) and synaptic terminals. GOC:dos ISBN:978-0-07-181001-2 Wikipedia:Neuropeptide&oldid=713905176 Any vesicle-mediated transport that occurs in a synapse. biological_process GO:0099003 vesicle-mediated transport in synapse Any vesicle-mediated transport that occurs in a synapse. GOC:dos The lipid bilayer surrounding a neuronal dense core vesicle. cellular_component GO:0099012 neuronal dense core vesicle membrane The lipid bilayer surrounding a neuronal dense core vesicle. GOC:dos A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuronal dense core vesicle. biological_process GO:0099014 neuronal dense core vesicle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuronal dense core vesicle. GOC:dos The aggregation, arrangement and bonding together of a set of components to form a presynapse. presynapse biogenesis presynaptic terminal assembly biological_process GO:0099054 presynapse assembly The aggregation, arrangement and bonding together of a set of components to form a presynapse. GOC:PARL GOC:bf GOC:dos PMID:24449494 presynapse biogenesis GOC:mah presynaptic terminal assembly PMID:24449494 The aggregation, arrangement and bonding together of a set of components to form a postsynapse. postsynapse biogenesis biological_process GO:0099068 postsynapse assembly The aggregation, arrangement and bonding together of a set of components to form a postsynapse. GOC:bf GOC:dos GOCL:PARL postsynapse biogenesis GOC:mah A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber. cellular_component GO:0099080 supramolecular complex A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber. GOC:dos A polymeric supramolecular structure. cellular_component GO:0099081 supramolecular polymer A polymeric supramolecular structure. GOC:dos Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a neuropeptide. biological_process GO:0099082 retrograde trans-synaptic signaling by neuropeptide Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a neuropeptide. GOC:PARL GOC:bf GOC:dos PMID:19448629 Modulation of synaptic transmittion by cell-cell signaling across the synaptic cleft from postsynapse to presynapse, mediated by a neuropeptide. biological_process GO:0099083 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission Modulation of synaptic transmittion by cell-cell signaling across the synaptic cleft from postsynapse to presynapse, mediated by a neuropeptide. GOC:PARL GOC:bf GOC:dos PMID:19448629 The movement of a cellular component as a result of microtubule polymerization. biological_process GO:0099098 microtubule polymerization based movement The movement of a cellular component as a result of microtubule polymerization. GOC:cjm ISBN:0815316194 A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. biological_process GO:0099111 microtubule-based transport A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. GOC:cjm ISBN:0815316194 The transport of a protein driven by polymerization of a microtubule to which it is attached. biological_process GO:0099112 microtubule polymerization based protein transport The transport of a protein driven by polymerization of a microtubule to which it is attached. GOC:dos GOC:vw PMID:11018050 A microtubule-based process that results in the transport of proteins. biological_process GO:0099118 microtubule-based protein transport A microtubule-based process that results in the transport of proteins. GOC:vw A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the presynaptic actin cytoskeleton. dos 2017-06-09T18:34:19Z biological_process GO:0099140 presynaptic actin cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the presynaptic actin cytoskeleton. GOC:dos The actin cytoskeleton that is part of a presynapse. dos 2017-06-09T18:36:19Z cellular_component GO:0099143 presynaptic actin cytoskeleton The actin cytoskeleton that is part of a presynapse. GOC:dos Cell-cell signaling in which the ligand is carried between cells by an exosome. dos 2017-07-05T16:40:45Z exosome mediated biological_process GO:0099156 cell-cell signaling via exosome Cell-cell signaling in which the ligand is carried between cells by an exosome. GOC:dos PMID:19837038 Transynaptic signaling in which the ligand is carried across the synapse by an exosome. dos 2017-07-05T16:49:44Z exosome mediated transynaptic signalling trans-synaptic signalling via exosome biological_process GO:0099157 trans-synaptic signaling via exosome Transynaptic signaling in which the ligand is carried across the synapse by an exosome. GOC:dos PMID:19837038 Any process, acting in the postsynapse that results in modulation of chemical synaptic transmission. dos 2017-09-11T17:09:17Z biological_process GO:0099170 postsynaptic modulation of chemical synaptic transmission Any process, acting in the postsynapse that results in modulation of chemical synaptic transmission. GOC:dos Any process, acting in the presynapse that results in modulation of chemical synaptic transmission. dos 2017-09-11T17:09:31Z biological_process GO:0099171 presynaptic modulation of chemical synaptic transmission Any process, acting in the presynapse that results in modulation of chemical synaptic transmission. GOC:dos A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a presynapse. presynapse development presynapse organisation biological_process presynapse morphogenesis presynapse organization and biogenesis GO:0099172 presynapse organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a presynapse. GOC:dos presynapse morphogenesis GOC:BHF presynapse organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a postsynapse. postsynapse development postsynapse organisation biological_process postsynapse morphogenesis postsynapse organization and biogenesis GO:0099173 postsynapse organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a postsynapse. GOC:dos postsynapse morphogenesis GOC:BHF postsynapse organization and biogenesis GOC:mah Any process that modulates the physical form of a presynapse. regulation of presynapse organisation regulation of presynapse structure biological_process regulation of presynapse organization and biogenesis GO:0099174 regulation of presynapse organization Any process that modulates the physical form of a presynapse. GOC:ai GOC:dph GOC:tb regulation of presynapse organisation GOC:mah regulation of presynapse organization and biogenesis GOC:mah Any process that modulates the physical form of a postsynapse. regulation of postsynapse organisation regulation of postsynapse structure biological_process regulation of postsynapse organization and biogenesis GO:0099175 regulation of postsynapse organization Any process that modulates the physical form of a postsynapse. GOC:ai GOC:dph GOC:tb regulation of postsynapse organisation GOC:mah regulation of postsynapse organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of trans-synaptic signaling. biological_process GO:0099177 regulation of trans-synaptic signaling Any process that modulates the frequency, rate or extent of trans-synaptic signaling. GOC:dos A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures and their associated proteins in the presynaptic cytoskeleton. dos 2017-12-20T15:05:34Z biological_process GO:0099187 presynaptic cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures and their associated proteins in the presynaptic cytoskeleton. GOC:dos A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising cytoskeletal filaments and their associated proteins in the postsynaptic cytoskeleton. dos 2017-12-20T15:06:57Z biological_process GO:0099188 postsynaptic cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising cytoskeletal filaments and their associated proteins in the postsynaptic cytoskeleton. GOC:dos Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space. biological_process GO:0099500 vesicle fusion to plasma membrane Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space. GOC:aruk GOC:bc ISBN:0071120009 PMID:18618940 The lipid bilayer surrounding an exocytic vesicle. secretory vesicle membrane cellular_component GO:0099501 exocytic vesicle membrane The lipid bilayer surrounding an exocytic vesicle. GOC:dos A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. cellular_component GO:0099503 secretory vesicle A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. GOC:dos A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GO:0043205 cellular_component fibril GO:0099512 supramolecular fiber A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GOC:dos A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. cellular_component GO:0099513 polymeric cytoskeletal fiber A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. GOC:dos The transport of organelles or other particles from one location in the cell to another along actin filaments. tb 2009-05-27T10:56:08Z biological_process GO:0099515 actin filament-based transport The transport of organelles or other particles from one location in the cell to another along actin filaments. GOC:dos GOC:dph GOC:mah GOC:tb The directed movement of a vesicle along a cytoskeletal fiber such as a microtubule or and actin filament, mediated by motor proteins. cytoskeletal fiber-based vesicle localization vesicle cytoskeletal transport biological_process GO:0099518 vesicle cytoskeletal trafficking The directed movement of a vesicle along a cytoskeletal fiber such as a microtubule or and actin filament, mediated by motor proteins. GOC:ecd GOC:rl cytoskeletal fiber-based vesicle localization GOC:rl The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission. biological_process GO:0099531 presynaptic process involved in chemical synaptic transmission The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission. GOC:dos Cell-cell signaling to, from or within a synapse. biological_process GO:0099536 synaptic signaling Cell-cell signaling to, from or within a synapse. GOC:dos Cell-cell signaling in either direction across the synaptic cleft. biological_process GO:0099537 trans-synaptic signaling Cell-cell signaling in either direction across the synaptic cleft. GOC:dos Cell-cell signaling to or from a synapse, mediated by a peptide. biological_process GO:0099538 synaptic signaling via neuropeptide Cell-cell signaling to or from a synapse, mediated by a peptide. GOC:dos Cell-cell signaling between presynapse and postsynapse mediated by a peptide ligand crossing the synaptic cleft. biological_process GO:0099540 trans-synaptic signaling by neuropeptide Cell-cell signaling between presynapse and postsynapse mediated by a peptide ligand crossing the synaptic cleft. GOC:dos Cell-cell signaling from post to pre-synapse, across the synaptic cleft, mediated by a lipid. biological_process GO:0099541 trans-synaptic signaling by lipid Cell-cell signaling from post to pre-synapse, across the synaptic cleft, mediated by a lipid. GOC:dos Any protein degradation process, occurring at a presynapse, that regulates synaptic transmission. biological_process GO:0099546 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. protein catabolic process, modulating synaptic transmission Any protein degradation process, occurring at a presynapse, that regulates synaptic transmission. GOC:dos PMID:23083742 Any process that modulates synaptic transmission by regulating translation occurring at the synapse. biological_process GO:0099547 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at synapse, modulating synaptic transmission Any process that modulates synaptic transmission by regulating translation occurring at the synapse. GOC:dos Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse. biological_process GO:0099550 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. trans-synaptic signaling, modulating synaptic transmission Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse. GOC:dos Cell-cell signaling between presynapse and postsynapse, via the vesicular release and reception of neuropeptide molecules, that modulates the synaptic transmission properties of the synapse. biological_process GO:0099551 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. trans-synaptic signaling by neuropeptide, modulating synaptic transmission Cell-cell signaling between presynapse and postsynapse, via the vesicular release and reception of neuropeptide molecules, that modulates the synaptic transmission properties of the synapse. GOC:dos Cell-cell signaling between presynapse and postsynapse, via the release and reception of lipid molecules, that modulates the synaptic transmission properties of the synapse. biological_process GO:0099552 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. trans-synaptic signaling by lipid, modulating synaptic transmission Cell-cell signaling between presynapse and postsynapse, via the release and reception of lipid molecules, that modulates the synaptic transmission properties of the synapse. GOC:dos PMID:21531987 Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. cellular_component GO:0099568 cytoplasmic region Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. GOC:dos The portion of the cytoskeleton contained within the presynapse. cellular_component GO:0099569 presynaptic cytoskeleton The portion of the cytoskeleton contained within the presynapse. GOC:dos The portion of the cytoskeleton contained within the postsynapse. cellular_component GO:0099571 postsynaptic cytoskeleton The portion of the cytoskeleton contained within the postsynapse. GOC:dos PMID:19889835 Any process that modulates synaptic transmission by regulating protein degradation at the synapse. biological_process GO:0099574 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of protein catabolic process at synapse, modulating synaptic transmission Any process that modulates synaptic transmission by regulating protein degradation at the synapse. GOC:dos Any process that modulates synaptic transmission by regulating a catabolic process occurring at a presynapse. biological_process GO:0099575 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of protein catabolic process at presynapse, modulating synaptic transmission Any process that modulates synaptic transmission by regulating a catabolic process occurring at a presynapse. GOC:dos Any process that modulates synaptic transmission by regulating a catabolic process occurring at a postsynapse. biological_process GO:0099576 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of protein catabolic process at postsynapse, modulating synaptic transmission Any process that modulates synaptic transmission by regulating a catabolic process occurring at a postsynapse. GOC:dos Any process that modulates synaptic transmission by regulating translation occurring at the presynapse. biological_process GO:0099577 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at presynapse, modulating synaptic transmission Any process that modulates synaptic transmission by regulating translation occurring at the presynapse. GOC:dos Any process that modulates synaptic transmission by regulating translation occurring at the postsynapse. biological_process GO:0099578 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at postsynapse, modulating synaptic transmission Any process that modulates synaptic transmission by regulating translation occurring at the postsynapse. GOC:dos A process in which protein is transported from one region of the plasma membrane to another. biological_process GO:0099632 protein transport within plasma membrane A process in which protein is transported from one region of the plasma membrane to another. GOC:dos The directed movement of proteins along microtubules in neuron projections. axonal protein transport biological_process GO:0099640 axo-dendritic protein transport The directed movement of proteins along microtubules in neuron projections. ISBN:0815316194 Any signal release from a synapse. biological_process GO:0099643 signal release from synapse Any signal release from a synapse. GOC:dos The complete extent of cell cortex that underlies some some region of the plasma membrane. perimembrane region cellular_component GO:0099738 cell cortex region The complete extent of cell cortex that underlies some some region of the plasma membrane. GOC:dos Any action potential process that regulates skeletal muscle contraction. cjm 2015-04-02T04:13:19Z biological_process GO:0100001 regulation of skeletal muscle contraction by action potential Any action potential process that regulates skeletal muscle contraction. GOC:cjm GOC:obol The multiplication or reproduction of blood vessel endothelial cells, resulting in the expansion of a cell population. biological_process GO:0101023 vascular endothelial cell proliferation The multiplication or reproduction of blood vessel endothelial cells, resulting in the expansion of a cell population. GOC:BHF GOC:BHF_telomere GOC:nc PMID:23201774 A mitotic cell cycle process which results in the assembly, arrangement, or disassembly of the nuclear inner or outer membrane during mitosis. https://github.com/geneontology/go-ontology/issues/19949 nuclear membrane organization involved in mitotic nuclear division biological_process GO:0101024 This process only occurs in organisms which undergo 'closed mitosis' without nuclear breakdown. mitotic nuclear membrane organization A mitotic cell cycle process which results in the assembly, arrangement, or disassembly of the nuclear inner or outer membrane during mitosis. GOC:vw PMID:15147872 The process in which a nuclear membrane is synthesized, aggregates, and bonds together. biological_process GO:0101025 nuclear membrane biogenesis The process in which a nuclear membrane is synthesized, aggregates, and bonds together. GOC:vw Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an environmental stimulus. dos 2017-02-17T16:02:42Z biological_process GO:0104004 cellular response to environmental stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an environmental stimulus. GOC:dos A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a neuron, e.g. an axon, or a dendrite. hjd 2017-06-23T18:30:18Z biological_process GO:0106027 neuron projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a neuron, e.g. an axon, or a dendrite. GOC:aruk GOC:bc PMID:11585923 Any process that modulates the frequency, rate or extent of vesicle fusion with Golgi apparatus. hjd 2019-06-27T15:12:22Z biological_process GO:0106214 regulation of vesicle fusion with Golgi apparatus Any process that modulates the frequency, rate or extent of vesicle fusion with Golgi apparatus. GOC:se PMID:26195667 Any process that stops, prevents or reduces the frequency, rate or extent of vesicle fustion with Golgi apparatus. hjd 2019-06-27T15:17:17Z biological_process GO:0106215 negative regulation of vesicle fusion with Golgi apparatus Any process that stops, prevents or reduces the frequency, rate or extent of vesicle fustion with Golgi apparatus. GOC:se PMID:26195667 Any process that activates or increases the frequency, rate or extent of vesicle fusion with Golgi apparatus. hjd 2019-06-27T15:20:59Z biological_process GO:0106216 positive regulation of vesicle fusion with Golgi apparatus Any process that activates or increases the frequency, rate or extent of vesicle fusion with Golgi apparatus. GOC:se PMID:26195667 Any process that modulates the frequency, rate or extent of the assembly, disassembly or arrangement of constituent parts of the basement membrane. kmv biological_process GO:0110011 regulation of basement membrane organization Any process that modulates the frequency, rate or extent of the assembly, disassembly or arrangement of constituent parts of the basement membrane. GOC:ha PMID:27404358 Any process that modulates the frequency, rate or extent of the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. kmv 2017-06-20T19:28:58Z biological_process GO:0110020 regulation of actomyosin structure organization Any process that modulates the frequency, rate or extent of the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. GOC:lf PMID:22790195 The multiplication or reproduction of cardiac muscle myoblasts, resulting in the expansion of a cardiac muscle myoblast cell population. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life. kmv 2017-06-29T14:35:24Z biological_process GO:0110021 cardiac muscle myoblast proliferation The multiplication or reproduction of cardiac muscle myoblasts, resulting in the expansion of a cardiac muscle myoblast cell population. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26512644 Any process that modulates the frequency, rate or extent of cardiac muscle myoblast proliferation. kmv 2017-06-29T15:11:47Z biological_process GO:0110022 regulation of cardiac muscle myoblast proliferation Any process that modulates the frequency, rate or extent of cardiac muscle myoblast proliferation. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26512644 Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle myoblast proliferation. kmv 2017-06-29T15:18:30Z biological_process GO:0110023 negative regulation of cardiac muscle myoblast proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle myoblast proliferation. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26512644 Any process that activates or increases the frequency, rate or extent of cardiac muscle myoblast proliferation. kmv 2017-06-29T15:24:16Z biological_process GO:0110024 positive regulation of cardiac muscle myoblast proliferation Any process that activates or increases the frequency, rate or extent of cardiac muscle myoblast proliferation. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26512644 Any process that modulates the frequency, rate or extent of actin filament organization. kmv 2017-09-20T19:52:57Z biological_process GO:0110053 regulation of actin filament organization Any process that modulates the frequency, rate or extent of actin filament organization. GOC:kmv Any process that modulates the frequency, rate or extent of blood vessel endothelial cell differentiation. kmv 2017-10-23T14:32:09Z biological_process GO:0110057 regulation of blood vessel endothelial cell differentiation Any process that modulates the frequency, rate or extent of blood vessel endothelial cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:23072816 Any process that activates or increases the frequency, rate or extent of blood vessel endothelial cell differentiation. kmv 2017-10-23T14:38:19Z biological_process GO:0110058 positive regulation of blood vessel endothelial cell differentiation Any process that activates or increases the frequency, rate or extent of blood vessel endothelial cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:23072816 Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel endothelial cell differentiation. kmv 2017-10-23T14:47:29Z biological_process GO:0110059 negative regulation of blood vessel endothelial cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel endothelial cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:23072816 A cellular transport process in which transported substances are moved in extracellular vesicles between cells; transported substances are enclosed in the vesicle lumen or located in the extracellular vesicle membrane. kmv 2018-01-29T14:46:52Z biological_process GO:0110077 vesicle-mediated intercellular transport A cellular transport process in which transported substances are moved in extracellular vesicles between cells; transported substances are enclosed in the vesicle lumen or located in the extracellular vesicle membrane. GOC:sp PMID:29328915 PMID:29328916 Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis. kmv 2018-07-05T14:10:14Z biological_process GO:0110110 positive regulation of animal organ morphogenesis Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis. GOC:kmv Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis. kmv 2018-07-05T14:25:21Z biological_process GO:0110111 negative regulation of animal organ morphogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis. GOC:kmv Any process that modulates the frequency, rate, or extent of lipid transporter activity. kmv 2018-07-06T18:53:55Z biological_process GO:0110112 regulation of lipid transporter activity Any process that modulates the frequency, rate, or extent of lipid transporter activity. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:27365390 Any process that increases the frequency, rate, or extent of lipid transporter activity. kmv 2018-07-06T19:14:13Z biological_process GO:0110113 positive regulation of lipid transporter activity Any process that increases the frequency, rate, or extent of lipid transporter activity. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:27365390 Any process that decreases the frequency, rate, or extent of lipid transporter activity. kmv 2018-07-06T19:21:44Z biological_process GO:0110114 negative regulation of lipid transporter activity Any process that decreases the frequency, rate, or extent of lipid transporter activity. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:27365390 Any process that modulates the frequency, rate or extent of compound eye photoreceptor cell differentiation. kmv 2018-07-16T18:08:49Z biological_process GO:0110116 regulation of compound eye photoreceptor cell differentiation Any process that modulates the frequency, rate or extent of compound eye photoreceptor cell differentiation. GOC:ha PMID:16377567 Any process that activates or increases the frequency, rate or extent of compound eye photoreceptor cell differentiation. kmv 2018-07-16T18:13:28Z biological_process GO:0110117 positive regulation of compound eye photoreceptor cell differentiation Any process that activates or increases the frequency, rate or extent of compound eye photoreceptor cell differentiation. GOC:ha PMID:16377567 Any process that stops, prevents, or reduces the frequency, rate or extent of compound eye photoreceptor cell differentiation. kmv 2018-07-16T18:15:52Z biological_process GO:0110118 negative regulation of compound eye photoreceptor cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of compound eye photoreceptor cell differentiation. GOC:ha PMID:16377567 A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 kmv 2019-08-12T18:01:37Z cellular_component GO:0110165 cellular anatomical entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. GOC:kmv A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 krc 2017-03-21T17:26:07Z cellular_component GO:0120025 plasma membrane bounded cell projection A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. GOC:krc Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-24T23:56:08Z eupodium biological_process GO:0120031 plasma membrane bounded cell projection assembly Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. GOC:krc eupodium GOC:krc GOC:rjd PMID:10328951 PMID:9096956 Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:27:04Z biological_process GO:0120032 regulation of plasma membrane bounded cell projection assembly Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:34:31Z biological_process GO:0120033 negative regulation of plasma membrane bounded cell projection assembly Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:34:45Z biological_process GO:0120034 positive regulation of plasma membrane bounded cell projection assembly Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T16:02:06Z biological_process GO:0120035 regulation of plasma membrane bounded cell projection organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections. GOC:krc A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T16:07:02Z biological_process GO:0120036 plasma membrane bounded cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. GOC:krc The process in which the anatomical structures of a plasma membrane bounded cell projection are generated and organized. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-28T23:39:37Z biological_process GO:0120039 plasma membrane bounded cell projection morphogenesis The process in which the anatomical structures of a plasma membrane bounded cell projection are generated and organized. GOC:krc All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection. https://github.com/geneontology/go-ontology/issues/14472 krc 2017-11-01T18:58:12Z cellular_component GO:0120111 neuron projection cytoplasm All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection. GOC:ha Any process that activates or increases the frequency, rate or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix. https://github.com/geneontology/go-ontology/issues/15720 krc 2018-05-11T16:31:42Z positive regulation of collagen breakdown positive regulation of collagen catabolism positive regulation of collagen degradation up regulation of collagen catabolic process up-regulation of collagen catabolic process upregulation of collagen catabolic process activation of collagen catabolic process biological_process GO:0120158 positive regulation of collagen catabolic process Any process that activates or increases the frequency, rate or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix. GOC:dph GOC:tb positive regulation of collagen breakdown GOC:dph GOC:tb positive regulation of collagen catabolism GOC:dph GOC:tb positive regulation of collagen degradation GOC:dph GOC:tb up regulation of collagen catabolic process GOC:dph GOC:tb up-regulation of collagen catabolic process GOC:dph GOC:tb upregulation of collagen catabolic process GOC:dph GOC:tb activation of collagen catabolic process GOC:dph GOC:tb The chemical reactions and pathways resulting in the formation of any steroid hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. https://github.com/geneontology/go-ontology/issues/16000 krc 2019-05-20T22:34:00Z biological_process GO:0120178 steroid hormone biosynthetic process The chemical reactions and pathways resulting in the formation of any steroid hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. GOC:krc GOC:nln Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin. https://github.com/geneontology/go-ontology/issues/16012 krc 2018-07-14T00:19:32Z negative regulation of protein localisation to chromatin biological_process GO:0120186 negative regulation of protein localization to chromatin Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin. PMID:20889714 PMID:29899453 negative regulation of protein localisation to chromatin GOC:krc Any process that activates or increases the frequency, rate or extent of protein localization to chromatin. https://github.com/geneontology/go-ontology/issues/16012 krc 2018-07-14T00:21:28Z positive regulation of protein localisation to chromatin biological_process GO:0120187 positive regulation of protein localization to chromatin Any process that activates or increases the frequency, rate or extent of protein localization to chromatin. PMID:20889714 PMID:29899453 positive regulation of protein localisation to chromatin GOC:krc Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. https://github.com/geneontology/go-ontology/issues/16040 krc 2018-07-16T22:28:58Z biological_process GO:0120188 regulation of bile acid secretion Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. https://github.com/geneontology/go-ontology/issues/16040 krc 2018-07-16T22:36:17Z biological_process GO:0120189 positive regulation of bile acid secretion Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. https://github.com/geneontology/go-ontology/issues/16040 krc 2018-07-16T22:38:34Z biological_process GO:0120190 negative regulation of bile acid secretion Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 Any process that modulates the frequency, rate or extent of blastocyst development. https://github.com/geneontology/go-ontology/issues/18871 krc 2020-02-17T19:59:20Z biological_process GO:0120222 regulation of blastocyst development Any process that modulates the frequency, rate or extent of blastocyst development. GOC:krc PMID:29593216 Any process that modulates the frequency, rate or extent of the deposition or modulates the distribution of coloring matter in an organism. https://github.com/geneontology/go-ontology/issues/20524 krc 2021-02-09T19:37:35Z biological_process GO:0120305 regulation of pigmentation Any process that modulates the frequency, rate or extent of the deposition or modulates the distribution of coloring matter in an organism. GOC:krc The developmental process pertaining to the initial formation of an endothelial tube. https://github.com/geneontology/go-ontology/issues/22302 krc 2022-05-25T16:17:59Z biological_process GO:0120331 endothelial tube formation The developmental process pertaining to the initial formation of an endothelial tube. GOC:sl PMID:23239824 One of the two nuclear divisions that occur as part of the meiotic cell cycle. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T09:40:00Z meiosis biological_process GO:0140013 meiotic nuclear division One of the two nuclear divisions that occur as part of the meiotic cell cycle. PMID:9334324 A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T14:44:23Z mitosis biological_process GO:0140014 mitotic nuclear division A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. ISBN:0198547684 The cellular processes that contribute to exocytosis. pg 2017-05-15T13:20:45Z biological_process GO:0140029 exocytic process The cellular processes that contribute to exocytosis. Wikipedia:Exocytosis The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other. pg 2017-06-27T09:58:51Z biological_process GO:0140056 organelle localization by membrane tethering The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other. PMID:27875684 Catalytic activity that acts to modify a protein. https://github.com/geneontology/go-ontology/issues/14225 pg 2017-09-14T10:32:59Z molecular_function GO:0140096 catalytic activity, acting on a protein Catalytic activity that acts to modify a protein. GOC:molecular_function_refactoring GOC:pdt Catalytic activity that acts to modify DNA. https://github.com/geneontology/go-ontology/issues/14225 pg 2017-09-14T12:03:51Z molecular_function GO:0140097 catalytic activity, acting on DNA Catalytic activity that acts to modify DNA. GOC:molecular_function_refactoring GOC:pdt Catalytic activity that acts to modify RNA, driven by ATP hydrolysis. https://github.com/geneontology/go-ontology/issues/14225 https://github.com/geneontology/go-ontology/issues/21612 pg 2017-09-14T12:05:21Z molecular_function GO:0140098 catalytic activity, acting on RNA Catalytic activity that acts to modify RNA, driven by ATP hydrolysis. GOC:molecular_function_refactoring GOC:pdt Catalysis of a biochemical reaction at physiological temperatures in which one of the substrates is a glycoprotein. https://github.com/geneontology/go-ontology/issues/14225 pg 2017-09-15T19:27:54Z molecular_function GO:0140103 catalytic activity, acting on a glycoprotein Catalysis of a biochemical reaction at physiological temperatures in which one of the substrates is a glycoprotein. GOC:molecular_function_refactoring GOC:pdt The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process GO:0140112 extracellular vesicle biogenesis The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. PMID:28736435 Translation that occurs at the presynapse. https://github.com/geneontology/synapse/issues/216 pg 2018-07-13T13:00:33Z biological_process GO:0140236 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. translation at presynapse Translation that occurs at the presynapse. PMID:27321671 Translation that occurs at the presynapse, and that modulates chemical synaptic transmission. https://github.com/geneontology/synapse/issues/216 pg 2018-07-13T13:07:23Z biological_process GO:0140237 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. translation at presynapse, modulating chemical synaptic transmission Translation that occurs at the presynapse, and that modulates chemical synaptic transmission. PMID:27321671 Translation that occurs at the synapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T09:23:12Z biological_process GO:0140241 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. translation at synapse Translation that occurs at the synapse. PMID:23083742 Translation that occurs at the postsynapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T09:26:27Z biological_process GO:0140242 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. translation at postsynapse Translation that occurs at the postsynapse. PMID:20427644 Any process that regulates translation occurring at the synapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T09:38:26Z biological_process GO:0140243 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at synapse Any process that regulates translation occurring at the synapse. PMID:20427644 Any process that regulates translation occurring at the presynapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T09:38:33Z biological_process GO:0140244 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at presynapse Any process that regulates translation occurring at the presynapse. PMID:20427644 Any process that regulates translation occurring at the postsynapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T09:38:54Z biological_process GO:0140245 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at postsynapse Any process that regulates translation occurring at the postsynapse. PMID:20427644 The chemical reactions and pathways resulting in the breakdown of a protein at a synapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T10:12:51Z biological_process GO:0140246 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. protein catabolic process at synapse The chemical reactions and pathways resulting in the breakdown of a protein at a synapse. PMID:17062563 The chemical reactions and pathways resulting in the breakdown of a protein at a presynapse. https://github.com/geneontology/synapse/issues/204 pg 2018-07-15T10:23:49Z biological_process GO:0140247 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. protein catabolic process at presynapse The chemical reactions and pathways resulting in the breakdown of a protein at a presynapse. PMID:27764673 The chemical reactions and pathways resulting in the breakdown of a protein at a postsynapse. https://github.com/geneontology/synapse/issues/204 pg 2018-07-15T10:25:04Z biological_process GO:0140249 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. protein catabolic process at postsynapse The chemical reactions and pathways resulting in the breakdown of a protein at a postsynapse. PMID:17062563 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the synapse. https://github.com/geneontology/synapse/issues/204 pg 2018-07-15T10:34:56Z biological_process GO:0140250 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation protein catabolic process at synapse Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the synapse. PMID:23083742 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the presynapse. https://github.com/geneontology/synapse/issues/204 pg 2018-07-15T10:35:39Z biological_process GO:0140251 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation protein catabolic process at presynapse Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the presynapse. PMID:27764673 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the postsynapse. https://github.com/geneontology/synapse/issues/204 pg 2018-07-15T10:35:56Z biological_process GO:0140252 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation protein catabolic process at postsynapse Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the postsynapse. PMID:17062563 A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. https://github.com/geneontology/go-ontology/issues/15939 pg 2018-08-13T18:38:18Z cell fusion cell cell fusion biological_process GO:0140253 cell-cell fusion A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. Wikipedia:Cell_fusion Directly binding to a specific protein and delivering it to a specific cellular location. https://github.com/geneontology/go-ontology/issues/17073 pg 2019-04-01T10:41:38Z Reactome:R-HSA-9662747 Reactome:R-HSA-9662818 molecular_function protein carrier activity protein transport chaperone GO:0140318 Examples of protein carriers include the soluble TIM chaperone complexes of S. cerevisiae Tim9-Tim10 and Tim8-Tim13, that provide a shuttle system between TOM and the membrane insertases TIM22 and SAM and, thus, ensure that precursors are kept in a translocation-competent conformation. protein transporter activity Directly binding to a specific protein and delivering it to a specific cellular location. PMID:18706423 Reactome:R-HSA-9662747 iRHOM2 transports ADAM17 from ER to the Golgi-network Reactome:R-HSA-9662818 iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. pg 2019-05-22T11:20:45Z efflux biological_process GO:0140352 export from cell The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. GOC:pg The directed movement of a lipid from a cell, into the extracellular region. pg 2019-05-22T11:33:07Z lipid efflux biological_process GO:0140353 lipid export from cell The directed movement of a lipid from a cell, into the extracellular region. GOC:pg The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. pg 2019-05-22T11:38:15Z lipid uptake biological_process GO:0140354 lipid import into cell The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. GOC:pg A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus. pg 2020-09-09T05:12:38Z nuclear complex cellular_component GO:0140513 nuclear protein-containing complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus. GOC:pg The division of a vacuole within a cell to form two or more separate vacuoles. https://github.com/geneontology/go-ontology/issues/20639 pg 2021-01-04T10:17:58Z biological_process GO:0140572 vacuole fission The division of a vacuole within a cell to form two or more separate vacuoles. PMID:19643199 Catalytic activity that acts to modify a nucleic acid. https://github.com/geneontology/go-ontology/issues/21402 pg 2021-05-11T06:31:07Z molecular_function GO:0140640 catalytic activity, acting on a nucleic acid Catalytic activity that acts to modify a nucleic acid. GOC:pg The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle. https://github.com/geneontology/go-ontology/issues/21939 pg 2021-08-09T15:30:06Z non-membrane-bounded organelle formation non-membrane-enclosed organelle assembly non-membrane-enclosed organelle formation biological_process GO:0140694 non-membrane-bounded organelle assembly The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle. PMID:28225081 The elimination of ammonium ions from an excretory cell. https://github.com/geneontology/go-ontology/issues/22368 pg 2021-11-24T17:55:51Z biological_process ammonia excretion GO:0140734 ammonium excretion The elimination of ammonium ions from an excretory cell. PMID:25740900 Any process carried out at the cellular level that reduces or removes the toxicity of a metal ion. pg 2022-12-07T15:35:18Z cellular detoxification of metal cation biological_process GO:0140961 cellular detoxification of metal ion Any process carried out at the cellular level that reduces or removes the toxicity of a metal ion. PMID:26729300 PMID:33046888 PMID:34442707 Any process that modulates the frequency, rate or extent of postsynapse assembly, the aggregation, arrangement and bonding together of a set of components to form a postsynapse. bc 2018-05-08T16:38:55Z biological_process GO:0150052 regulation of postsynapse assembly Any process that modulates the frequency, rate or extent of postsynapse assembly, the aggregation, arrangement and bonding together of a set of components to form a postsynapse. GOC:aruk GOC:bc PMID:16394100 PMID:16672654 PMID:28185854 The process whose specific outcome is the progression of the visual system over time, from its formation to the mature structure, including the eye, parts of the central nervous system (CNS) involved in processing of visual inputs, and connecting nerve pathways. bc 2018-07-23T10:31:58Z biological_process optic pathway development visual pathway development GO:0150063 visual system development The process whose specific outcome is the progression of the visual system over time, from its formation to the mature structure, including the eye, parts of the central nervous system (CNS) involved in processing of visual inputs, and connecting nerve pathways. GOC:aruk GOC:bc GOC:krc PMID:15004427 PMID:20647017 PMID:22632727 Cell-cell signaling that mediates the transfer of information from a glial cell to a neuron. This signaling has been shown to be mediated by various molecules, depending on which glial cells release them, and in which tissues the signaling occurs, e.g. microglial cell-derived nerve growth factor (NGF) in the retina, or microglial cell-derived superoxide ions in the cerebellum. bc 2018-12-17T12:28:09Z glia-neuron signaling glia-neuron signalling glia-neurone signaling glia-neurone signalling glial cell- neuron signalling glial cell-neurone signalling glial cell-neurone singaling biological_process GO:0150098 glial cell-neuron signaling Cell-cell signaling that mediates the transfer of information from a glial cell to a neuron. This signaling has been shown to be mediated by various molecules, depending on which glial cells release them, and in which tissues the signaling occurs, e.g. microglial cell-derived nerve growth factor (NGF) in the retina, or microglial cell-derived superoxide ions in the cerebellum. GOC:aruk GOC:bc PMID:14980203 PMID:16144764 PMID:16547515 PMID:18685038 PMID:27788368 PMID:9459440 Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine. bc 2018-12-17T12:30:12Z neuron-glia signaling neuron-glia signalling neuron-glial cell signalling neurone-glia signaling neurone-glia signalling neurone-glial cell signaling neurone-glial cell signalling biological_process GO:0150099 neuron-glial cell signaling Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine. GOC:aruk GOC:bc PMID:10195197 PMID:10196584 PMID:10377338 PMID:10493741 PMID:11356870 PMID:11399439 PMID:15252819 PMID:27788368 A process in which a protein is transported to, or maintained, in a location within a cell-cell junction. bc 2019-06-11T11:00:18Z biological_process GO:0150105 protein localization to cell-cell junction A process in which a protein is transported to, or maintained, in a location within a cell-cell junction. GOC:aruk GOC:bc PMID:26706435 Any process that modulates the frequency, rate or extent of protein localization to cell-cell junction. bc 2019-06-11T11:17:15Z biological_process GO:0150106 regulation of protein localization to cell-cell junction Any process that modulates the frequency, rate or extent of protein localization to cell-cell junction. GOC:aruk GOC:bc PMID:26706435 Any process that activates or increases the frequency, rate or extent of protein localization to cell-cell junction. bc 2019-06-11T11:23:58Z biological_process GO:0150107 positive regulation of protein localization to cell-cell junction Any process that activates or increases the frequency, rate or extent of protein localization to cell-cell junction. GOC:aruk GOC:bc PMID:26706435 Any process that modulates the frequency, rate or extent of transepithelial transport. bc 2019-09-15T07:16:49Z biological_process GO:0150111 regulation of transepithelial transport Any process that modulates the frequency, rate or extent of transepithelial transport. GOC:aruk PMID:27593915 Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell-cell junction. bc 2019-11-21T13:53:34Z negative regulation of protein localisation to cell-cell junction biological_process GO:0150119 negative regulation of protein localization to cell-cell junction Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell-cell junction. GOC:aruk GOC:bc The disaggregation of a cell junction into its constituent components. bc 2019-12-08T11:12:13Z biological_process GO:0150146 cell junction disassembly The disaggregation of a cell junction into its constituent components. GOC:aruk PMID:25490267 The disaggregation of a cell-cell junction into its constituent components. bc 2019-12-08T11:16:14Z biological_process GO:0150147 cell-cell junction disassembly The disaggregation of a cell-cell junction into its constituent components. GOC:aruk PMID:25490267 The process whose specific outcome is the progression of a somatic sensory system over time from its formation to the mature structure. Somatic sensory system is the sensory system for the sense of touch and pain. rynl 2022-07-07T16:49:26Z somatosensory system development biological_process GO:0160038 somatic sensory system development The process whose specific outcome is the progression of a somatic sensory system over time from its formation to the mature structure. Somatic sensory system is the sensory system for the sense of touch and pain. PMID:25832476 PMID:31399790 The regulated release of catecholamine by a cell in which the catecholamine acts as a neurotransmitter. https://github.com/geneontology/go-ontology/issues/23804 rynl 2022-08-17T00:36:44Z biological_process GO:0160043 catecholamine secretion, neurotransmission The regulated release of catecholamine by a cell in which the catecholamine acts as a neurotransmitter. PMID:10191060 The process whose specific outcome is the progression of cordate pharynx over time, from its formation to the mature structure. https://github.com/geneontology/go-ontology/issues/18285 rynl 2023-08-29T21:05:28Z biological_process GO:0160093 chordate pharynx development The process whose specific outcome is the progression of cordate pharynx over time, from its formation to the mature structure. PMID:23020903 Any regulation of signal transduction that takes place in the extracellular region. bf 2012-02-22T10:21:48Z regulation of signaling pathway in extracellular region regulation of signalling pathway in extracellular region biological_process GO:1900115 extracellular regulation of signal transduction Any regulation of signal transduction that takes place in the extracellular region. GOC:TermGenie GOC:signaling regulation of signaling pathway in extracellular region GOC:TermGenie regulation of signalling pathway in extracellular region GOC:TermGenie Any negative regulation of signal transduction that takes place in extracellular region. bf 2012-02-22T10:27:56Z down regulation of signal transduction in extracellular region down-regulation of signal transduction in extracellular region downregulation of signal transduction in extracellular region negative regulation of signaling pathway in extracellular region negative regulation of signalling pathway in extracellular region extracellular inhibition of signaling pathway inhibition of signal transduction in extracellular region biological_process GO:1900116 extracellular negative regulation of signal transduction Any negative regulation of signal transduction that takes place in extracellular region. GOC:TermGenie GOC:signaling down regulation of signal transduction in extracellular region GOC:TermGenie down-regulation of signal transduction in extracellular region GOC:TermGenie downregulation of signal transduction in extracellular region GOC:TermGenie negative regulation of signaling pathway in extracellular region GOC:TermGenie negative regulation of signalling pathway in extracellular region GOC:TermGenie extracellular inhibition of signaling pathway GOC:bf inhibition of signal transduction in extracellular region GOC:TermGenie Any process that modulates the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:20Z biological_process GO:1900117 regulation of execution phase of apoptosis Any process that modulates the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:24Z down regulation of execution phase of apoptosis down-regulation of execution phase of apoptosis downregulation of execution phase of apoptosis inhibition of execution phase of apoptosis biological_process GO:1900118 negative regulation of execution phase of apoptosis Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis down regulation of execution phase of apoptosis GOC:TermGenie down-regulation of execution phase of apoptosis GOC:TermGenie downregulation of execution phase of apoptosis GOC:TermGenie inhibition of execution phase of apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:27Z up regulation of execution phase of apoptosis up-regulation of execution phase of apoptosis upregulation of execution phase of apoptosis activation of execution phase of apoptosis biological_process GO:1900119 positive regulation of execution phase of apoptosis Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis up regulation of execution phase of apoptosis GOC:TermGenie up-regulation of execution phase of apoptosis GOC:TermGenie upregulation of execution phase of apoptosis GOC:TermGenie activation of execution phase of apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of hyaluronan biosynthetic process. yaf 2012-02-23T01:09:21Z regulation of hyaluronan anabolism regulation of hyaluronan biosynthesis regulation of hyaluronan formation regulation of hyaluronan synthesis biological_process GO:1900125 regulation of hyaluronan biosynthetic process Any process that modulates the frequency, rate or extent of hyaluronan biosynthetic process. GOC:TermGenie GOC:yaf regulation of hyaluronan anabolism GOC:TermGenie regulation of hyaluronan biosynthesis GOC:TermGenie regulation of hyaluronan formation GOC:TermGenie regulation of hyaluronan synthesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process. yaf 2012-02-23T01:09:29Z down regulation of hyaluronan anabolism down regulation of hyaluronan biosynthesis down regulation of hyaluronan biosynthetic process down regulation of hyaluronan formation down regulation of hyaluronan synthesis down-regulation of hyaluronan anabolism down-regulation of hyaluronan biosynthesis down-regulation of hyaluronan biosynthetic process down-regulation of hyaluronan formation down-regulation of hyaluronan synthesis downregulation of hyaluronan anabolism downregulation of hyaluronan biosynthesis downregulation of hyaluronan biosynthetic process downregulation of hyaluronan formation downregulation of hyaluronan synthesis inhibition of hyaluronan anabolism inhibition of hyaluronan biosynthesis inhibition of hyaluronan formation inhibition of hyaluronan synthesis negative regulation of hyaluronan anabolism negative regulation of hyaluronan biosynthesis negative regulation of hyaluronan formation negative regulation of hyaluronan synthesis inhibition of hyaluronan biosynthetic process biological_process GO:1900126 negative regulation of hyaluronan biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process. GOC:TermGenie GOC:yaf down regulation of hyaluronan anabolism GOC:TermGenie down regulation of hyaluronan biosynthesis GOC:TermGenie down regulation of hyaluronan biosynthetic process GOC:TermGenie down regulation of hyaluronan formation GOC:TermGenie down regulation of hyaluronan synthesis GOC:TermGenie down-regulation of hyaluronan anabolism GOC:TermGenie down-regulation of hyaluronan biosynthesis GOC:TermGenie down-regulation of hyaluronan biosynthetic process GOC:TermGenie down-regulation of hyaluronan formation GOC:TermGenie down-regulation of hyaluronan synthesis GOC:TermGenie downregulation of hyaluronan anabolism GOC:TermGenie downregulation of hyaluronan biosynthesis GOC:TermGenie downregulation of hyaluronan biosynthetic process GOC:TermGenie downregulation of hyaluronan formation GOC:TermGenie downregulation of hyaluronan synthesis GOC:TermGenie inhibition of hyaluronan anabolism GOC:TermGenie inhibition of hyaluronan biosynthesis GOC:TermGenie inhibition of hyaluronan formation GOC:TermGenie inhibition of hyaluronan synthesis GOC:TermGenie negative regulation of hyaluronan anabolism GOC:TermGenie negative regulation of hyaluronan biosynthesis GOC:TermGenie negative regulation of hyaluronan formation GOC:TermGenie negative regulation of hyaluronan synthesis GOC:TermGenie inhibition of hyaluronan biosynthetic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process. yaf 2012-02-23T01:09:33Z activation of hyaluronan anabolism activation of hyaluronan biosynthesis activation of hyaluronan formation activation of hyaluronan synthesis positive regulation of hyaluronan anabolism positive regulation of hyaluronan biosynthesis positive regulation of hyaluronan formation positive regulation of hyaluronan synthesis up regulation of hyaluronan anabolism up regulation of hyaluronan biosynthesis up regulation of hyaluronan biosynthetic process up regulation of hyaluronan formation up regulation of hyaluronan synthesis up-regulation of hyaluronan anabolism up-regulation of hyaluronan biosynthesis up-regulation of hyaluronan biosynthetic process up-regulation of hyaluronan formation up-regulation of hyaluronan synthesis upregulation of hyaluronan anabolism upregulation of hyaluronan biosynthesis upregulation of hyaluronan biosynthetic process upregulation of hyaluronan formation upregulation of hyaluronan synthesis activation of hyaluronan biosynthetic process biological_process GO:1900127 positive regulation of hyaluronan biosynthetic process Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process. GOC:TermGenie GOC:yaf activation of hyaluronan anabolism GOC:TermGenie activation of hyaluronan biosynthesis GOC:TermGenie activation of hyaluronan formation GOC:TermGenie activation of hyaluronan synthesis GOC:TermGenie positive regulation of hyaluronan anabolism GOC:TermGenie positive regulation of hyaluronan biosynthesis GOC:TermGenie positive regulation of hyaluronan formation GOC:TermGenie positive regulation of hyaluronan synthesis GOC:TermGenie up regulation of hyaluronan anabolism GOC:TermGenie up regulation of hyaluronan biosynthesis GOC:TermGenie up regulation of hyaluronan biosynthetic process GOC:TermGenie up regulation of hyaluronan formation GOC:TermGenie up regulation of hyaluronan synthesis GOC:TermGenie up-regulation of hyaluronan anabolism GOC:TermGenie up-regulation of hyaluronan biosynthesis GOC:TermGenie up-regulation of hyaluronan biosynthetic process GOC:TermGenie up-regulation of hyaluronan formation GOC:TermGenie up-regulation of hyaluronan synthesis GOC:TermGenie upregulation of hyaluronan anabolism GOC:TermGenie upregulation of hyaluronan biosynthesis GOC:TermGenie upregulation of hyaluronan biosynthetic process GOC:TermGenie upregulation of hyaluronan formation GOC:TermGenie upregulation of hyaluronan synthesis GOC:TermGenie activation of hyaluronan biosynthetic process GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:44Z regulation of protein localisation to nucleus regulation of protein localization in cell nucleus regulation of protein localization in nucleus biological_process GO:1900180 regulation of protein localization to nucleus Any process that modulates the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie regulation of protein localisation to nucleus GOC:TermGenie regulation of protein localization in cell nucleus GOC:TermGenie regulation of protein localization in nucleus GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:48Z down regulation of protein localisation to nucleus down regulation of protein localization in cell nucleus down regulation of protein localization in nucleus down regulation of protein localization to nucleus down-regulation of protein localisation to nucleus down-regulation of protein localization in cell nucleus down-regulation of protein localization in nucleus down-regulation of protein localization to nucleus downregulation of protein localisation to nucleus downregulation of protein localization in cell nucleus downregulation of protein localization in nucleus downregulation of protein localization to nucleus negative regulation of protein localisation to nucleus negative regulation of protein localization in cell nucleus negative regulation of protein localization in nucleus inhibition of protein localisation to nucleus inhibition of protein localization in cell nucleus inhibition of protein localization in nucleus inhibition of protein localization to nucleus biological_process GO:1900181 negative regulation of protein localization to nucleus Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie down regulation of protein localisation to nucleus GOC:TermGenie down regulation of protein localization in cell nucleus GOC:TermGenie down regulation of protein localization in nucleus GOC:TermGenie down regulation of protein localization to nucleus GOC:TermGenie down-regulation of protein localisation to nucleus GOC:TermGenie down-regulation of protein localization in cell nucleus GOC:TermGenie down-regulation of protein localization in nucleus GOC:TermGenie down-regulation of protein localization to nucleus GOC:TermGenie downregulation of protein localisation to nucleus GOC:TermGenie downregulation of protein localization in cell nucleus GOC:TermGenie downregulation of protein localization in nucleus GOC:TermGenie downregulation of protein localization to nucleus GOC:TermGenie negative regulation of protein localisation to nucleus GOC:TermGenie negative regulation of protein localization in cell nucleus GOC:TermGenie negative regulation of protein localization in nucleus GOC:TermGenie inhibition of protein localisation to nucleus GOC:TermGenie inhibition of protein localization in cell nucleus GOC:TermGenie inhibition of protein localization in nucleus GOC:TermGenie inhibition of protein localization to nucleus GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to nucleus. bf 2012-03-12T01:23:52Z activation of protein localization in nucleus positive regulation of protein localisation to nucleus positive regulation of protein localization in cell nucleus positive regulation of protein localization in nucleus up regulation of protein localisation to nucleus up regulation of protein localization in cell nucleus up regulation of protein localization in nucleus up regulation of protein localization to nucleus up-regulation of protein localisation to nucleus up-regulation of protein localization in cell nucleus up-regulation of protein localization in nucleus up-regulation of protein localization to nucleus upregulation of protein localisation to nucleus upregulation of protein localization in cell nucleus upregulation of protein localization in nucleus upregulation of protein localization to nucleus activation of protein localisation to nucleus activation of protein localization in cell nucleus activation of protein localization to nucleus biological_process GO:1900182 positive regulation of protein localization to nucleus Any process that activates or increases the frequency, rate or extent of protein localization to nucleus. GOC:TermGenie activation of protein localization in nucleus GOC:TermGenie positive regulation of protein localisation to nucleus GOC:TermGenie positive regulation of protein localization in cell nucleus GOC:TermGenie positive regulation of protein localization in nucleus GOC:TermGenie up regulation of protein localisation to nucleus GOC:TermGenie up regulation of protein localization in cell nucleus GOC:TermGenie up regulation of protein localization in nucleus GOC:TermGenie up regulation of protein localization to nucleus GOC:TermGenie up-regulation of protein localisation to nucleus GOC:TermGenie up-regulation of protein localization in cell nucleus GOC:TermGenie up-regulation of protein localization in nucleus GOC:TermGenie up-regulation of protein localization to nucleus GOC:TermGenie upregulation of protein localisation to nucleus GOC:TermGenie upregulation of protein localization in cell nucleus GOC:TermGenie upregulation of protein localization in nucleus GOC:TermGenie upregulation of protein localization to nucleus GOC:TermGenie activation of protein localisation to nucleus GOC:TermGenie activation of protein localization in cell nucleus GOC:TermGenie activation of protein localization to nucleus GOC:TermGenie Any process that modulates the frequency, rate or extent of oocyte maturation. kmv 2012-03-19T09:41:18Z biological_process GO:1900193 regulation of oocyte maturation Any process that modulates the frequency, rate or extent of oocyte maturation. GOC:TermGenie GOC:kmv Any process that stops, prevents or reduces the frequency, rate or extent of oocyte maturation. kmv 2012-03-19T09:41:27Z down regulation of oocyte maturation down-regulation of oocyte maturation downregulation of oocyte maturation inhibition of oocyte maturation biological_process GO:1900194 negative regulation of oocyte maturation Any process that stops, prevents or reduces the frequency, rate or extent of oocyte maturation. GOC:TermGenie GOC:kmv down regulation of oocyte maturation GOC:TermGenie down-regulation of oocyte maturation GOC:TermGenie downregulation of oocyte maturation GOC:TermGenie inhibition of oocyte maturation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of oocyte maturation. kmv 2012-03-19T09:41:35Z up regulation of oocyte maturation up-regulation of oocyte maturation upregulation of oocyte maturation activation of oocyte maturation biological_process GO:1900195 positive regulation of oocyte maturation Any process that activates or increases the frequency, rate or extent of oocyte maturation. GOC:TermGenie GOC:kmv up regulation of oocyte maturation GOC:TermGenie up-regulation of oocyte maturation GOC:TermGenie upregulation of oocyte maturation GOC:TermGenie activation of oocyte maturation GOC:TermGenie Any process that modulates the frequency, rate or extent of secondary metabolite biosynthetic process. di 2012-04-17T01:55:23Z regulation of secondary metabolite biosynthesis biological_process GO:1900376 regulation of secondary metabolite biosynthetic process Any process that modulates the frequency, rate or extent of secondary metabolite biosynthetic process. GOC:TermGenie GOC:di regulation of secondary metabolite biosynthesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of secondary metabolite biosynthetic process. di 2012-04-17T01:55:32Z down regulation of secondary metabolite biosynthesis down regulation of secondary metabolite biosynthetic process down-regulation of secondary metabolite biosynthesis down-regulation of secondary metabolite biosynthetic process downregulation of secondary metabolite biosynthesis downregulation of secondary metabolite biosynthetic process inhibition of secondary metabolite biosynthesis negative regulation of secondary metabolite biosynthesis inhibition of secondary metabolite biosynthetic process biological_process GO:1900377 negative regulation of secondary metabolite biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of secondary metabolite biosynthetic process. GOC:TermGenie GOC:di down regulation of secondary metabolite biosynthesis GOC:TermGenie down regulation of secondary metabolite biosynthetic process GOC:TermGenie down-regulation of secondary metabolite biosynthesis GOC:TermGenie down-regulation of secondary metabolite biosynthetic process GOC:TermGenie downregulation of secondary metabolite biosynthesis GOC:TermGenie downregulation of secondary metabolite biosynthetic process GOC:TermGenie inhibition of secondary metabolite biosynthesis GOC:TermGenie negative regulation of secondary metabolite biosynthesis GOC:TermGenie inhibition of secondary metabolite biosynthetic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of secondary metabolite biosynthetic process. di 2012-04-17T01:55:41Z activation of secondary metabolite biosynthesis positive regulation of secondary metabolite biosynthesis up regulation of secondary metabolite biosynthesis up regulation of secondary metabolite biosynthetic process up-regulation of secondary metabolite biosynthesis up-regulation of secondary metabolite biosynthetic process upregulation of secondary metabolite biosynthesis upregulation of secondary metabolite biosynthetic process activation of secondary metabolite biosynthetic process biological_process GO:1900378 positive regulation of secondary metabolite biosynthetic process Any process that activates or increases the frequency, rate or extent of secondary metabolite biosynthetic process. GOC:TermGenie GOC:di activation of secondary metabolite biosynthesis GOC:TermGenie positive regulation of secondary metabolite biosynthesis GOC:TermGenie up regulation of secondary metabolite biosynthesis GOC:TermGenie up regulation of secondary metabolite biosynthetic process GOC:TermGenie up-regulation of secondary metabolite biosynthesis GOC:TermGenie up-regulation of secondary metabolite biosynthetic process GOC:TermGenie upregulation of secondary metabolite biosynthesis GOC:TermGenie upregulation of secondary metabolite biosynthetic process GOC:TermGenie activation of secondary metabolite biosynthetic process GOC:TermGenie The chemical reactions and pathways involving an acetate ester, any carboxylic ester where the carboxylic acid component is acetic acid. bf 2012-05-16T12:29:51Z acetate ester metabolism acetyl ester metabolic process acetyl ester metabolism biological_process GO:1900619 acetate ester metabolic process The chemical reactions and pathways involving an acetate ester, any carboxylic ester where the carboxylic acid component is acetic acid. GOC:TermGenie acetate ester metabolism GOC:TermGenie acetyl ester metabolic process CHEBI:47622 acetyl ester metabolism CHEBI:47622 The chemical reactions and pathways resulting in the formation of an acetate esteran acetate ester, any carboxylic ester where the carboxylic acid component is acetic acid. bf 2012-05-16T12:30:12Z acetate ester anabolism acetate ester biosynthesis acetate ester formation acetate ester synthesis acetyl ester biosynthesis acetyl ester biosynthetic process biological_process GO:1900620 acetate ester biosynthetic process The chemical reactions and pathways resulting in the formation of an acetate esteran acetate ester, any carboxylic ester where the carboxylic acid component is acetic acid. GOC:TermGenie PMID:15042596 acetate ester anabolism GOC:TermGenie acetate ester biosynthesis GOC:TermGenie acetate ester formation GOC:TermGenie acetate ester synthesis GOC:TermGenie acetyl ester biosynthesis CHEBI:47622 acetyl ester biosynthetic process CHEBI:47622 The chemical reactions and pathways involving carbohydrate derivative. bf 2012-07-12T04:05:09Z carbohydrate derivative metabolism biological_process GO:1901135 carbohydrate derivative metabolic process The chemical reactions and pathways involving carbohydrate derivative. GOC:TermGenie carbohydrate derivative metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative. bf 2012-07-12T04:05:31Z carbohydrate derivative breakdown carbohydrate derivative catabolism carbohydrate derivative degradation biological_process GO:1901136 carbohydrate derivative catabolic process The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative. GOC:TermGenie carbohydrate derivative breakdown GOC:TermGenie carbohydrate derivative catabolism GOC:TermGenie carbohydrate derivative degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of carbohydrate derivative. bf 2012-07-12T04:05:39Z carbohydrate derivative anabolism carbohydrate derivative biosynthesis carbohydrate derivative formation carbohydrate derivative synthesis biological_process GO:1901137 carbohydrate derivative biosynthetic process The chemical reactions and pathways resulting in the formation of carbohydrate derivative. GOC:TermGenie carbohydrate derivative anabolism GOC:TermGenie carbohydrate derivative biosynthesis GOC:TermGenie carbohydrate derivative formation GOC:TermGenie carbohydrate derivative synthesis GOC:TermGenie The chemical reactions and pathways involving insulin. pm 2012-07-13T12:32:40Z insulin metabolism biological_process GO:1901142 insulin metabolic process The chemical reactions and pathways involving insulin. GOC:TermGenie insulin metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of insulin. pm 2012-07-13T12:33:03Z insulin breakdown insulin catabolism insulin degradation biological_process GO:1901143 insulin catabolic process The chemical reactions and pathways resulting in the breakdown of insulin. GOC:TermGenie insulin breakdown GOC:TermGenie insulin catabolism GOC:TermGenie insulin degradation GOC:TermGenie Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form. bf 2012-07-16T03:29:30Z expression of extracellular matrix proteins biological_process extracellular matrix protein production GO:1901148 gene expression involved in extracellular matrix organization Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form. GOC:TermGenie GOC:pg PMID:18668558 expression of extracellular matrix proteins GOC:bf extracellular matrix protein production GOC:pg The chemical reactions and pathways involving primary amino compound. bf 2012-07-18T04:44:39Z primary amino compound metabolism biological_process GO:1901160 primary amino compound metabolic process The chemical reactions and pathways involving primary amino compound. GOC:TermGenie primary amino compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of primary amino compound. bf 2012-07-18T04:45:06Z primary amino compound breakdown primary amino compound catabolism primary amino compound degradation biological_process GO:1901161 primary amino compound catabolic process The chemical reactions and pathways resulting in the breakdown of primary amino compound. GOC:TermGenie primary amino compound breakdown GOC:TermGenie primary amino compound catabolism GOC:TermGenie primary amino compound degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of primary amino compound. bf 2012-07-18T04:45:14Z primary amino compound anabolism primary amino compound biosynthesis primary amino compound formation primary amino compound synthesis biological_process GO:1901162 primary amino compound biosynthetic process The chemical reactions and pathways resulting in the formation of primary amino compound. GOC:TermGenie primary amino compound anabolism GOC:TermGenie primary amino compound biosynthesis GOC:TermGenie primary amino compound formation GOC:TermGenie primary amino compound synthesis GOC:TermGenie Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex. ss 2012-07-25T02:26:58Z regulation of translation initiation ternary complex assembly biological_process GO:1901190 regulation of formation of translation initiation ternary complex Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex. GOC:TermGenie regulation of translation initiation ternary complex assembly GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex. ss 2012-07-25T02:27:21Z down regulation of formation of translation initiation ternary complex down regulation of translation initiation ternary complex assembly down-regulation of formation of translation initiation ternary complex down-regulation of translation initiation ternary complex assembly downregulation of formation of translation initiation ternary complex downregulation of translation initiation ternary complex assembly inhibition of translation initiation ternary complex assembly negative regulation of translation initiation ternary complex assembly inhibition of formation of translation initiation ternary complex biological_process GO:1901191 negative regulation of formation of translation initiation ternary complex Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex. GOC:TermGenie down regulation of formation of translation initiation ternary complex GOC:TermGenie down regulation of translation initiation ternary complex assembly GOC:TermGenie down-regulation of formation of translation initiation ternary complex GOC:TermGenie down-regulation of translation initiation ternary complex assembly GOC:TermGenie downregulation of formation of translation initiation ternary complex GOC:TermGenie downregulation of translation initiation ternary complex assembly GOC:TermGenie inhibition of translation initiation ternary complex assembly GOC:TermGenie negative regulation of translation initiation ternary complex assembly GOC:TermGenie inhibition of formation of translation initiation ternary complex GOC:TermGenie Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex. ss 2012-07-25T02:27:29Z activation of translation initiation ternary complex assembly positive regulation of translation initiation ternary complex assembly up regulation of formation of translation initiation ternary complex up regulation of translation initiation ternary complex assembly up-regulation of formation of translation initiation ternary complex up-regulation of translation initiation ternary complex assembly upregulation of formation of translation initiation ternary complex upregulation of translation initiation ternary complex assembly activation of formation of translation initiation ternary complex biological_process GO:1901192 positive regulation of formation of translation initiation ternary complex Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex. GOC:TermGenie activation of translation initiation ternary complex assembly GOC:TermGenie positive regulation of translation initiation ternary complex assembly GOC:TermGenie up regulation of formation of translation initiation ternary complex GOC:TermGenie up regulation of translation initiation ternary complex assembly GOC:TermGenie up-regulation of formation of translation initiation ternary complex GOC:TermGenie up-regulation of translation initiation ternary complex assembly GOC:TermGenie upregulation of formation of translation initiation ternary complex GOC:TermGenie upregulation of translation initiation ternary complex assembly GOC:TermGenie activation of formation of translation initiation ternary complex GOC:TermGenie Any process that modulates the frequency, rate or extent of extracellular matrix assembly. rl 2012-07-27T04:04:00Z biological_process GO:1901201 regulation of extracellular matrix assembly Any process that modulates the frequency, rate or extent of extracellular matrix assembly. GOC:BHF GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix assembly. rl 2012-07-27T04:04:24Z down regulation of extracellular matrix assembly down-regulation of extracellular matrix assembly downregulation of extracellular matrix assembly inhibition of extracellular matrix assembly biological_process GO:1901202 negative regulation of extracellular matrix assembly Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix assembly. GOC:BHF GOC:TermGenie down regulation of extracellular matrix assembly GOC:TermGenie down-regulation of extracellular matrix assembly GOC:TermGenie downregulation of extracellular matrix assembly GOC:TermGenie inhibition of extracellular matrix assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly. rl 2012-07-27T04:04:32Z up regulation of extracellular matrix assembly up-regulation of extracellular matrix assembly upregulation of extracellular matrix assembly activation of extracellular matrix assembly biological_process GO:1901203 positive regulation of extracellular matrix assembly Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly. GOC:BHF GOC:TermGenie up regulation of extracellular matrix assembly GOC:TermGenie up-regulation of extracellular matrix assembly GOC:TermGenie upregulation of extracellular matrix assembly GOC:TermGenie activation of extracellular matrix assembly GOC:TermGenie Any process that modulates the frequency, rate or extent of cardiac chamber formation. rl 2012-07-31T07:18:35Z regulation of heart chamber formation biological_process GO:1901210 regulation of cardiac chamber formation Any process that modulates the frequency, rate or extent of cardiac chamber formation. GOC:BHF GOC:TermGenie regulation of heart chamber formation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber formation. rl 2012-07-31T07:18:57Z down regulation of cardiac chamber formation down regulation of heart chamber formation down-regulation of cardiac chamber formation down-regulation of heart chamber formation downregulation of cardiac chamber formation downregulation of heart chamber formation inhibition of heart chamber formation negative regulation of heart chamber formation inhibition of cardiac chamber formation biological_process GO:1901211 negative regulation of cardiac chamber formation Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber formation. GOC:BHF GOC:TermGenie down regulation of cardiac chamber formation GOC:TermGenie down regulation of heart chamber formation GOC:TermGenie down-regulation of cardiac chamber formation GOC:TermGenie down-regulation of heart chamber formation GOC:TermGenie downregulation of cardiac chamber formation GOC:TermGenie downregulation of heart chamber formation GOC:TermGenie inhibition of heart chamber formation GOC:TermGenie negative regulation of heart chamber formation GOC:TermGenie inhibition of cardiac chamber formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cardiac chamber formation. rl 2012-07-31T07:19:05Z activation of heart chamber formation positive regulation of heart chamber formation up regulation of cardiac chamber formation up regulation of heart chamber formation up-regulation of cardiac chamber formation up-regulation of heart chamber formation upregulation of cardiac chamber formation upregulation of heart chamber formation activation of cardiac chamber formation biological_process GO:1901212 positive regulation of cardiac chamber formation Any process that activates or increases the frequency, rate or extent of cardiac chamber formation. GOC:BHF GOC:TermGenie activation of heart chamber formation GOC:TermGenie positive regulation of heart chamber formation GOC:TermGenie up regulation of cardiac chamber formation GOC:TermGenie up regulation of heart chamber formation GOC:TermGenie up-regulation of cardiac chamber formation GOC:TermGenie up-regulation of heart chamber formation GOC:TermGenie upregulation of cardiac chamber formation GOC:TermGenie upregulation of heart chamber formation GOC:TermGenie activation of cardiac chamber formation GOC:TermGenie Any process that modulates the frequency, rate or extent of cardiac chamber morphogenesis. rl 2012-08-06T17:59:11Z regulation of heart chamber morphogenesis biological_process GO:1901219 regulation of cardiac chamber morphogenesis Any process that modulates the frequency, rate or extent of cardiac chamber morphogenesis. GOC:BHF GOC:TermGenie regulation of heart chamber morphogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber morphogenesis. rl 2012-08-06T17:59:34Z down regulation of cardiac chamber morphogenesis down regulation of heart chamber morphogenesis down-regulation of cardiac chamber morphogenesis down-regulation of heart chamber morphogenesis downregulation of cardiac chamber morphogenesis downregulation of heart chamber morphogenesis negative regulation of heart chamber morphogenesis inhibition of cardiac chamber morphogenesis inhibition of heart chamber morphogenesis biological_process GO:1901220 negative regulation of cardiac chamber morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber morphogenesis. GOC:BHF GOC:TermGenie down regulation of cardiac chamber morphogenesis GOC:TermGenie down regulation of heart chamber morphogenesis GOC:TermGenie down-regulation of cardiac chamber morphogenesis GOC:TermGenie down-regulation of heart chamber morphogenesis GOC:TermGenie downregulation of cardiac chamber morphogenesis GOC:TermGenie downregulation of heart chamber morphogenesis GOC:TermGenie negative regulation of heart chamber morphogenesis GOC:TermGenie inhibition of cardiac chamber morphogenesis GOC:TermGenie inhibition of heart chamber morphogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cardiac chamber morphogenesis. rl 2012-08-06T17:59:42Z positive regulation of heart chamber morphogenesis up regulation of cardiac chamber morphogenesis up regulation of heart chamber morphogenesis up-regulation of cardiac chamber morphogenesis up-regulation of heart chamber morphogenesis upregulation of cardiac chamber morphogenesis upregulation of heart chamber morphogenesis activation of cardiac chamber morphogenesis activation of heart chamber morphogenesis biological_process GO:1901221 positive regulation of cardiac chamber morphogenesis Any process that activates or increases the frequency, rate or extent of cardiac chamber morphogenesis. GOC:BHF GOC:TermGenie positive regulation of heart chamber morphogenesis GOC:TermGenie up regulation of cardiac chamber morphogenesis GOC:TermGenie up regulation of heart chamber morphogenesis GOC:TermGenie up-regulation of cardiac chamber morphogenesis GOC:TermGenie up-regulation of heart chamber morphogenesis GOC:TermGenie upregulation of cardiac chamber morphogenesis GOC:TermGenie upregulation of heart chamber morphogenesis GOC:TermGenie activation of cardiac chamber morphogenesis GOC:TermGenie activation of heart chamber morphogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of lung ciliated cell differentiation. vk 2012-08-08T08:58:34Z biological_process GO:1901246 regulation of lung ciliated cell differentiation Any process that modulates the frequency, rate or extent of lung ciliated cell differentiation. GOC:BHF GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of lung ciliated cell differentiation. vk 2012-08-08T08:58:58Z down regulation of lung ciliated cell differentiation down-regulation of lung ciliated cell differentiation downregulation of lung ciliated cell differentiation inhibition of lung ciliated cell differentiation biological_process GO:1901247 negative regulation of lung ciliated cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of lung ciliated cell differentiation. GOC:BHF GOC:TermGenie down regulation of lung ciliated cell differentiation GOC:TermGenie down-regulation of lung ciliated cell differentiation GOC:TermGenie downregulation of lung ciliated cell differentiation GOC:TermGenie inhibition of lung ciliated cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of lung ciliated cell differentiation. vk 2012-08-08T08:59:05Z up regulation of lung ciliated cell differentiation up-regulation of lung ciliated cell differentiation upregulation of lung ciliated cell differentiation activation of lung ciliated cell differentiation biological_process GO:1901248 positive regulation of lung ciliated cell differentiation Any process that activates or increases the frequency, rate or extent of lung ciliated cell differentiation. GOC:BHF GOC:TermGenie up regulation of lung ciliated cell differentiation GOC:TermGenie up-regulation of lung ciliated cell differentiation GOC:TermGenie upregulation of lung ciliated cell differentiation GOC:TermGenie activation of lung ciliated cell differentiation GOC:TermGenie The directed movement of a carbohydrate derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. bf 2012-08-16T14:51:22Z biological_process GO:1901264 carbohydrate derivative transport The directed movement of a carbohydrate derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:TermGenie GOC:bf GOC:jl Any process that modulates the frequency, rate or extent of vasculature development. bf 2012-09-06T09:16:15Z biological_process regulation of vascular system development GO:1901342 regulation of vasculature development Any process that modulates the frequency, rate or extent of vasculature development. GOC:TermGenie regulation of vascular system development GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of vasculature development. bf 2012-09-06T09:17:24Z down regulation of vasculature development down-regulation of vasculature development downregulation of vasculature development inhibition of vasculature development biological_process down regulation of vascular system development down-regulation of vascular system development downregulation of vascular system development inhibition of vascular system development negative regulation of vascular system development GO:1901343 negative regulation of vasculature development Any process that stops, prevents or reduces the frequency, rate or extent of vasculature development. GOC:TermGenie down regulation of vasculature development GOC:TermGenie down-regulation of vasculature development GOC:TermGenie downregulation of vasculature development GOC:TermGenie inhibition of vasculature development GOC:TermGenie down regulation of vascular system development GOC:TermGenie down-regulation of vascular system development GOC:TermGenie downregulation of vascular system development GOC:TermGenie inhibition of vascular system development GOC:TermGenie negative regulation of vascular system development GOC:TermGenie The chemical reactions and pathways involving organic cyclic compound. bf 2012-09-14T09:03:51Z organic cyclic compound metabolism biological_process GO:1901360 organic cyclic compound metabolic process The chemical reactions and pathways involving organic cyclic compound. GOC:TermGenie organic cyclic compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. bf 2012-09-14T09:05:04Z organic cyclic compound breakdown organic cyclic compound catabolism organic cyclic compound degradation biological_process GO:1901361 organic cyclic compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. GOC:TermGenie organic cyclic compound breakdown GOC:TermGenie organic cyclic compound catabolism GOC:TermGenie organic cyclic compound degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of organic cyclic compound. bf 2012-09-14T09:05:22Z organic cyclic compound anabolism organic cyclic compound biosynthesis organic cyclic compound formation organic cyclic compound synthesis biological_process GO:1901362 organic cyclic compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic cyclic compound. GOC:TermGenie organic cyclic compound anabolism GOC:TermGenie organic cyclic compound biosynthesis GOC:TermGenie organic cyclic compound formation GOC:TermGenie organic cyclic compound synthesis GOC:TermGenie The directed movement of an acetate ester into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. bf 2012-09-28T10:42:13Z biological_process GO:1901374 acetate ester transport The directed movement of an acetate ester into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:TermGenie Enables the transfer of an acetate ester from one side of a membrane to the other. bf 2012-09-28T10:47:08Z molecular_function GO:1901375 acetate ester transmembrane transporter activity Enables the transfer of an acetate ester from one side of a membrane to the other. GOC:TermGenie Any process that modulates the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:34:03Z regulation of tetrapyrrole metabolism biological_process GO:1901401 regulation of tetrapyrrole metabolic process Any process that modulates the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators regulation of tetrapyrrole metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:35:11Z down regulation of tetrapyrrole metabolic process down regulation of tetrapyrrole metabolism down-regulation of tetrapyrrole metabolic process down-regulation of tetrapyrrole metabolism downregulation of tetrapyrrole metabolic process downregulation of tetrapyrrole metabolism inhibition of tetrapyrrole metabolism negative regulation of tetrapyrrole metabolism inhibition of tetrapyrrole metabolic process biological_process GO:1901402 negative regulation of tetrapyrrole metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators down regulation of tetrapyrrole metabolic process GOC:TermGenie down regulation of tetrapyrrole metabolism GOC:TermGenie down-regulation of tetrapyrrole metabolic process GOC:TermGenie down-regulation of tetrapyrrole metabolism GOC:TermGenie downregulation of tetrapyrrole metabolic process GOC:TermGenie downregulation of tetrapyrrole metabolism GOC:TermGenie inhibition of tetrapyrrole metabolism GOC:TermGenie negative regulation of tetrapyrrole metabolism GOC:TermGenie inhibition of tetrapyrrole metabolic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:35:29Z activation of tetrapyrrole metabolism positive regulation of tetrapyrrole metabolism up regulation of tetrapyrrole metabolic process up regulation of tetrapyrrole metabolism up-regulation of tetrapyrrole metabolic process up-regulation of tetrapyrrole metabolism upregulation of tetrapyrrole metabolic process upregulation of tetrapyrrole metabolism activation of tetrapyrrole metabolic process biological_process GO:1901403 positive regulation of tetrapyrrole metabolic process Any process that activates or increases the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators activation of tetrapyrrole metabolism GOC:TermGenie positive regulation of tetrapyrrole metabolism GOC:TermGenie up regulation of tetrapyrrole metabolic process GOC:TermGenie up regulation of tetrapyrrole metabolism GOC:TermGenie up-regulation of tetrapyrrole metabolic process GOC:TermGenie up-regulation of tetrapyrrole metabolism GOC:TermGenie upregulation of tetrapyrrole metabolic process GOC:TermGenie upregulation of tetrapyrrole metabolism GOC:TermGenie activation of tetrapyrrole metabolic process GOC:TermGenie Any process that modulates the frequency, rate or extent of tetrapyrrole catabolic process. tt 2012-10-01T14:38:12Z regulation of tetrapyrrole breakdown regulation of tetrapyrrole catabolism regulation of tetrapyrrole degradation biological_process GO:1901404 regulation of tetrapyrrole catabolic process Any process that modulates the frequency, rate or extent of tetrapyrrole catabolic process. GOC:TermGenie GOC:mengo_curators regulation of tetrapyrrole breakdown GOC:TermGenie regulation of tetrapyrrole catabolism GOC:TermGenie regulation of tetrapyrrole degradation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole catabolic process. tt 2012-10-01T14:39:22Z down regulation of tetrapyrrole breakdown down regulation of tetrapyrrole catabolic process down regulation of tetrapyrrole catabolism down regulation of tetrapyrrole degradation down-regulation of tetrapyrrole breakdown down-regulation of tetrapyrrole catabolic process down-regulation of tetrapyrrole catabolism down-regulation of tetrapyrrole degradation downregulation of tetrapyrrole breakdown downregulation of tetrapyrrole catabolic process downregulation of tetrapyrrole catabolism downregulation of tetrapyrrole degradation inhibition of tetrapyrrole breakdown inhibition of tetrapyrrole catabolism inhibition of tetrapyrrole degradation negative regulation of tetrapyrrole breakdown negative regulation of tetrapyrrole catabolism negative regulation of tetrapyrrole degradation inhibition of tetrapyrrole catabolic process biological_process GO:1901405 negative regulation of tetrapyrrole catabolic process Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole catabolic process. GOC:TermGenie GOC:mengo_curators down regulation of tetrapyrrole breakdown GOC:TermGenie down regulation of tetrapyrrole catabolic process GOC:TermGenie down regulation of tetrapyrrole catabolism GOC:TermGenie down regulation of tetrapyrrole degradation GOC:TermGenie down-regulation of tetrapyrrole breakdown GOC:TermGenie down-regulation of tetrapyrrole catabolic process GOC:TermGenie down-regulation of tetrapyrrole catabolism GOC:TermGenie down-regulation of tetrapyrrole degradation GOC:TermGenie downregulation of tetrapyrrole breakdown GOC:TermGenie downregulation of tetrapyrrole catabolic process GOC:TermGenie downregulation of tetrapyrrole catabolism GOC:TermGenie downregulation of tetrapyrrole degradation GOC:TermGenie inhibition of tetrapyrrole breakdown GOC:TermGenie inhibition of tetrapyrrole catabolism GOC:TermGenie inhibition of tetrapyrrole degradation GOC:TermGenie negative regulation of tetrapyrrole breakdown GOC:TermGenie negative regulation of tetrapyrrole catabolism GOC:TermGenie negative regulation of tetrapyrrole degradation GOC:TermGenie inhibition of tetrapyrrole catabolic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of tetrapyrrole catabolic process. tt 2012-10-01T14:39:40Z activation of tetrapyrrole breakdown activation of tetrapyrrole catabolism activation of tetrapyrrole degradation positive regulation of tetrapyrrole breakdown positive regulation of tetrapyrrole catabolism positive regulation of tetrapyrrole degradation up regulation of tetrapyrrole breakdown up regulation of tetrapyrrole catabolic process up regulation of tetrapyrrole catabolism up regulation of tetrapyrrole degradation up-regulation of tetrapyrrole breakdown up-regulation of tetrapyrrole catabolic process up-regulation of tetrapyrrole catabolism up-regulation of tetrapyrrole degradation upregulation of tetrapyrrole breakdown upregulation of tetrapyrrole catabolic process upregulation of tetrapyrrole catabolism upregulation of tetrapyrrole degradation activation of tetrapyrrole catabolic process biological_process GO:1901406 positive regulation of tetrapyrrole catabolic process Any process that activates or increases the frequency, rate or extent of tetrapyrrole catabolic process. GOC:TermGenie GOC:mengo_curators activation of tetrapyrrole breakdown GOC:TermGenie activation of tetrapyrrole catabolism GOC:TermGenie activation of tetrapyrrole degradation GOC:TermGenie positive regulation of tetrapyrrole breakdown GOC:TermGenie positive regulation of tetrapyrrole catabolism GOC:TermGenie positive regulation of tetrapyrrole degradation GOC:TermGenie up regulation of tetrapyrrole breakdown GOC:TermGenie up regulation of tetrapyrrole catabolic process GOC:TermGenie up regulation of tetrapyrrole catabolism GOC:TermGenie up regulation of tetrapyrrole degradation GOC:TermGenie up-regulation of tetrapyrrole breakdown GOC:TermGenie up-regulation of tetrapyrrole catabolic process GOC:TermGenie up-regulation of tetrapyrrole catabolism GOC:TermGenie up-regulation of tetrapyrrole degradation GOC:TermGenie upregulation of tetrapyrrole breakdown GOC:TermGenie upregulation of tetrapyrrole catabolic process GOC:TermGenie upregulation of tetrapyrrole catabolism GOC:TermGenie upregulation of tetrapyrrole degradation GOC:TermGenie activation of tetrapyrrole catabolic process GOC:TermGenie Any process that modulates the frequency, rate or extent of response to acetate. tt 2012-10-02T14:25:06Z biological_process GO:1901457 regulation of response to acetate Any process that modulates the frequency, rate or extent of response to acetate. GOC:TermGenie GOC:mengo_curators Any process that stops, prevents or reduces the frequency, rate or extent of response to acetate. tt 2012-10-02T14:26:15Z down regulation of response to acetate down-regulation of response to acetate downregulation of response to acetate inhibition of response to acetate biological_process GO:1901458 negative regulation of response to acetate Any process that stops, prevents or reduces the frequency, rate or extent of response to acetate. GOC:TermGenie GOC:mengo_curators down regulation of response to acetate GOC:TermGenie down-regulation of response to acetate GOC:TermGenie downregulation of response to acetate GOC:TermGenie inhibition of response to acetate GOC:TermGenie Any process that activates or increases the frequency, rate or extent of response to acetate. tt 2012-10-02T14:26:34Z up regulation of response to acetate up-regulation of response to acetate upregulation of response to acetate activation of response to acetate biological_process GO:1901459 positive regulation of response to acetate Any process that activates or increases the frequency, rate or extent of response to acetate. GOC:TermGenie GOC:mengo_curators up regulation of response to acetate GOC:TermGenie up-regulation of response to acetate GOC:TermGenie upregulation of response to acetate GOC:TermGenie activation of response to acetate GOC:TermGenie Any process that modulates the frequency, rate or extent of tetrapyrrole biosynthetic process. tt 2012-10-02T14:34:14Z regulation of tetrapyrrole anabolism regulation of tetrapyrrole biosynthesis regulation of tetrapyrrole formation regulation of tetrapyrrole synthesis biological_process GO:1901463 regulation of tetrapyrrole biosynthetic process Any process that modulates the frequency, rate or extent of tetrapyrrole biosynthetic process. GOC:TermGenie GOC:mengo_curators regulation of tetrapyrrole anabolism GOC:TermGenie regulation of tetrapyrrole biosynthesis GOC:TermGenie regulation of tetrapyrrole formation GOC:TermGenie regulation of tetrapyrrole synthesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole biosynthetic process. tt 2012-10-02T14:35:26Z down regulation of tetrapyrrole anabolism down regulation of tetrapyrrole biosynthesis down regulation of tetrapyrrole biosynthetic process down regulation of tetrapyrrole formation down regulation of tetrapyrrole synthesis down-regulation of tetrapyrrole anabolism down-regulation of tetrapyrrole biosynthesis down-regulation of tetrapyrrole biosynthetic process down-regulation of tetrapyrrole formation down-regulation of tetrapyrrole synthesis downregulation of tetrapyrrole anabolism downregulation of tetrapyrrole biosynthesis downregulation of tetrapyrrole biosynthetic process downregulation of tetrapyrrole formation downregulation of tetrapyrrole synthesis inhibition of tetrapyrrole anabolism inhibition of tetrapyrrole biosynthesis inhibition of tetrapyrrole formation inhibition of tetrapyrrole synthesis negative regulation of tetrapyrrole anabolism negative regulation of tetrapyrrole biosynthesis negative regulation of tetrapyrrole formation negative regulation of tetrapyrrole synthesis inhibition of tetrapyrrole biosynthetic process biological_process GO:1901464 negative regulation of tetrapyrrole biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole biosynthetic process. GOC:TermGenie GOC:mengo_curators down regulation of tetrapyrrole anabolism GOC:TermGenie down regulation of tetrapyrrole biosynthesis GOC:TermGenie down regulation of tetrapyrrole biosynthetic process GOC:TermGenie down regulation of tetrapyrrole formation GOC:TermGenie down regulation of tetrapyrrole synthesis GOC:TermGenie down-regulation of tetrapyrrole anabolism GOC:TermGenie down-regulation of tetrapyrrole biosynthesis GOC:TermGenie down-regulation of tetrapyrrole biosynthetic process GOC:TermGenie down-regulation of tetrapyrrole formation GOC:TermGenie down-regulation of tetrapyrrole synthesis GOC:TermGenie downregulation of tetrapyrrole anabolism GOC:TermGenie downregulation of tetrapyrrole biosynthesis GOC:TermGenie downregulation of tetrapyrrole biosynthetic process GOC:TermGenie downregulation of tetrapyrrole formation GOC:TermGenie downregulation of tetrapyrrole synthesis GOC:TermGenie inhibition of tetrapyrrole anabolism GOC:TermGenie inhibition of tetrapyrrole biosynthesis GOC:TermGenie inhibition of tetrapyrrole formation GOC:TermGenie inhibition of tetrapyrrole synthesis GOC:TermGenie negative regulation of tetrapyrrole anabolism GOC:TermGenie negative regulation of tetrapyrrole biosynthesis GOC:TermGenie negative regulation of tetrapyrrole formation GOC:TermGenie negative regulation of tetrapyrrole synthesis GOC:TermGenie inhibition of tetrapyrrole biosynthetic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of tetrapyrrole biosynthetic process. tt 2012-10-02T14:35:43Z activation of tetrapyrrole anabolism activation of tetrapyrrole biosynthesis activation of tetrapyrrole formation activation of tetrapyrrole synthesis positive regulation of tetrapyrrole anabolism positive regulation of tetrapyrrole biosynthesis positive regulation of tetrapyrrole formation positive regulation of tetrapyrrole synthesis up regulation of tetrapyrrole anabolism up regulation of tetrapyrrole biosynthesis up regulation of tetrapyrrole biosynthetic process up regulation of tetrapyrrole formation up regulation of tetrapyrrole synthesis up-regulation of tetrapyrrole anabolism up-regulation of tetrapyrrole biosynthesis up-regulation of tetrapyrrole biosynthetic process up-regulation of tetrapyrrole formation up-regulation of tetrapyrrole synthesis upregulation of tetrapyrrole anabolism upregulation of tetrapyrrole biosynthesis upregulation of tetrapyrrole biosynthetic process upregulation of tetrapyrrole formation upregulation of tetrapyrrole synthesis activation of tetrapyrrole biosynthetic process biological_process GO:1901465 positive regulation of tetrapyrrole biosynthetic process Any process that activates or increases the frequency, rate or extent of tetrapyrrole biosynthetic process. GOC:TermGenie GOC:mengo_curators activation of tetrapyrrole anabolism GOC:TermGenie activation of tetrapyrrole biosynthesis GOC:TermGenie activation of tetrapyrrole formation GOC:TermGenie activation of tetrapyrrole synthesis GOC:TermGenie positive regulation of tetrapyrrole anabolism GOC:TermGenie positive regulation of tetrapyrrole biosynthesis GOC:TermGenie positive regulation of tetrapyrrole formation GOC:TermGenie positive regulation of tetrapyrrole synthesis GOC:TermGenie up regulation of tetrapyrrole anabolism GOC:TermGenie up regulation of tetrapyrrole biosynthesis GOC:TermGenie up regulation of tetrapyrrole biosynthetic process GOC:TermGenie up regulation of tetrapyrrole formation GOC:TermGenie up regulation of tetrapyrrole synthesis GOC:TermGenie up-regulation of tetrapyrrole anabolism GOC:TermGenie up-regulation of tetrapyrrole biosynthesis GOC:TermGenie up-regulation of tetrapyrrole biosynthetic process GOC:TermGenie up-regulation of tetrapyrrole formation GOC:TermGenie up-regulation of tetrapyrrole synthesis GOC:TermGenie upregulation of tetrapyrrole anabolism GOC:TermGenie upregulation of tetrapyrrole biosynthesis GOC:TermGenie upregulation of tetrapyrrole biosynthetic process GOC:TermGenie upregulation of tetrapyrrole formation GOC:TermGenie upregulation of tetrapyrrole synthesis GOC:TermGenie activation of tetrapyrrole biosynthetic process GOC:TermGenie Enables the transfer of carbohydrate derivative from one side of a membrane to the other. pr 2012-10-17T10:31:22Z molecular_function carbohydrate derivative transporter activity GO:1901505 carbohydrate derivative transmembrane transporter activity GO_REF:0000090 Enables the transfer of carbohydrate derivative from one side of a membrane to the other. GOC:TermGenie GOC:pr Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis. dph 2012-10-17T14:30:40Z biological_process GO:1901509 regulation of endothelial tube morphogenesis Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis. GOC:TermGenie GOC:dph Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:01Z regulation of haematopoietic progenitor cell differentiation regulation of haemopoietic progenitor cell differentiation regulation of hemopoietic progenitor cell differentiation biological_process GO:1901532 regulation of hematopoietic progenitor cell differentiation Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl regulation of haematopoietic progenitor cell differentiation GOC:TermGenie regulation of haemopoietic progenitor cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:06Z down regulation of haematopoietic progenitor cell differentiation down regulation of haemopoietic progenitor cell differentiation down regulation of hemopoietic progenitor cell differentiation down-regulation of haematopoietic progenitor cell differentiation down-regulation of haemopoietic progenitor cell differentiation down-regulation of hemopoietic progenitor cell differentiation downregulation of haematopoietic progenitor cell differentiation downregulation of haemopoietic progenitor cell differentiation downregulation of hemopoietic progenitor cell differentiation inhibition of haematopoietic progenitor cell differentiation inhibition of haemopoietic progenitor cell differentiation negative regulation of haematopoietic progenitor cell differentiation negative regulation of haemopoietic progenitor cell differentiation negative regulation of hemopoietic progenitor cell differentiation inhibition of hemopoietic progenitor cell differentiation biological_process down regulation of hematopoietic progenitor cell differentiation down-regulation of hematopoietic progenitor cell differentiation downregulation of hematopoietic progenitor cell differentiation inhibition of hematopoietic progenitor cell differentiation GO:1901533 negative regulation of hematopoietic progenitor cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl down regulation of haematopoietic progenitor cell differentiation GOC:TermGenie down regulation of haemopoietic progenitor cell differentiation GOC:TermGenie down regulation of hemopoietic progenitor cell differentiation GOC:TermGenie down-regulation of haematopoietic progenitor cell differentiation GOC:TermGenie down-regulation of haemopoietic progenitor cell differentiation GOC:TermGenie down-regulation of hemopoietic progenitor cell differentiation GOC:TermGenie downregulation of haematopoietic progenitor cell differentiation GOC:TermGenie downregulation of haemopoietic progenitor cell differentiation GOC:TermGenie downregulation of hemopoietic progenitor cell differentiation GOC:TermGenie inhibition of haematopoietic progenitor cell differentiation GOC:TermGenie inhibition of haemopoietic progenitor cell differentiation GOC:TermGenie negative regulation of haematopoietic progenitor cell differentiation GOC:TermGenie negative regulation of haemopoietic progenitor cell differentiation GOC:TermGenie inhibition of hemopoietic progenitor cell differentiation GOC:TermGenie down regulation of hematopoietic progenitor cell differentiation GOC:TermGenie down-regulation of hematopoietic progenitor cell differentiation GOC:TermGenie downregulation of hematopoietic progenitor cell differentiation GOC:TermGenie inhibition of hematopoietic progenitor cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:14Z activation of haematopoietic progenitor cell differentiation activation of haemopoietic progenitor cell differentiation positive regulation of haematopoietic progenitor cell differentiation positive regulation of haemopoietic progenitor cell differentiation positive regulation of hemopoietic progenitor cell differentiation up regulation of haematopoietic progenitor cell differentiation up regulation of haemopoietic progenitor cell differentiation up regulation of hemopoietic progenitor cell differentiation up-regulation of haematopoietic progenitor cell differentiation up-regulation of haemopoietic progenitor cell differentiation up-regulation of hemopoietic progenitor cell differentiation upregulation of haematopoietic progenitor cell differentiation upregulation of haemopoietic progenitor cell differentiation upregulation of hemopoietic progenitor cell differentiation activation of hemopoietic progenitor cell differentiation biological_process activation of hematopoietic progenitor cell differentiation up regulation of hematopoietic progenitor cell differentiation up-regulation of hematopoietic progenitor cell differentiation upregulation of hematopoietic progenitor cell differentiation GO:1901534 positive regulation of hematopoietic progenitor cell differentiation Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl activation of haematopoietic progenitor cell differentiation GOC:TermGenie activation of haemopoietic progenitor cell differentiation GOC:TermGenie positive regulation of haematopoietic progenitor cell differentiation GOC:TermGenie positive regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up regulation of haematopoietic progenitor cell differentiation GOC:TermGenie up regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up regulation of hemopoietic progenitor cell differentiation GOC:TermGenie up-regulation of haematopoietic progenitor cell differentiation GOC:TermGenie up-regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up-regulation of hemopoietic progenitor cell differentiation GOC:TermGenie upregulation of haematopoietic progenitor cell differentiation GOC:TermGenie upregulation of haemopoietic progenitor cell differentiation GOC:TermGenie upregulation of hemopoietic progenitor cell differentiation GOC:TermGenie activation of hemopoietic progenitor cell differentiation GOC:TermGenie activation of hematopoietic progenitor cell differentiation GOC:TermGenie up regulation of hematopoietic progenitor cell differentiation GOC:TermGenie up-regulation of hematopoietic progenitor cell differentiation GOC:TermGenie upregulation of hematopoietic progenitor cell differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of endothelial cell development. pr 2012-10-30T12:59:50Z biological_process GO:1901550 regulation of endothelial cell development Any process that modulates the frequency, rate or extent of endothelial cell development. GOC:TermGenie GOC:pr PMID:19470579 Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell development. pr 2012-10-30T12:59:54Z down regulation of endothelial cell development down-regulation of endothelial cell development downregulation of endothelial cell development inhibition of endothelial cell development biological_process GO:1901551 negative regulation of endothelial cell development Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell development. GOC:TermGenie GOC:pr PMID:19470579 down regulation of endothelial cell development GOC:TermGenie down-regulation of endothelial cell development GOC:TermGenie downregulation of endothelial cell development GOC:TermGenie inhibition of endothelial cell development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of endothelial cell development. pr 2012-10-30T12:59:58Z up regulation of endothelial cell development up-regulation of endothelial cell development upregulation of endothelial cell development activation of endothelial cell development biological_process GO:1901552 positive regulation of endothelial cell development Any process that activates or increases the frequency, rate or extent of endothelial cell development. GOC:TermGenie GOC:pr PMID:19470579 up regulation of endothelial cell development GOC:TermGenie up-regulation of endothelial cell development GOC:TermGenie upregulation of endothelial cell development GOC:TermGenie activation of endothelial cell development GOC:TermGenie The chemical reactions and pathways involving organonitrogen compound. pr 2012-11-04T15:17:52Z organonitrogen compound metabolism biological_process GO:1901564 organonitrogen compound metabolic process The chemical reactions and pathways involving organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. pr 2012-11-04T15:17:56Z organonitrogen compound breakdown organonitrogen compound catabolism organonitrogen compound degradation biological_process GO:1901565 organonitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound breakdown GOC:TermGenie organonitrogen compound catabolism GOC:TermGenie organonitrogen compound degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of organonitrogen compound. pr 2012-11-04T15:18:00Z organonitrogen compound anabolism organonitrogen compound biosynthesis organonitrogen compound formation organonitrogen compound synthesis biological_process GO:1901566 organonitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound anabolism GOC:TermGenie organonitrogen compound biosynthesis GOC:TermGenie organonitrogen compound formation GOC:TermGenie organonitrogen compound synthesis GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:36Z organic molecular entity breakdown organic molecular entity catabolic process organic molecular entity catabolism organic molecular entity degradation organic substance breakdown organic substance catabolism organic substance degradation biological_process GO:1901575 organic substance catabolic process The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity breakdown GOC:TermGenie organic molecular entity catabolism GOC:TermGenie organic molecular entity degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:40Z organic molecular entity anabolism organic molecular entity biosynthesis organic molecular entity biosynthetic process organic molecular entity formation organic molecular entity synthesis organic substance anabolism organic substance biosynthesis organic substance formation organic substance synthesis biological_process GO:1901576 organic substance biosynthetic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity anabolism GOC:TermGenie organic molecular entity biosynthesis GOC:TermGenie organic molecular entity formation GOC:TermGenie organic molecular entity synthesis GOC:TermGenie The chemical reactions and pathways involving an alpha-amino acid. tb 2012-11-08T17:39:50Z alpha-amino acid metabolism biological_process GO:1901605 alpha-amino acid metabolic process The chemical reactions and pathways involving an alpha-amino acid. GOC:TermGenie alpha-amino acid metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid. tb 2012-11-08T17:39:54Z alpha-amino acid breakdown alpha-amino acid catabolism alpha-amino acid degradation biological_process GO:1901606 alpha-amino acid catabolic process The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid. GOC:TermGenie alpha-amino acid breakdown GOC:TermGenie alpha-amino acid catabolism GOC:TermGenie alpha-amino acid degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of an alpha-amino acid. tb 2012-11-08T17:39:58Z alpha-amino acid anabolism alpha-amino acid biosynthesis alpha-amino acid formation alpha-amino acid synthesis biological_process GO:1901607 alpha-amino acid biosynthetic process The chemical reactions and pathways resulting in the formation of an alpha-amino acid. GOC:TermGenie alpha-amino acid anabolism GOC:TermGenie alpha-amino acid biosynthesis GOC:TermGenie alpha-amino acid formation GOC:TermGenie alpha-amino acid synthesis GOC:TermGenie Any process that modulates the frequency, rate or extent of vesicle transport along microtubule. hjd 2012-11-08T21:49:44Z regulation of microtubule-based vesicle localization biological_process GO:1901608 regulation of vesicle transport along microtubule Any process that modulates the frequency, rate or extent of vesicle transport along microtubule. GOC:TermGenie regulation of microtubule-based vesicle localization GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of vesicle transport along microtubule. hjd 2012-11-08T21:49:48Z down regulation of microtubule-based vesicle localization down regulation of vesicle transport along microtubule down-regulation of microtubule-based vesicle localization down-regulation of vesicle transport along microtubule downregulation of microtubule-based vesicle localization downregulation of vesicle transport along microtubule inhibition of microtubule-based vesicle localization negative regulation of microtubule-based vesicle localization inhibition of vesicle transport along microtubule biological_process GO:1901609 negative regulation of vesicle transport along microtubule Any process that stops, prevents or reduces the frequency, rate or extent of vesicle transport along microtubule. GOC:TermGenie down regulation of microtubule-based vesicle localization GOC:TermGenie down regulation of vesicle transport along microtubule GOC:TermGenie down-regulation of microtubule-based vesicle localization GOC:TermGenie down-regulation of vesicle transport along microtubule GOC:TermGenie downregulation of microtubule-based vesicle localization GOC:TermGenie downregulation of vesicle transport along microtubule GOC:TermGenie inhibition of microtubule-based vesicle localization GOC:TermGenie negative regulation of microtubule-based vesicle localization GOC:TermGenie inhibition of vesicle transport along microtubule GOC:TermGenie Any process that activates or increases the frequency, rate or extent of vesicle transport along microtubule. hjd 2012-11-08T21:49:53Z activation of microtubule-based vesicle localization positive regulation of microtubule-based vesicle localization up regulation of microtubule-based vesicle localization up regulation of vesicle transport along microtubule up-regulation of microtubule-based vesicle localization up-regulation of vesicle transport along microtubule upregulation of microtubule-based vesicle localization upregulation of vesicle transport along microtubule activation of vesicle transport along microtubule biological_process GO:1901610 positive regulation of vesicle transport along microtubule Any process that activates or increases the frequency, rate or extent of vesicle transport along microtubule. GOC:TermGenie activation of microtubule-based vesicle localization GOC:TermGenie positive regulation of microtubule-based vesicle localization GOC:TermGenie up regulation of microtubule-based vesicle localization GOC:TermGenie up regulation of vesicle transport along microtubule GOC:TermGenie up-regulation of microtubule-based vesicle localization GOC:TermGenie up-regulation of vesicle transport along microtubule GOC:TermGenie upregulation of microtubule-based vesicle localization GOC:TermGenie upregulation of vesicle transport along microtubule GOC:TermGenie activation of vesicle transport along microtubule GOC:TermGenie The chemical reactions and pathways involving organic hydroxy compound. pr 2012-11-13T12:54:27Z organic hydroxy compound metabolism biological_process GO:1901615 organic hydroxy compound metabolic process The chemical reactions and pathways involving organic hydroxy compound. GOC:TermGenie GOC:pr organic hydroxy compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of organic hydroxy compound. pr 2012-11-13T12:54:31Z organic hydroxy compound breakdown organic hydroxy compound catabolism organic hydroxy compound degradation biological_process GO:1901616 organic hydroxy compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic hydroxy compound. GOC:TermGenie GOC:pr organic hydroxy compound breakdown GOC:TermGenie organic hydroxy compound catabolism GOC:TermGenie organic hydroxy compound degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of organic hydroxy compound. pr 2012-11-13T12:54:36Z organic hydroxy compound anabolism organic hydroxy compound biosynthesis organic hydroxy compound formation organic hydroxy compound synthesis biological_process GO:1901617 organic hydroxy compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic hydroxy compound. GOC:TermGenie GOC:pr organic hydroxy compound anabolism GOC:TermGenie organic hydroxy compound biosynthesis GOC:TermGenie organic hydroxy compound formation GOC:TermGenie organic hydroxy compound synthesis GOC:TermGenie Enables the transfer of organic hydroxy compound from one side of a membrane to the other. pr 2012-11-13T12:59:01Z molecular_function GO:1901618 organic hydroxy compound transmembrane transporter activity Enables the transfer of organic hydroxy compound from one side of a membrane to the other. GOC:TermGenie GOC:pr Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus. pr 2012-11-20T09:45:15Z biological_process GO:1901652 response to peptide Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus. GOC:TermGenie GOC:pr A response that results in a state of tolerance to ketone. pr 2012-11-20T10:55:47Z GO:1990369 process resulting in tolerance to ketone biological_process GO:1901654 response to ketone A response that results in a state of tolerance to ketone. GOC:mengo_curators PMID:23356676 Enables the transfer of a sulfur compound from one side of a membrane to the other. pr 2012-11-26T20:45:29Z sulfur molecular entity transmembrane transporter activity molecular_function GO:1901682 sulfur compound transmembrane transporter activity Enables the transfer of a sulfur compound from one side of a membrane to the other. GOC:TermGenie GOC:pr Any process that modulates the frequency, rate or extent of compound eye retinal cell apoptotic process. pr 2012-12-12T10:28:35Z biological_process GO:1901692 regulation of compound eye retinal cell apoptotic process Any process that modulates the frequency, rate or extent of compound eye retinal cell apoptotic process. GOC:TermGenie GOC:mtg_apoptosis PMID:12021768 Any process that stops, prevents or reduces the frequency, rate or extent of compound eye retinal cell apoptotic process. pr 2012-12-12T10:28:40Z down regulation of compound eye retinal cell apoptotic process down-regulation of compound eye retinal cell apoptotic process downregulation of compound eye retinal cell apoptotic process inhibition of compound eye retinal cell apoptotic process biological_process GO:1901693 negative regulation of compound eye retinal cell apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of compound eye retinal cell apoptotic process. GOC:TermGenie GOC:mtg_apoptosis PMID:12021768 down regulation of compound eye retinal cell apoptotic process GOC:TermGenie down-regulation of compound eye retinal cell apoptotic process GOC:TermGenie downregulation of compound eye retinal cell apoptotic process GOC:TermGenie inhibition of compound eye retinal cell apoptotic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of compound eye retinal cell apoptotic process. pr 2012-12-12T10:28:45Z GO:0046675 up regulation of compound eye retinal cell apoptotic process up-regulation of compound eye retinal cell apoptotic process upregulation of compound eye retinal cell apoptotic process activation of compound eye retinal cell apoptotic process biological_process induction of compound eye retinal cell programmed cell death GO:1901694 positive regulation of compound eye retinal cell apoptotic process Any process that activates or increases the frequency, rate or extent of compound eye retinal cell apoptotic process. GOC:TermGenie GOC:mtg_apoptosis PMID:12021768 up regulation of compound eye retinal cell apoptotic process GOC:TermGenie up-regulation of compound eye retinal cell apoptotic process GOC:TermGenie upregulation of compound eye retinal cell apoptotic process GOC:TermGenie activation of compound eye retinal cell apoptotic process GOC:TermGenie Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus. pr 2012-12-13T15:06:08Z response to nitrogen molecular entity biological_process GO:1901698 response to nitrogen compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus. GOC:TermGenie GOC:pr Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus. pr 2012-12-13T15:11:37Z response to oxygen molecular entity biological_process GO:1901700 response to oxygen-containing compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus. GOC:TermGenie GOC:pr Enables the transfer of salt from one side of a membrane to the other. pr 2012-12-13T15:14:47Z molecular_function GO:1901702 salt transmembrane transporter activity Enables the transfer of salt from one side of a membrane to the other. GOC:TermGenie GOC:pr The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of bone as it progresses from its formation to the mature state. hjd 2012-12-14T16:04:16Z biological_process GO:1901706 mesenchymal cell differentiation involved in bone development The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of bone as it progresses from its formation to the mature state. GOC:TermGenie GOC:hjd PMID:21571217 Any process that modulates the frequency, rate or extent of muscle tissue development. yaf 2013-02-01T10:30:47Z biological_process GO:1901861 regulation of muscle tissue development Any process that modulates the frequency, rate or extent of muscle tissue development. GOC:TermGenie GOC:yaf PMID:23150719 Any process that stops, prevents or reduces the frequency, rate or extent of muscle tissue development. yaf 2013-02-01T10:30:52Z down regulation of muscle tissue development down-regulation of muscle tissue development downregulation of muscle tissue development inhibition of muscle tissue development biological_process GO:1901862 negative regulation of muscle tissue development Any process that stops, prevents or reduces the frequency, rate or extent of muscle tissue development. GOC:TermGenie GOC:yaf PMID:23150719 down regulation of muscle tissue development GOC:TermGenie down-regulation of muscle tissue development GOC:TermGenie downregulation of muscle tissue development GOC:TermGenie inhibition of muscle tissue development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of muscle tissue development. yaf 2013-02-01T10:30:57Z up regulation of muscle tissue development up-regulation of muscle tissue development upregulation of muscle tissue development activation of muscle tissue development biological_process GO:1901863 positive regulation of muscle tissue development Any process that activates or increases the frequency, rate or extent of muscle tissue development. GOC:TermGenie GOC:yaf PMID:23150719 up regulation of muscle tissue development GOC:TermGenie up-regulation of muscle tissue development GOC:TermGenie upregulation of muscle tissue development GOC:TermGenie activation of muscle tissue development GOC:TermGenie Any process that modulates the frequency, rate or extent of protein depolymerization. rl 2013-02-06T13:57:23Z regulation of protein polymer breakdown regulation of protein polymer catabolic process regulation of protein polymer catabolism regulation of protein polymer degradation biological_process GO:1901879 regulation of protein depolymerization Any process that modulates the frequency, rate or extent of protein depolymerization. GOC:BHF GOC:TermGenie GOC:rl PMID:12032137 regulation of protein polymer breakdown GOC:TermGenie regulation of protein polymer catabolic process GOC:TermGenie regulation of protein polymer catabolism GOC:TermGenie regulation of protein polymer degradation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein depolymerization. rl 2013-02-06T13:57:28Z down regulation of protein depolymerization down regulation of protein polymer breakdown down regulation of protein polymer catabolic process down regulation of protein polymer catabolism down regulation of protein polymer degradation down-regulation of protein depolymerization down-regulation of protein polymer breakdown down-regulation of protein polymer catabolic process down-regulation of protein polymer catabolism down-regulation of protein polymer degradation downregulation of protein depolymerization downregulation of protein polymer breakdown downregulation of protein polymer catabolic process downregulation of protein polymer catabolism downregulation of protein polymer degradation inhibition of protein polymer breakdown inhibition of protein polymer catabolic process inhibition of protein polymer catabolism inhibition of protein polymer degradation negative regulation of protein polymer breakdown negative regulation of protein polymer catabolic process negative regulation of protein polymer catabolism negative regulation of protein polymer degradation inhibition of protein depolymerization biological_process GO:1901880 negative regulation of protein depolymerization Any process that stops, prevents or reduces the frequency, rate or extent of protein depolymerization. GOC:BHF GOC:TermGenie GOC:rl PMID:12032137 down regulation of protein depolymerization GOC:TermGenie down regulation of protein polymer breakdown GOC:TermGenie down regulation of protein polymer catabolic process GOC:TermGenie down regulation of protein polymer catabolism GOC:TermGenie down regulation of protein polymer degradation GOC:TermGenie down-regulation of protein depolymerization GOC:TermGenie down-regulation of protein polymer breakdown GOC:TermGenie down-regulation of protein polymer catabolic process GOC:TermGenie down-regulation of protein polymer catabolism GOC:TermGenie down-regulation of protein polymer degradation GOC:TermGenie downregulation of protein depolymerization GOC:TermGenie downregulation of protein polymer breakdown GOC:TermGenie downregulation of protein polymer catabolic process GOC:TermGenie downregulation of protein polymer catabolism GOC:TermGenie downregulation of protein polymer degradation GOC:TermGenie inhibition of protein polymer breakdown GOC:TermGenie inhibition of protein polymer catabolic process GOC:TermGenie inhibition of protein polymer catabolism GOC:TermGenie inhibition of protein polymer degradation GOC:TermGenie negative regulation of protein polymer breakdown GOC:TermGenie negative regulation of protein polymer catabolic process GOC:TermGenie negative regulation of protein polymer catabolism GOC:TermGenie negative regulation of protein polymer degradation GOC:TermGenie inhibition of protein depolymerization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein depolymerization. rl 2013-02-06T13:57:32Z activation of protein polymer breakdown activation of protein polymer catabolic process activation of protein polymer catabolism activation of protein polymer degradation positive regulation of protein polymer breakdown positive regulation of protein polymer catabolic process positive regulation of protein polymer catabolism positive regulation of protein polymer degradation up regulation of protein depolymerization up regulation of protein polymer breakdown up regulation of protein polymer catabolic process up regulation of protein polymer catabolism up regulation of protein polymer degradation up-regulation of protein depolymerization up-regulation of protein polymer breakdown up-regulation of protein polymer catabolic process up-regulation of protein polymer catabolism up-regulation of protein polymer degradation upregulation of protein depolymerization upregulation of protein polymer breakdown upregulation of protein polymer catabolic process upregulation of protein polymer catabolism upregulation of protein polymer degradation activation of protein depolymerization biological_process GO:1901881 positive regulation of protein depolymerization Any process that activates or increases the frequency, rate or extent of protein depolymerization. GOC:BHF GOC:TermGenie GOC:rl PMID:12032137 activation of protein polymer breakdown GOC:TermGenie activation of protein polymer catabolic process GOC:TermGenie activation of protein polymer catabolism GOC:TermGenie activation of protein polymer degradation GOC:TermGenie positive regulation of protein polymer breakdown GOC:TermGenie positive regulation of protein polymer catabolic process GOC:TermGenie positive regulation of protein polymer catabolism GOC:TermGenie positive regulation of protein polymer degradation GOC:TermGenie up regulation of protein depolymerization GOC:TermGenie up regulation of protein polymer breakdown GOC:TermGenie up regulation of protein polymer catabolic process GOC:TermGenie up regulation of protein polymer catabolism GOC:TermGenie up regulation of protein polymer degradation GOC:TermGenie up-regulation of protein depolymerization GOC:TermGenie up-regulation of protein polymer breakdown GOC:TermGenie up-regulation of protein polymer catabolic process GOC:TermGenie up-regulation of protein polymer catabolism GOC:TermGenie up-regulation of protein polymer degradation GOC:TermGenie upregulation of protein depolymerization GOC:TermGenie upregulation of protein polymer breakdown GOC:TermGenie upregulation of protein polymer catabolic process GOC:TermGenie upregulation of protein polymer catabolism GOC:TermGenie upregulation of protein polymer degradation GOC:TermGenie activation of protein depolymerization GOC:TermGenie Any process that modulates the frequency, rate or extent of cell junction assembly. tb 2013-02-06T19:40:32Z biological_process GO:1901888 regulation of cell junction assembly Any process that modulates the frequency, rate or extent of cell junction assembly. GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cell junction assembly. tb 2013-02-06T19:40:41Z down regulation of cell junction assembly down-regulation of cell junction assembly downregulation of cell junction assembly inhibition of cell junction assembly biological_process GO:1901889 negative regulation of cell junction assembly Any process that stops, prevents or reduces the frequency, rate or extent of cell junction assembly. GOC:TermGenie down regulation of cell junction assembly GOC:TermGenie down-regulation of cell junction assembly GOC:TermGenie downregulation of cell junction assembly GOC:TermGenie inhibition of cell junction assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cell junction assembly. tb 2013-02-06T19:40:46Z up regulation of cell junction assembly up-regulation of cell junction assembly upregulation of cell junction assembly activation of cell junction assembly biological_process GO:1901890 positive regulation of cell junction assembly Any process that activates or increases the frequency, rate or extent of cell junction assembly. GOC:TermGenie up regulation of cell junction assembly GOC:TermGenie up-regulation of cell junction assembly GOC:TermGenie upregulation of cell junction assembly GOC:TermGenie activation of cell junction assembly GOC:TermGenie Any process that modulates the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis. dph 2013-02-20T20:30:26Z biological_process GO:1901963 regulation of cell proliferation involved in outflow tract morphogenesis Any process that modulates the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis. GOC:TermGenie GOC:dph GOC:mtg_heart PMID:21419760 Any process that activates or increases the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis. dph 2013-02-20T20:30:31Z up regulation of cell proliferation involved in outflow tract morphogenesis up-regulation of cell proliferation involved in outflow tract morphogenesis upregulation of cell proliferation involved in outflow tract morphogenesis activation of cell proliferation involved in outflow tract morphogenesis biological_process GO:1901964 positive regulation of cell proliferation involved in outflow tract morphogenesis Any process that activates or increases the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis. GOC:TermGenie GOC:dph GOC:mtg_heart PMID:21419760 up regulation of cell proliferation involved in outflow tract morphogenesis GOC:TermGenie up-regulation of cell proliferation involved in outflow tract morphogenesis GOC:TermGenie upregulation of cell proliferation involved in outflow tract morphogenesis GOC:TermGenie activation of cell proliferation involved in outflow tract morphogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of cilium assembly. dph 2013-03-26T18:10:51Z regulation of ciliogenesis biological_process regulation of cilium biogenesis GO:1902017 regulation of cilium assembly Any process that modulates the frequency, rate or extent of cilium assembly. GOC:TermGenie GOC:cilia GOC:dph PMID:17719545 regulation of ciliogenesis GOC:TermGenie regulation of cilium biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly. dph 2013-03-26T18:10:56Z down regulation of ciliogenesis down regulation of cilium assembly down-regulation of ciliogenesis down-regulation of cilium assembly downregulation of ciliogenesis downregulation of cilium assembly inhibition of ciliogenesis negative regulation of ciliogenesis inhibition of cilium assembly biological_process down regulation of cilium biogenesis down-regulation of cilium biogenesis downregulation of cilium biogenesis inhibition of cilium biogenesis negative regulation of cilium biogenesis GO:1902018 negative regulation of cilium assembly Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly. GOC:TermGenie GOC:cilia GOC:dph PMID:17719545 down regulation of ciliogenesis GOC:TermGenie down regulation of cilium assembly GOC:TermGenie down-regulation of ciliogenesis GOC:TermGenie down-regulation of cilium assembly GOC:TermGenie downregulation of ciliogenesis GOC:TermGenie downregulation of cilium assembly GOC:TermGenie inhibition of ciliogenesis GOC:TermGenie negative regulation of ciliogenesis GOC:TermGenie inhibition of cilium assembly GOC:TermGenie down regulation of cilium biogenesis GOC:TermGenie down-regulation of cilium biogenesis GOC:TermGenie downregulation of cilium biogenesis GOC:TermGenie inhibition of cilium biogenesis GOC:TermGenie negative regulation of cilium biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of hematopoietic stem cell proliferation. ss 2013-04-02T05:13:19Z regulation of hemopoietic stem cell proliferation biological_process GO:1902033 regulation of hematopoietic stem cell proliferation Any process that modulates the frequency, rate or extent of hematopoietic stem cell proliferation. GOC:TermGenie PMID:23403623 regulation of hemopoietic stem cell proliferation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell proliferation. ss 2013-04-02T05:13:24Z down regulation of hematopoietic stem cell proliferation down regulation of hemopoietic stem cell proliferation down-regulation of hematopoietic stem cell proliferation down-regulation of hemopoietic stem cell proliferation downregulation of hematopoietic stem cell proliferation downregulation of hemopoietic stem cell proliferation negative regulation of hemopoietic stem cell proliferation inhibition of hematopoietic stem cell proliferation inhibition of hemopoietic stem cell proliferation biological_process GO:1902034 negative regulation of hematopoietic stem cell proliferation Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell proliferation. GOC:TermGenie PMID:23403623 down regulation of hematopoietic stem cell proliferation GOC:TermGenie down regulation of hemopoietic stem cell proliferation GOC:TermGenie down-regulation of hematopoietic stem cell proliferation GOC:TermGenie down-regulation of hemopoietic stem cell proliferation GOC:TermGenie downregulation of hematopoietic stem cell proliferation GOC:TermGenie downregulation of hemopoietic stem cell proliferation GOC:TermGenie negative regulation of hemopoietic stem cell proliferation GOC:TermGenie inhibition of hematopoietic stem cell proliferation GOC:TermGenie inhibition of hemopoietic stem cell proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell proliferation. ss 2013-04-02T05:13:31Z positive regulation of hemopoietic stem cell proliferation up regulation of hematopoietic stem cell proliferation up regulation of hemopoietic stem cell proliferation up-regulation of hematopoietic stem cell proliferation up-regulation of hemopoietic stem cell proliferation upregulation of hematopoietic stem cell proliferation upregulation of hemopoietic stem cell proliferation activation of hematopoietic stem cell proliferation activation of hemopoietic stem cell proliferation biological_process GO:1902035 positive regulation of hematopoietic stem cell proliferation Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell proliferation. GOC:TermGenie PMID:23403623 positive regulation of hemopoietic stem cell proliferation GOC:TermGenie up regulation of hematopoietic stem cell proliferation GOC:TermGenie up regulation of hemopoietic stem cell proliferation GOC:TermGenie up-regulation of hematopoietic stem cell proliferation GOC:TermGenie up-regulation of hemopoietic stem cell proliferation GOC:TermGenie upregulation of hematopoietic stem cell proliferation GOC:TermGenie upregulation of hemopoietic stem cell proliferation GOC:TermGenie activation of hematopoietic stem cell proliferation GOC:TermGenie activation of hemopoietic stem cell proliferation GOC:TermGenie Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation. ss 2013-04-02T05:19:09Z regulation of haematopoietic stem cell differentiation regulation of haemopoietic stem cell differentiation regulation of hemopoietic stem cell differentiation biological_process GO:1902036 regulation of hematopoietic stem cell differentiation Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation. GOC:TermGenie PMID:23403623 regulation of haematopoietic stem cell differentiation GOC:TermGenie regulation of haemopoietic stem cell differentiation GOC:TermGenie regulation of hemopoietic stem cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell differentiation. ss 2013-04-02T05:19:14Z down regulation of haematopoietic stem cell differentiation down regulation of haemopoietic stem cell differentiation down regulation of hematopoietic stem cell differentiation down regulation of hemopoietic stem cell differentiation down-regulation of haematopoietic stem cell differentiation down-regulation of haemopoietic stem cell differentiation down-regulation of hematopoietic stem cell differentiation down-regulation of hemopoietic stem cell differentiation downregulation of haematopoietic stem cell differentiation downregulation of haemopoietic stem cell differentiation downregulation of hematopoietic stem cell differentiation downregulation of hemopoietic stem cell differentiation negative regulation of haematopoietic stem cell differentiation negative regulation of haemopoietic stem cell differentiation negative regulation of hemopoietic stem cell differentiation inhibition of haematopoietic stem cell differentiation inhibition of haemopoietic stem cell differentiation inhibition of hematopoietic stem cell differentiation inhibition of hemopoietic stem cell differentiation biological_process GO:1902037 negative regulation of hematopoietic stem cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell differentiation. GOC:TermGenie PMID:23403623 down regulation of haematopoietic stem cell differentiation GOC:TermGenie down regulation of haemopoietic stem cell differentiation GOC:TermGenie down regulation of hematopoietic stem cell differentiation GOC:TermGenie down regulation of hemopoietic stem cell differentiation GOC:TermGenie down-regulation of haematopoietic stem cell differentiation GOC:TermGenie down-regulation of haemopoietic stem cell differentiation GOC:TermGenie down-regulation of hematopoietic stem cell differentiation GOC:TermGenie down-regulation of hemopoietic stem cell differentiation GOC:TermGenie downregulation of haematopoietic stem cell differentiation GOC:TermGenie downregulation of haemopoietic stem cell differentiation GOC:TermGenie downregulation of hematopoietic stem cell differentiation GOC:TermGenie downregulation of hemopoietic stem cell differentiation GOC:TermGenie negative regulation of haematopoietic stem cell differentiation GOC:TermGenie negative regulation of haemopoietic stem cell differentiation GOC:TermGenie negative regulation of hemopoietic stem cell differentiation GOC:TermGenie inhibition of haematopoietic stem cell differentiation GOC:TermGenie inhibition of haemopoietic stem cell differentiation GOC:TermGenie inhibition of hematopoietic stem cell differentiation GOC:TermGenie inhibition of hemopoietic stem cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell differentiation. ss 2013-04-02T05:19:19Z positive regulation of haematopoietic stem cell differentiation positive regulation of haemopoietic stem cell differentiation positive regulation of hemopoietic stem cell differentiation up regulation of haematopoietic stem cell differentiation up regulation of haemopoietic stem cell differentiation up regulation of hematopoietic stem cell differentiation up regulation of hemopoietic stem cell differentiation up-regulation of haematopoietic stem cell differentiation up-regulation of haemopoietic stem cell differentiation up-regulation of hematopoietic stem cell differentiation up-regulation of hemopoietic stem cell differentiation upregulation of haematopoietic stem cell differentiation upregulation of haemopoietic stem cell differentiation upregulation of hematopoietic stem cell differentiation upregulation of hemopoietic stem cell differentiation activation of haematopoietic stem cell differentiation activation of haemopoietic stem cell differentiation activation of hematopoietic stem cell differentiation activation of hemopoietic stem cell differentiation biological_process GO:1902038 positive regulation of hematopoietic stem cell differentiation Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell differentiation. GOC:TermGenie PMID:23403623 positive regulation of haematopoietic stem cell differentiation GOC:TermGenie positive regulation of haemopoietic stem cell differentiation GOC:TermGenie positive regulation of hemopoietic stem cell differentiation GOC:TermGenie up regulation of haematopoietic stem cell differentiation GOC:TermGenie up regulation of haemopoietic stem cell differentiation GOC:TermGenie up regulation of hematopoietic stem cell differentiation GOC:TermGenie up regulation of hemopoietic stem cell differentiation GOC:TermGenie up-regulation of haematopoietic stem cell differentiation GOC:TermGenie up-regulation of haemopoietic stem cell differentiation GOC:TermGenie up-regulation of hematopoietic stem cell differentiation GOC:TermGenie up-regulation of hemopoietic stem cell differentiation GOC:TermGenie upregulation of haematopoietic stem cell differentiation GOC:TermGenie upregulation of haemopoietic stem cell differentiation GOC:TermGenie upregulation of hematopoietic stem cell differentiation GOC:TermGenie upregulation of hemopoietic stem cell differentiation GOC:TermGenie activation of haematopoietic stem cell differentiation GOC:TermGenie activation of haemopoietic stem cell differentiation GOC:TermGenie activation of hematopoietic stem cell differentiation GOC:TermGenie activation of hemopoietic stem cell differentiation GOC:TermGenie Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salt stimulus. mls 2013-04-22T15:41:57Z response to salinity biological_process GO:1902074 response to salt Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salt stimulus. GOC:TermGenie GOC:mls PMID:16666921 response to salinity GOC:mls Any process that modulates the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:42Z regulation of immune cell differentiation regulation of leucocyte differentiation biological_process GO:1902105 regulation of leukocyte differentiation Any process that modulates the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add regulation of immune cell differentiation GOC:TermGenie regulation of leucocyte differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:47Z down regulation of immune cell differentiation down regulation of leucocyte differentiation down regulation of leukocyte differentiation down-regulation of immune cell differentiation down-regulation of leucocyte differentiation down-regulation of leukocyte differentiation downregulation of immune cell differentiation downregulation of leucocyte differentiation downregulation of leukocyte differentiation negative regulation of immune cell differentiation negative regulation of leucocyte differentiation inhibition of immune cell differentiation inhibition of leucocyte differentiation inhibition of leukocyte differentiation biological_process GO:1902106 negative regulation of leukocyte differentiation Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add down regulation of immune cell differentiation GOC:TermGenie down regulation of leucocyte differentiation GOC:TermGenie down regulation of leukocyte differentiation GOC:TermGenie down-regulation of immune cell differentiation GOC:TermGenie down-regulation of leucocyte differentiation GOC:TermGenie down-regulation of leukocyte differentiation GOC:TermGenie downregulation of immune cell differentiation GOC:TermGenie downregulation of leucocyte differentiation GOC:TermGenie downregulation of leukocyte differentiation GOC:TermGenie negative regulation of immune cell differentiation GOC:TermGenie negative regulation of leucocyte differentiation GOC:TermGenie inhibition of immune cell differentiation GOC:TermGenie inhibition of leucocyte differentiation GOC:TermGenie inhibition of leukocyte differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:52Z positive regulation of immune cell differentiation positive regulation of leucocyte differentiation up regulation of immune cell differentiation up regulation of leucocyte differentiation up regulation of leukocyte differentiation up-regulation of immune cell differentiation up-regulation of leucocyte differentiation up-regulation of leukocyte differentiation upregulation of immune cell differentiation upregulation of leucocyte differentiation upregulation of leukocyte differentiation activation of immune cell differentiation activation of leucocyte differentiation activation of leukocyte differentiation biological_process GO:1902107 positive regulation of leukocyte differentiation Any process that activates or increases the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add positive regulation of immune cell differentiation GOC:TermGenie positive regulation of leucocyte differentiation GOC:TermGenie up regulation of immune cell differentiation GOC:TermGenie up regulation of leucocyte differentiation GOC:TermGenie up regulation of leukocyte differentiation GOC:TermGenie up-regulation of immune cell differentiation GOC:TermGenie up-regulation of leucocyte differentiation GOC:TermGenie up-regulation of leukocyte differentiation GOC:TermGenie upregulation of immune cell differentiation GOC:TermGenie upregulation of leucocyte differentiation GOC:TermGenie upregulation of leukocyte differentiation GOC:TermGenie activation of immune cell differentiation GOC:TermGenie activation of leucocyte differentiation GOC:TermGenie activation of leukocyte differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:21Z biological_process GO:1902115 regulation of organelle assembly Any process that modulates the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:31Z down regulation of organelle assembly down-regulation of organelle assembly downregulation of organelle assembly inhibition of organelle assembly biological_process GO:1902116 negative regulation of organelle assembly Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr down regulation of organelle assembly GOC:TermGenie down-regulation of organelle assembly GOC:TermGenie downregulation of organelle assembly GOC:TermGenie inhibition of organelle assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:36Z up regulation of organelle assembly up-regulation of organelle assembly upregulation of organelle assembly activation of organelle assembly biological_process GO:1902117 positive regulation of organelle assembly Any process that activates or increases the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr up regulation of organelle assembly GOC:TermGenie up-regulation of organelle assembly GOC:TermGenie upregulation of organelle assembly GOC:TermGenie activation of organelle assembly GOC:TermGenie Any apoptotic process in an erythrocyte. rl 2013-06-13T10:02:29Z RBC apoptotic process red blood cell apoptotic process RBC apoptosis erythrocyte apoptosis red blood cell apoptosis biological_process GO:1902217 erythrocyte apoptotic process Any apoptotic process in an erythrocyte. GOC:BHF GOC:TermGenie GOC:mtg_apoptosis GOC:rl PMID:14569084 RBC apoptotic process GOC:TermGenie red blood cell apoptotic process GOC:TermGenie RBC apoptosis GOC:TermGenie erythrocyte apoptosis GOC:TermGenie red blood cell apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of erythrocyte apoptotic process. rl 2013-06-20T19:30:53Z regulation of RBC apoptotic process regulation of red blood cell apoptotic process regulation of RBC apoptosis regulation of erythrocyte apoptosis regulation of red blood cell apoptosis biological_process GO:1902250 regulation of erythrocyte apoptotic process Any process that modulates the frequency, rate or extent of erythrocyte apoptotic process. GOC:BHF GOC:TermGenie GOC:mtg_apoptosis GOC:rl PMID:14569084 regulation of RBC apoptotic process GOC:TermGenie regulation of red blood cell apoptotic process GOC:TermGenie regulation of RBC apoptosis GOC:TermGenie regulation of erythrocyte apoptosis GOC:TermGenie regulation of red blood cell apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of erythrocyte apoptotic process. rl 2013-06-20T19:30:59Z down regulation of RBC apoptotic process down regulation of erythrocyte apoptotic process down regulation of red blood cell apoptotic process down-regulation of RBC apoptotic process down-regulation of erythrocyte apoptotic process down-regulation of red blood cell apoptotic process downregulation of RBC apoptotic process downregulation of erythrocyte apoptotic process downregulation of red blood cell apoptotic process negative regulation of RBC apoptotic process negative regulation of red blood cell apoptotic process down regulation of RBC apoptosis down regulation of erythrocyte apoptosis down regulation of red blood cell apoptosis down-regulation of RBC apoptosis down-regulation of erythrocyte apoptosis down-regulation of red blood cell apoptosis downregulation of RBC apoptosis downregulation of erythrocyte apoptosis downregulation of red blood cell apoptosis inhibition of RBC apoptosis inhibition of RBC apoptotic process inhibition of erythrocyte apoptosis inhibition of erythrocyte apoptotic process inhibition of red blood cell apoptosis inhibition of red blood cell apoptotic process negative regulation of RBC apoptosis negative regulation of erythrocyte apoptosis negative regulation of red blood cell apoptosis biological_process GO:1902251 negative regulation of erythrocyte apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of erythrocyte apoptotic process. GOC:BHF GOC:TermGenie GOC:mtg_apoptosis GOC:rl PMID:14569084 down regulation of RBC apoptotic process GOC:TermGenie down regulation of erythrocyte apoptotic process GOC:TermGenie down regulation of red blood cell apoptotic process GOC:TermGenie down-regulation of RBC apoptotic process GOC:TermGenie down-regulation of erythrocyte apoptotic process GOC:TermGenie down-regulation of red blood cell apoptotic process GOC:TermGenie downregulation of RBC apoptotic process GOC:TermGenie downregulation of erythrocyte apoptotic process GOC:TermGenie downregulation of red blood cell apoptotic process GOC:TermGenie negative regulation of RBC apoptotic process GOC:TermGenie negative regulation of red blood cell apoptotic process GOC:TermGenie down regulation of RBC apoptosis GOC:TermGenie down regulation of erythrocyte apoptosis GOC:TermGenie down regulation of red blood cell apoptosis GOC:TermGenie down-regulation of RBC apoptosis GOC:TermGenie down-regulation of erythrocyte apoptosis GOC:TermGenie down-regulation of red blood cell apoptosis GOC:TermGenie downregulation of RBC apoptosis GOC:TermGenie downregulation of erythrocyte apoptosis GOC:TermGenie downregulation of red blood cell apoptosis GOC:TermGenie inhibition of RBC apoptosis GOC:TermGenie inhibition of RBC apoptotic process GOC:TermGenie inhibition of erythrocyte apoptosis GOC:TermGenie inhibition of erythrocyte apoptotic process GOC:TermGenie inhibition of red blood cell apoptosis GOC:TermGenie inhibition of red blood cell apoptotic process GOC:TermGenie negative regulation of RBC apoptosis GOC:TermGenie negative regulation of erythrocyte apoptosis GOC:TermGenie negative regulation of red blood cell apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of erythrocyte apoptotic process. rl 2013-06-20T19:31:04Z positive regulation of RBC apoptotic process positive regulation of red blood cell apoptotic process up regulation of RBC apoptotic process up regulation of erythrocyte apoptotic process up regulation of red blood cell apoptotic process up-regulation of RBC apoptotic process up-regulation of erythrocyte apoptotic process up-regulation of red blood cell apoptotic process upregulation of RBC apoptotic process upregulation of erythrocyte apoptotic process upregulation of red blood cell apoptotic process activation of RBC apoptosis activation of RBC apoptotic process activation of erythrocyte apoptosis activation of erythrocyte apoptotic process activation of red blood cell apoptosis activation of red blood cell apoptotic process positive regulation of RBC apoptosis positive regulation of erythrocyte apoptosis positive regulation of red blood cell apoptosis up regulation of RBC apoptosis up regulation of erythrocyte apoptosis up regulation of red blood cell apoptosis up-regulation of RBC apoptosis up-regulation of erythrocyte apoptosis up-regulation of red blood cell apoptosis upregulation of RBC apoptosis upregulation of erythrocyte apoptosis upregulation of red blood cell apoptosis biological_process GO:1902252 positive regulation of erythrocyte apoptotic process Any process that activates or increases the frequency, rate or extent of erythrocyte apoptotic process. GOC:BHF GOC:TermGenie GOC:mtg_apoptosis GOC:rl PMID:14569084 positive regulation of RBC apoptotic process GOC:TermGenie positive regulation of red blood cell apoptotic process GOC:TermGenie up regulation of RBC apoptotic process GOC:TermGenie up regulation of erythrocyte apoptotic process GOC:TermGenie up regulation of red blood cell apoptotic process GOC:TermGenie up-regulation of RBC apoptotic process GOC:TermGenie up-regulation of erythrocyte apoptotic process GOC:TermGenie up-regulation of red blood cell apoptotic process GOC:TermGenie upregulation of RBC apoptotic process GOC:TermGenie upregulation of erythrocyte apoptotic process GOC:TermGenie upregulation of red blood cell apoptotic process GOC:TermGenie activation of RBC apoptosis GOC:TermGenie activation of RBC apoptotic process GOC:TermGenie activation of erythrocyte apoptosis GOC:TermGenie activation of erythrocyte apoptotic process GOC:TermGenie activation of red blood cell apoptosis GOC:TermGenie activation of red blood cell apoptotic process GOC:TermGenie positive regulation of RBC apoptosis GOC:TermGenie positive regulation of erythrocyte apoptosis GOC:TermGenie positive regulation of red blood cell apoptosis GOC:TermGenie up regulation of RBC apoptosis GOC:TermGenie up regulation of erythrocyte apoptosis GOC:TermGenie up regulation of red blood cell apoptosis GOC:TermGenie up-regulation of RBC apoptosis GOC:TermGenie up-regulation of erythrocyte apoptosis GOC:TermGenie up-regulation of red blood cell apoptosis GOC:TermGenie upregulation of RBC apoptosis GOC:TermGenie upregulation of erythrocyte apoptosis GOC:TermGenie upregulation of red blood cell apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis. dph 2013-06-24T19:12:24Z regulation of apoptosis involved in outflow tract morphogenesis biological_process GO:1902256 regulation of apoptotic process involved in outflow tract morphogenesis Any process that modulates the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis. GOC:TermGenie GOC:dph GOC:mtg_apoptosis PMID:16839542 regulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis. dph 2013-06-24T19:12:30Z down regulation of apoptotic process involved in outflow tract morphogenesis down-regulation of apoptotic process involved in outflow tract morphogenesis downregulation of apoptotic process involved in outflow tract morphogenesis down regulation of apoptosis involved in outflow tract morphogenesis down-regulation of apoptosis involved in outflow tract morphogenesis downregulation of apoptosis involved in outflow tract morphogenesis inhibition of apoptosis involved in outflow tract morphogenesis inhibition of apoptotic process involved in outflow tract morphogenesis negative regulation of apoptosis involved in outflow tract morphogenesis biological_process GO:1902257 negative regulation of apoptotic process involved in outflow tract morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis. GOC:TermGenie GOC:dph GOC:mtg_apoptosis PMID:16839542 down regulation of apoptotic process involved in outflow tract morphogenesis GOC:TermGenie down-regulation of apoptotic process involved in outflow tract morphogenesis GOC:TermGenie downregulation of apoptotic process involved in outflow tract morphogenesis GOC:TermGenie down regulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie down-regulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie downregulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie inhibition of apoptosis involved in outflow tract morphogenesis GOC:TermGenie inhibition of apoptotic process involved in outflow tract morphogenesis GOC:TermGenie negative regulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis. dph 2013-06-24T19:12:42Z up regulation of apoptotic process involved in outflow tract morphogenesis up-regulation of apoptotic process involved in outflow tract morphogenesis upregulation of apoptotic process involved in outflow tract morphogenesis activation of apoptosis involved in outflow tract morphogenesis activation of apoptotic process involved in outflow tract morphogenesis positive regulation of apoptosis involved in outflow tract morphogenesis up regulation of apoptosis involved in outflow tract morphogenesis up-regulation of apoptosis involved in outflow tract morphogenesis upregulation of apoptosis involved in outflow tract morphogenesis biological_process GO:1902258 positive regulation of apoptotic process involved in outflow tract morphogenesis Any process that activates or increases the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis. GOC:TermGenie GOC:dph GOC:mtg_apoptosis PMID:16839542 up regulation of apoptotic process involved in outflow tract morphogenesis GOC:TermGenie up-regulation of apoptotic process involved in outflow tract morphogenesis GOC:TermGenie upregulation of apoptotic process involved in outflow tract morphogenesis GOC:TermGenie activation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie activation of apoptotic process involved in outflow tract morphogenesis GOC:TermGenie positive regulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie up regulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie up-regulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie upregulation of apoptosis involved in outflow tract morphogenesis GOC:TermGenie Any apoptotic process that is involved in blood vessel morphogenesis. dph 2013-06-25T16:16:00Z apoptotic cell death involved in patterning of blood vessels apoptotic programmed cell death involved in patterning of blood vessels programmed cell death by apoptosis involved in patterning of blood vessels apoptosis involved in patterning of blood vessels apoptotic program involved in patterning of blood vessels type I programmed cell death involved in patterning of blood vessels biological_process signaling (initiator) caspase activity involved in patterning of blood vessels GO:1902262 apoptotic process involved in blood vessel morphogenesis Any apoptotic process that is involved in blood vessel morphogenesis. GOC:TermGenie GOC:dph GOC:mtg_apoptosis PMID:16163358 apoptotic cell death involved in patterning of blood vessels GOC:TermGenie apoptotic programmed cell death involved in patterning of blood vessels GOC:TermGenie programmed cell death by apoptosis involved in patterning of blood vessels GOC:TermGenie apoptosis involved in patterning of blood vessels GOC:TermGenie apoptotic program involved in patterning of blood vessels GOC:TermGenie type I programmed cell death involved in patterning of blood vessels GOC:TermGenie signaling (initiator) caspase activity involved in patterning of blood vessels GOC:TermGenie Any process that modulates the frequency, rate or extent of chromatin organization. bf 2013-07-01T13:21:52Z GO:0001672 GO:1903308 regulation of chromatin organisation regulation of establishment or maintenance of chromatin architecture biological_process regulation of chromatin assembly or disassembly regulation of chromatin assembly/disassembly regulation of chromatin modification GO:1902275 regulation of chromatin organization Any process that modulates the frequency, rate or extent of chromatin organization. GOC:TermGenie GOC:bf GOC:vw GO_REF:0000058 PMID:18314879 regulation of chromatin organisation GOC:TermGenie regulation of establishment or maintenance of chromatin architecture GOC:TermGenie Any process that modulates the frequency, rate or extent of sodium ion transmembrane transport. rl 2013-07-18T13:33:53Z regulation of sodium ion membrane transport biological_process GO:1902305 regulation of sodium ion transmembrane transport Any process that modulates the frequency, rate or extent of sodium ion transmembrane transport. GOC:BHF GOC:TermGenie GOC:mtg_cardiac_conduct_nov11 GOC:rl PMID:18591664 regulation of sodium ion membrane transport GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transport. rl 2013-07-18T13:34:01Z down regulation of sodium ion membrane transport down regulation of sodium ion transmembrane transport down-regulation of sodium ion membrane transport down-regulation of sodium ion transmembrane transport downregulation of sodium ion membrane transport downregulation of sodium ion transmembrane transport negative regulation of sodium ion membrane transport inhibition of sodium ion membrane transport inhibition of sodium ion transmembrane transport biological_process GO:1902306 negative regulation of sodium ion transmembrane transport Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transport. GOC:BHF GOC:TermGenie GOC:mtg_cardiac_conduct_nov11 GOC:rl PMID:18591664 down regulation of sodium ion membrane transport GOC:TermGenie down regulation of sodium ion transmembrane transport GOC:TermGenie down-regulation of sodium ion membrane transport GOC:TermGenie down-regulation of sodium ion transmembrane transport GOC:TermGenie downregulation of sodium ion membrane transport GOC:TermGenie downregulation of sodium ion transmembrane transport GOC:TermGenie negative regulation of sodium ion membrane transport GOC:TermGenie inhibition of sodium ion membrane transport GOC:TermGenie inhibition of sodium ion transmembrane transport GOC:TermGenie Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transport. rl 2013-07-18T13:34:18Z positive regulation of sodium ion membrane transport up regulation of sodium ion membrane transport up regulation of sodium ion transmembrane transport up-regulation of sodium ion membrane transport up-regulation of sodium ion transmembrane transport upregulation of sodium ion membrane transport upregulation of sodium ion transmembrane transport activation of sodium ion membrane transport activation of sodium ion transmembrane transport biological_process GO:1902307 positive regulation of sodium ion transmembrane transport Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transport. GOC:BHF GOC:TermGenie GOC:mtg_cardiac_conduct_nov11 GOC:rl PMID:18591664 positive regulation of sodium ion membrane transport GOC:TermGenie up regulation of sodium ion membrane transport GOC:TermGenie up regulation of sodium ion transmembrane transport GOC:TermGenie up-regulation of sodium ion membrane transport GOC:TermGenie up-regulation of sodium ion transmembrane transport GOC:TermGenie upregulation of sodium ion membrane transport GOC:TermGenie upregulation of sodium ion transmembrane transport GOC:TermGenie activation of sodium ion membrane transport GOC:TermGenie activation of sodium ion transmembrane transport GOC:TermGenie Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:16Z regulation of apoptosis involved in morphogenesis biological_process regulation of apoptosis involved in development regulation of morphogenetic apoptosis GO:1902337 regulation of apoptotic process involved in morphogenesis Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 regulation of apoptosis involved in morphogenesis GOC:TermGenie regulation of apoptosis involved in development GOC:TermGenie regulation of morphogenetic apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:25Z down regulation of apoptotic process involved in morphogenesis down-regulation of apoptotic process involved in morphogenesis downregulation of apoptotic process involved in morphogenesis down regulation of apoptosis involved in morphogenesis down-regulation of apoptosis involved in morphogenesis downregulation of apoptosis involved in morphogenesis inhibition of apoptosis involved in morphogenesis inhibition of apoptotic process involved in morphogenesis negative regulation of apoptosis involved in morphogenesis biological_process down regulation of apoptosis involved in development down regulation of morphogenetic apoptosis down-regulation of apoptosis involved in development down-regulation of morphogenetic apoptosis downregulation of apoptosis involved in development downregulation of morphogenetic apoptosis inhibition of apoptosis involved in development inhibition of morphogenetic apoptosis negative regulation of apoptosis involved in development negative regulation of morphogenetic apoptosis GO:1902338 negative regulation of apoptotic process involved in morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 down regulation of apoptotic process involved in morphogenesis GOC:TermGenie down-regulation of apoptotic process involved in morphogenesis GOC:TermGenie downregulation of apoptotic process involved in morphogenesis GOC:TermGenie down regulation of apoptosis involved in morphogenesis GOC:TermGenie down-regulation of apoptosis involved in morphogenesis GOC:TermGenie downregulation of apoptosis involved in morphogenesis GOC:TermGenie inhibition of apoptosis involved in morphogenesis GOC:TermGenie inhibition of apoptotic process involved in morphogenesis GOC:TermGenie negative regulation of apoptosis involved in morphogenesis GOC:TermGenie down regulation of apoptosis involved in development GOC:TermGenie down regulation of morphogenetic apoptosis GOC:TermGenie down-regulation of apoptosis involved in development GOC:TermGenie down-regulation of morphogenetic apoptosis GOC:TermGenie downregulation of apoptosis involved in development GOC:TermGenie downregulation of morphogenetic apoptosis GOC:TermGenie inhibition of apoptosis involved in development GOC:TermGenie inhibition of morphogenetic apoptosis GOC:TermGenie negative regulation of apoptosis involved in development GOC:TermGenie negative regulation of morphogenetic apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:33Z up regulation of apoptotic process involved in morphogenesis up-regulation of apoptotic process involved in morphogenesis upregulation of apoptotic process involved in morphogenesis activation of apoptosis involved in morphogenesis activation of apoptotic process involved in morphogenesis positive regulation of apoptosis involved in morphogenesis up regulation of apoptosis involved in morphogenesis up-regulation of apoptosis involved in morphogenesis upregulation of apoptosis involved in morphogenesis biological_process activation of apoptosis involved in development activation of morphogenetic apoptosis positive regulation of apoptosis involved in development positive regulation of morphogenetic apoptosis up regulation of apoptosis involved in development up regulation of morphogenetic apoptosis up-regulation of apoptosis involved in development up-regulation of morphogenetic apoptosis upregulation of apoptosis involved in development upregulation of morphogenetic apoptosis GO:1902339 positive regulation of apoptotic process involved in morphogenesis Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 up regulation of apoptotic process involved in morphogenesis GOC:TermGenie up-regulation of apoptotic process involved in morphogenesis GOC:TermGenie upregulation of apoptotic process involved in morphogenesis GOC:TermGenie activation of apoptosis involved in morphogenesis GOC:TermGenie activation of apoptotic process involved in morphogenesis GOC:TermGenie positive regulation of apoptosis involved in morphogenesis GOC:TermGenie up regulation of apoptosis involved in morphogenesis GOC:TermGenie up-regulation of apoptosis involved in morphogenesis GOC:TermGenie upregulation of apoptosis involved in morphogenesis GOC:TermGenie activation of apoptosis involved in development GOC:TermGenie activation of morphogenetic apoptosis GOC:TermGenie positive regulation of apoptosis involved in development GOC:TermGenie positive regulation of morphogenetic apoptosis GOC:TermGenie up regulation of apoptosis involved in development GOC:TermGenie up regulation of morphogenetic apoptosis GOC:TermGenie up-regulation of apoptosis involved in development GOC:TermGenie up-regulation of morphogenetic apoptosis GOC:TermGenie upregulation of apoptosis involved in development GOC:TermGenie upregulation of morphogenetic apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation. dgf 2013-07-29T20:54:14Z down regulation of chromosome condensation down regulation of eukaryotic chromosome condensation down regulation of nuclear chromosome condensation down-regulation of chromosome condensation down-regulation of eukaryotic chromosome condensation down-regulation of nuclear chromosome condensation downregulation of chromosome condensation downregulation of eukaryotic chromosome condensation downregulation of nuclear chromosome condensation negative regulation of eukaryotic chromosome condensation negative regulation of nuclear chromosome condensation inhibition of chromosome condensation inhibition of eukaryotic chromosome condensation inhibition of nuclear chromosome condensation biological_process GO:1902340 negative regulation of chromosome condensation Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation. GOC:TermGenie PMID:23219725 down regulation of chromosome condensation GOC:TermGenie down regulation of eukaryotic chromosome condensation GOC:TermGenie down regulation of nuclear chromosome condensation GOC:TermGenie down-regulation of chromosome condensation GOC:TermGenie down-regulation of eukaryotic chromosome condensation GOC:TermGenie down-regulation of nuclear chromosome condensation GOC:TermGenie downregulation of chromosome condensation GOC:TermGenie downregulation of eukaryotic chromosome condensation GOC:TermGenie downregulation of nuclear chromosome condensation GOC:TermGenie negative regulation of eukaryotic chromosome condensation GOC:TermGenie negative regulation of nuclear chromosome condensation GOC:TermGenie inhibition of chromosome condensation GOC:TermGenie inhibition of eukaryotic chromosome condensation GOC:TermGenie inhibition of nuclear chromosome condensation GOC:TermGenie The directed movement of sulfate across a membrane. dph 2013-08-14T14:46:04Z biological_process GO:1902358 sulfate transmembrane transport The directed movement of sulfate across a membrane. GOC:TermGenie GOC:dph PMID:9055073 Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process. bf 2013-08-22T14:59:39Z down regulation of RNA breakdown down regulation of RNA catabolic process down regulation of RNA catabolism down regulation of RNA degradation down-regulation of RNA breakdown down-regulation of RNA catabolic process down-regulation of RNA catabolism down-regulation of RNA degradation downregulation of RNA breakdown downregulation of RNA catabolic process downregulation of RNA catabolism downregulation of RNA degradation negative regulation of RNA breakdown negative regulation of RNA catabolism negative regulation of RNA degradation inhibition of RNA breakdown inhibition of RNA catabolic process inhibition of RNA catabolism inhibition of RNA degradation biological_process GO:1902369 negative regulation of RNA catabolic process Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process. GOC:TermGenie GOC:bf PMID:16640457 down regulation of RNA breakdown GOC:TermGenie down regulation of RNA catabolic process GOC:TermGenie down regulation of RNA catabolism GOC:TermGenie down regulation of RNA degradation GOC:TermGenie down-regulation of RNA breakdown GOC:TermGenie down-regulation of RNA catabolic process GOC:TermGenie down-regulation of RNA catabolism GOC:TermGenie down-regulation of RNA degradation GOC:TermGenie downregulation of RNA breakdown GOC:TermGenie downregulation of RNA catabolic process GOC:TermGenie downregulation of RNA catabolism GOC:TermGenie downregulation of RNA degradation GOC:TermGenie negative regulation of RNA breakdown GOC:TermGenie negative regulation of RNA catabolism GOC:TermGenie negative regulation of RNA degradation GOC:TermGenie inhibition of RNA breakdown GOC:TermGenie inhibition of RNA catabolic process GOC:TermGenie inhibition of RNA catabolism GOC:TermGenie inhibition of RNA degradation GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a cell junction. tb 2013-09-13T16:55:57Z protein localisation in cell junction protein localisation to cell junction protein localization in cell junction biological_process GO:1902414 protein localization to cell junction A process in which a protein is transported to, or maintained in, a location within a cell junction. GOC:TermGenie PMID:18332111 protein localisation in cell junction GOC:TermGenie protein localisation to cell junction GOC:TermGenie protein localization in cell junction GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a cell leading edge. jl 2013-10-22T12:36:07Z protein localisation in cell leading edge protein localisation to cell leading edge protein localization in cell leading edge biological_process GO:1902463 protein localization to cell leading edge A process in which a protein is transported to, or maintained in, a location within a cell leading edge. GOC:TermGenie GOC:lb PMID:21543326 protein localisation in cell leading edge GOC:TermGenie protein localisation to cell leading edge GOC:TermGenie protein localization in cell leading edge GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to synapse. kmv 2013-10-25T15:09:09Z regulation of protein localisation to synapse biological_process GO:1902473 regulation of protein localization to synapse Any process that modulates the frequency, rate or extent of protein localization to synapse. GOC:TermGenie GOC:kmv PMID:22588719 regulation of protein localisation to synapse GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to synapse. kmv 2013-10-25T15:09:18Z positive regulation of protein localisation to synapse up regulation of protein localisation to synapse up regulation of protein localization to synapse up-regulation of protein localisation to synapse up-regulation of protein localization to synapse upregulation of protein localisation to synapse upregulation of protein localization to synapse activation of protein localisation to synapse activation of protein localization to synapse biological_process GO:1902474 positive regulation of protein localization to synapse Any process that activates or increases the frequency, rate or extent of protein localization to synapse. GOC:TermGenie GOC:kmv PMID:22588719 positive regulation of protein localisation to synapse GOC:TermGenie up regulation of protein localisation to synapse GOC:TermGenie up regulation of protein localization to synapse GOC:TermGenie up-regulation of protein localisation to synapse GOC:TermGenie up-regulation of protein localization to synapse GOC:TermGenie upregulation of protein localisation to synapse GOC:TermGenie upregulation of protein localization to synapse GOC:TermGenie activation of protein localisation to synapse GOC:TermGenie activation of protein localization to synapse GOC:TermGenie Any apoptotic process in a cholangiocyte. cls 2013-11-12T15:30:08Z epithelial cell of bile duct apoptotic process cholangiocyte apoptosis epithelial cell of bile duct apoptosis biological_process GO:1902488 cholangiocyte apoptotic process Any apoptotic process in a cholangiocyte. GOC:TermGenie PMID:22961800 epithelial cell of bile duct apoptotic process GOC:TermGenie cholangiocyte apoptosis GOC:TermGenie epithelial cell of bile duct apoptosis GOC:TermGenie Any apoptotic process in a hepatoblast. cls 2013-11-12T17:02:52Z hepatoblast apoptosis biological_process GO:1902489 hepatoblast apoptotic process Any apoptotic process in a hepatoblast. GOC:TermGenie PMID:22412967 hepatoblast apoptosis GOC:TermGenie A protein complex which is capable of catalytic activity. https://github.com/geneontology/go-ontology/issues/19980 bhm 2013-11-13T16:18:47Z enzyme complex cellular_component GO:1902494 catalytic complex A protein complex which is capable of catalytic activity. GOC:TermGenie GOC:bhm PMID:8077207 enzyme complex GOC:bhm GOC:jl A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other. bhm 2013-11-13T16:23:04Z cellular_component GO:1902495 transmembrane transporter complex A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other. GOC:TermGenie GOC:bhm PMID:18024586 Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation. hjd 2013-11-15T18:28:32Z regulation of DNA fragmentation regulation of chromatinolysis regulation of DNA catabolic process during apoptosis regulation of DNA catabolism during apoptosis regulation of DNA fragmentation involved in apoptotic nuclear change regulation of endonucleolytic DNA catabolic process involved in apoptosis biological_process GO:1902510 DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases (see GO:0006309 'apoptotic DNA fragmentation'). Gene products involved in compartmentalization of such nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341). regulation of apoptotic DNA fragmentation Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation. GOC:TermGenie GOC:hjd PMID:15572351 PMID:15723341 regulation of DNA fragmentation GOC:TermGenie regulation of chromatinolysis GOC:TermGenie regulation of DNA catabolic process during apoptosis GOC:TermGenie regulation of DNA catabolism during apoptosis GOC:TermGenie regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation. hjd 2013-11-15T18:28:41Z down regulation of DNA catabolic process during apoptosis down regulation of DNA catabolism during apoptosis down regulation of DNA fragmentation involved in apoptotic nuclear change down regulation of apoptotic DNA fragmentation down regulation of endonucleolytic DNA catabolic process involved in apoptosis down-regulation of DNA catabolic process during apoptosis down-regulation of DNA catabolism during apoptosis down-regulation of DNA fragmentation involved in apoptotic nuclear change down-regulation of apoptotic DNA fragmentation down-regulation of endonucleolytic DNA catabolic process involved in apoptosis downregulation of DNA catabolic process during apoptosis downregulation of DNA catabolism during apoptosis downregulation of DNA fragmentation involved in apoptotic nuclear change downregulation of apoptotic DNA fragmentation downregulation of endonucleolytic DNA catabolic process involved in apoptosis negative regulation of DNA catabolic process during apoptosis negative regulation of DNA catabolism during apoptosis negative regulation of DNA fragmentation involved in apoptotic nuclear change negative regulation of endonucleolytic DNA catabolic process involved in apoptosis inhibition of DNA catabolic process during apoptosis inhibition of DNA catabolism during apoptosis inhibition of DNA fragmentation involved in apoptotic nuclear change inhibition of apoptotic DNA fragmentation inhibition of endonucleolytic DNA catabolic process involved in apoptosis biological_process GO:1902511 negative regulation of apoptotic DNA fragmentation Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation. GOC:TermGenie GOC:hjd PMID:15572351 down regulation of DNA catabolic process during apoptosis GOC:TermGenie down regulation of DNA catabolism during apoptosis GOC:TermGenie down regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie down regulation of apoptotic DNA fragmentation GOC:TermGenie down regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie down-regulation of DNA catabolic process during apoptosis GOC:TermGenie down-regulation of DNA catabolism during apoptosis GOC:TermGenie down-regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie down-regulation of apoptotic DNA fragmentation GOC:TermGenie down-regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie downregulation of DNA catabolic process during apoptosis GOC:TermGenie downregulation of DNA catabolism during apoptosis GOC:TermGenie downregulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie downregulation of apoptotic DNA fragmentation GOC:TermGenie downregulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie negative regulation of DNA catabolic process during apoptosis GOC:TermGenie negative regulation of DNA catabolism during apoptosis GOC:TermGenie negative regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie negative regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie inhibition of DNA catabolic process during apoptosis GOC:TermGenie inhibition of DNA catabolism during apoptosis GOC:TermGenie inhibition of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie inhibition of apoptotic DNA fragmentation GOC:TermGenie inhibition of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation. hjd 2013-11-15T18:28:50Z positive regulation of DNA catabolic process during apoptosis positive regulation of DNA catabolism during apoptosis positive regulation of DNA fragmentation involved in apoptotic nuclear change positive regulation of endonucleolytic DNA catabolic process involved in apoptosis up regulation of DNA catabolic process during apoptosis up regulation of DNA catabolism during apoptosis up regulation of DNA fragmentation involved in apoptotic nuclear change up regulation of apoptotic DNA fragmentation up regulation of endonucleolytic DNA catabolic process involved in apoptosis up-regulation of DNA catabolic process during apoptosis up-regulation of DNA catabolism during apoptosis up-regulation of DNA fragmentation involved in apoptotic nuclear change up-regulation of apoptotic DNA fragmentation up-regulation of endonucleolytic DNA catabolic process involved in apoptosis upregulation of DNA catabolic process during apoptosis upregulation of DNA catabolism during apoptosis upregulation of DNA fragmentation involved in apoptotic nuclear change upregulation of apoptotic DNA fragmentation upregulation of endonucleolytic DNA catabolic process involved in apoptosis activation of DNA catabolic process during apoptosis activation of DNA catabolism during apoptosis activation of DNA fragmentation involved in apoptotic nuclear change activation of apoptotic DNA fragmentation activation of endonucleolytic DNA catabolic process involved in apoptosis biological_process GO:1902512 positive regulation of apoptotic DNA fragmentation Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation. GOC:TermGenie GOC:hjd PMID:15572351 positive regulation of DNA catabolic process during apoptosis GOC:TermGenie positive regulation of DNA catabolism during apoptosis GOC:TermGenie positive regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie positive regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie up regulation of DNA catabolic process during apoptosis GOC:TermGenie up regulation of DNA catabolism during apoptosis GOC:TermGenie up regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie up regulation of apoptotic DNA fragmentation GOC:TermGenie up regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie up-regulation of DNA catabolic process during apoptosis GOC:TermGenie up-regulation of DNA catabolism during apoptosis GOC:TermGenie up-regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie up-regulation of apoptotic DNA fragmentation GOC:TermGenie up-regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie upregulation of DNA catabolic process during apoptosis GOC:TermGenie upregulation of DNA catabolism during apoptosis GOC:TermGenie upregulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie upregulation of apoptotic DNA fragmentation GOC:TermGenie upregulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie activation of DNA catabolic process during apoptosis GOC:TermGenie activation of DNA catabolism during apoptosis GOC:TermGenie activation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie activation of apoptotic DNA fragmentation GOC:TermGenie activation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of organelle transport along microtubule. dph 2013-11-15T20:15:17Z regulation of microtubule-based organelle localization biological_process GO:1902513 regulation of organelle transport along microtubule Any process that modulates the frequency, rate or extent of organelle transport along microtubule. GOC:TermGenie GOC:dph PMID:21147087 regulation of microtubule-based organelle localization GOC:TermGenie Any process that modulates the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:32:52Z GO:0010627 regulation of intracellular signaling cascade regulation of intracellular signaling chain regulation of intracellular protein kinase cascade regulation of intracellular signal transduction pathway regulation of signal transmission via intracellular cascade biological_process regulation of intracellular signaling pathway regulation of signal transduction via intracellular signaling cascade GO:1902531 regulation of intracellular signal transduction Any process that modulates the frequency, rate or extent of intracellular signal transduction. GOC:TermGenie GOC:dph GOC:signaling GOC:tb regulation of intracellular signaling cascade GOC:TermGenie regulation of intracellular signaling chain GOC:TermGenie regulation of intracellular signal transduction pathway GOC:TermGenie regulation of signal transmission via intracellular cascade GOC:TermGenie regulation of intracellular signaling pathway GOC:TermGenie regulation of signal transduction via intracellular signaling cascade GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:33:01Z GO:0010741 down regulation of intracellular signal transduction down regulation of intracellular signaling chain down-regulation of intracellular signal transduction down-regulation of intracellular signaling chain downregulation of intracellular signal transduction downregulation of intracellular signaling chain negative regulation of intracellular protein kinase cascade negative regulation of intracellular signaling cascade negative regulation of intracellular signaling chain down regulation of intracellular signal transduction pathway down regulation of intracellular signaling cascade down regulation of signal transmission via intracellular cascade down-regulation of intracellular signal transduction pathway downregulation of intracellular signal transduction pathway downregulation of intracellular signaling cascade downregulation of signal transmission via intracellular cascade inhibition of intracellular signal transduction inhibition of intracellular signal transduction pathway inhibition of intracellular signaling cascade inhibition of intracellular signaling chain inhibition of signal transmission via intracellular cascade negative regulation of intracellular signal transduction pathway negative regulation of signal transmission via intracellular cascade biological_process down regulation of intracellular signaling pathway down regulation of signal transduction via intracellular signaling cascade down-regulation of intracellular signaling cascade down-regulation of intracellular signaling pathway down-regulation of signal transduction via intracellular signaling cascade down-regulation of signal transmission via intracellular cascade downregulation of intracellular signaling pathway downregulation of signal transduction via intracellular signaling cascade inhibition of intracellular signaling pathway inhibition of signal transduction via intracellular signaling cascade negative regulation of intracellular signaling pathway negative regulation of signal transduction via intracellular signaling cascade GO:1902532 negative regulation of intracellular signal transduction Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. GOC:TermGenie GOC:dph GOC:signaling GOC:tb down regulation of intracellular signal transduction GOC:TermGenie down regulation of intracellular signaling chain GOC:TermGenie down-regulation of intracellular signal transduction GOC:TermGenie down-regulation of intracellular signaling chain GOC:TermGenie downregulation of intracellular signal transduction GOC:TermGenie downregulation of intracellular signaling chain GOC:TermGenie negative regulation of intracellular signaling cascade GOC:TermGenie negative regulation of intracellular signaling chain GOC:TermGenie down regulation of intracellular signal transduction pathway GOC:TermGenie down regulation of intracellular signaling cascade GOC:TermGenie down regulation of signal transmission via intracellular cascade GOC:TermGenie down-regulation of intracellular signal transduction pathway GOC:TermGenie downregulation of intracellular signal transduction pathway GOC:TermGenie downregulation of intracellular signaling cascade GOC:TermGenie downregulation of signal transmission via intracellular cascade GOC:TermGenie inhibition of intracellular signal transduction GOC:TermGenie inhibition of intracellular signal transduction pathway GOC:TermGenie inhibition of intracellular signaling cascade GOC:TermGenie inhibition of intracellular signaling chain GOC:TermGenie inhibition of signal transmission via intracellular cascade GOC:TermGenie negative regulation of intracellular signal transduction pathway GOC:TermGenie negative regulation of signal transmission via intracellular cascade GOC:TermGenie down regulation of intracellular signaling pathway GOC:TermGenie down regulation of signal transduction via intracellular signaling cascade GOC:TermGenie down-regulation of intracellular signaling cascade GOC:TermGenie down-regulation of intracellular signaling pathway GOC:TermGenie down-regulation of signal transduction via intracellular signaling cascade GOC:TermGenie down-regulation of signal transmission via intracellular cascade GOC:TermGenie downregulation of intracellular signaling pathway GOC:TermGenie downregulation of signal transduction via intracellular signaling cascade GOC:TermGenie inhibition of intracellular signaling pathway GOC:TermGenie inhibition of signal transduction via intracellular signaling cascade GOC:TermGenie negative regulation of intracellular signaling pathway GOC:TermGenie negative regulation of signal transduction via intracellular signaling cascade GOC:TermGenie Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:33:10Z GO:0010740 positive regulation of intracellular signaling chain up regulation of intracellular signal transduction up regulation of intracellular signaling chain up-regulation of intracellular signal transduction up-regulation of intracellular signaling chain upregulation of intracellular signal transduction upregulation of intracellular signaling chain activation of intracellular signal transduction activation of intracellular signal transduction pathway activation of intracellular signaling cascade activation of intracellular signaling chain activation of signal transmission via intracellular cascade positive regulation of intracellular protein kinase cascade positive regulation of intracellular signal transduction pathway positive regulation of signal transmission via intracellular cascade up regulation of intracellular signal transduction pathway up regulation of signal transmission via intracellular cascade up-regulation of intracellular signal transduction pathway up-regulation of signal transmission via intracellular cascade upregulation of intracellular signal transduction pathway upregulation of signal transmission via intracellular cascade biological_process activation of intracellular signaling pathway activation of signal transduction via intracellular signaling cascade positive regulation of intracellular signaling cascade positive regulation of intracellular signaling pathway positive regulation of signal transduction via intracellular signaling cascade up regulation of intracellular signaling cascade up regulation of intracellular signaling pathway up regulation of signal transduction via intracellular signaling cascade up-regulation of intracellular signaling cascade up-regulation of intracellular signaling pathway up-regulation of signal transduction via intracellular signaling cascade upregulation of intracellular signaling cascade upregulation of intracellular signaling pathway upregulation of signal transduction via intracellular signaling cascade GO:1902533 positive regulation of intracellular signal transduction Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. GOC:BHF GOC:TermGenie GOC:dph GOC:signaling GOC:tb positive regulation of intracellular signaling chain GOC:TermGenie up regulation of intracellular signal transduction GOC:TermGenie up regulation of intracellular signaling chain GOC:TermGenie up-regulation of intracellular signal transduction GOC:TermGenie up-regulation of intracellular signaling chain GOC:TermGenie upregulation of intracellular signal transduction GOC:TermGenie upregulation of intracellular signaling chain GOC:TermGenie activation of intracellular signal transduction GOC:TermGenie activation of intracellular signal transduction pathway GOC:TermGenie activation of intracellular signaling cascade GOC:TermGenie activation of intracellular signaling chain GOC:TermGenie activation of signal transmission via intracellular cascade GOC:TermGenie positive regulation of intracellular signal transduction pathway GOC:TermGenie positive regulation of signal transmission via intracellular cascade GOC:TermGenie up regulation of intracellular signal transduction pathway GOC:TermGenie up regulation of signal transmission via intracellular cascade GOC:TermGenie up-regulation of intracellular signal transduction pathway GOC:TermGenie up-regulation of signal transmission via intracellular cascade GOC:TermGenie upregulation of intracellular signal transduction pathway GOC:TermGenie upregulation of signal transmission via intracellular cascade GOC:TermGenie activation of intracellular signaling pathway GOC:TermGenie activation of signal transduction via intracellular signaling cascade GOC:TermGenie positive regulation of intracellular signaling cascade GOC:TermGenie positive regulation of intracellular signaling pathway GOC:TermGenie positive regulation of signal transduction via intracellular signaling cascade GOC:TermGenie up regulation of intracellular signaling cascade GOC:TermGenie up regulation of intracellular signaling pathway GOC:TermGenie up regulation of signal transduction via intracellular signaling cascade GOC:TermGenie up-regulation of intracellular signaling cascade GOC:TermGenie up-regulation of intracellular signaling pathway GOC:TermGenie up-regulation of signal transduction via intracellular signaling cascade GOC:TermGenie upregulation of intracellular signaling cascade GOC:TermGenie upregulation of intracellular signaling pathway GOC:TermGenie upregulation of signal transduction via intracellular signaling cascade GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a nucleolus. mah 2013-12-10T16:25:28Z protein localisation in nucleolus protein localisation to nucleolus protein localization in nucleolus biological_process GO:1902570 protein localization to nucleolus A process in which a protein is transported to, or maintained in, a location within a nucleolus. GOC:TermGenie PMID:22809626 protein localisation in nucleolus GOC:TermGenie protein localisation to nucleolus GOC:TermGenie protein localization in nucleolus GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process. jl 2014-02-05T16:32:01Z down regulation of RNA anabolism down regulation of RNA biosynthesis down regulation of RNA biosynthetic process down regulation of RNA formation down regulation of RNA synthesis down-regulation of RNA anabolism down-regulation of RNA biosynthesis down-regulation of RNA biosynthetic process down-regulation of RNA formation down-regulation of RNA synthesis downregulation of RNA anabolism downregulation of RNA biosynthesis downregulation of RNA biosynthetic process downregulation of RNA formation downregulation of RNA synthesis negative regulation of RNA anabolism negative regulation of RNA biosynthesis negative regulation of RNA formation negative regulation of RNA synthesis inhibition of RNA anabolism inhibition of RNA biosynthesis inhibition of RNA biosynthetic process inhibition of RNA formation inhibition of RNA synthesis biological_process GO:1902679 negative regulation of RNA biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process. GO:jl GOC:TermGenie GO_REF:0000058 down regulation of RNA anabolism GOC:TermGenie down regulation of RNA biosynthesis GOC:TermGenie down regulation of RNA biosynthetic process GOC:TermGenie down regulation of RNA formation GOC:TermGenie down regulation of RNA synthesis GOC:TermGenie down-regulation of RNA anabolism GOC:TermGenie down-regulation of RNA biosynthesis GOC:TermGenie down-regulation of RNA biosynthetic process GOC:TermGenie down-regulation of RNA formation GOC:TermGenie down-regulation of RNA synthesis GOC:TermGenie downregulation of RNA anabolism GOC:TermGenie downregulation of RNA biosynthesis GOC:TermGenie downregulation of RNA biosynthetic process GOC:TermGenie downregulation of RNA formation GOC:TermGenie downregulation of RNA synthesis GOC:TermGenie negative regulation of RNA anabolism GOC:TermGenie negative regulation of RNA biosynthesis GOC:TermGenie negative regulation of RNA formation GOC:TermGenie negative regulation of RNA synthesis GOC:TermGenie inhibition of RNA anabolism GOC:TermGenie inhibition of RNA biosynthesis GOC:TermGenie inhibition of RNA biosynthetic process GOC:TermGenie inhibition of RNA formation GOC:TermGenie inhibition of RNA synthesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process. jl 2014-02-05T16:32:10Z positive regulation of RNA anabolism positive regulation of RNA biosynthesis positive regulation of RNA formation positive regulation of RNA synthesis up regulation of RNA anabolism up regulation of RNA biosynthesis up regulation of RNA biosynthetic process up regulation of RNA formation up regulation of RNA synthesis up-regulation of RNA anabolism up-regulation of RNA biosynthesis up-regulation of RNA biosynthetic process up-regulation of RNA formation up-regulation of RNA synthesis upregulation of RNA anabolism upregulation of RNA biosynthesis upregulation of RNA biosynthetic process upregulation of RNA formation upregulation of RNA synthesis activation of RNA anabolism activation of RNA biosynthesis activation of RNA biosynthetic process activation of RNA formation activation of RNA synthesis biological_process GO:1902680 positive regulation of RNA biosynthetic process Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process. GO:jl GOC:TermGenie GO_REF:0000058 positive regulation of RNA anabolism GOC:TermGenie positive regulation of RNA biosynthesis GOC:TermGenie positive regulation of RNA formation GOC:TermGenie positive regulation of RNA synthesis GOC:TermGenie up regulation of RNA anabolism GOC:TermGenie up regulation of RNA biosynthesis GOC:TermGenie up regulation of RNA biosynthetic process GOC:TermGenie up regulation of RNA formation GOC:TermGenie up regulation of RNA synthesis GOC:TermGenie up-regulation of RNA anabolism GOC:TermGenie up-regulation of RNA biosynthesis GOC:TermGenie up-regulation of RNA biosynthetic process GOC:TermGenie up-regulation of RNA formation GOC:TermGenie up-regulation of RNA synthesis GOC:TermGenie upregulation of RNA anabolism GOC:TermGenie upregulation of RNA biosynthesis GOC:TermGenie upregulation of RNA biosynthetic process GOC:TermGenie upregulation of RNA formation GOC:TermGenie upregulation of RNA synthesis GOC:TermGenie activation of RNA anabolism GOC:TermGenie activation of RNA biosynthesis GOC:TermGenie activation of RNA biosynthetic process GOC:TermGenie activation of RNA formation GOC:TermGenie activation of RNA synthesis GOC:TermGenie Any process that modulates the frequency, rate or extent of neuroblast proliferation. rl 2014-02-18T10:03:31Z biological_process GO:1902692 regulation of neuroblast proliferation Any process that modulates the frequency, rate or extent of neuroblast proliferation. GOC:PARL GOC:TermGenie GOC:rl GO_REF:0000058 PMID:21168496 Any process that modulates the rate, frequency, or extent of the process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage. mr 2014-02-26T15:36:15Z biological_process GO:1902738 regulation of chondrocyte differentiation involved in endochondral bone morphogenesis Any process that modulates the rate, frequency, or extent of the process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage. GOC:TermGenie GO_REF:0000058 PMID:8662546 Any apoptotic process that is involved in anatomical structure development. pr 2014-02-28T13:09:43Z apoptotic cell death involved in anatomical structure development apoptotic cell death involved in development of an anatomical structure apoptotic process involved in anatomical structure development apoptotic process involved in development of an anatomical structure apoptotic programmed cell death involved in anatomical structure development apoptotic programmed cell death involved in development of an anatomical structure programmed cell death by apoptosis involved in anatomical structure development programmed cell death by apoptosis involved in development of an anatomical structure activation of apoptosis involved in anatomical structure development activation of apoptosis involved in development of an anatomical structure apoptosis involved in anatomical structure development apoptosis involved in development of an anatomical structure apoptosis signaling involved in anatomical structure development apoptosis signaling involved in development of an anatomical structure apoptotic program involved in anatomical structure development apoptotic program involved in development of an anatomical structure type I programmed cell death involved in anatomical structure development type I programmed cell death involved in development of an anatomical structure biological_process apoptosis activator activity involved in anatomical structure development apoptosis activator activity involved in development of an anatomical structure commitment to apoptosis involved in anatomical structure development commitment to apoptosis involved in development of an anatomical structure induction of apoptosis by p53 involved in anatomical structure development induction of apoptosis by p53 involved in development of an anatomical structure induction of apoptosis involved in anatomical structure development induction of apoptosis involved in development of an anatomical structure signaling (initiator) caspase activity involved in anatomical structure development signaling (initiator) caspase activity involved in development of an anatomical structure GO:1902742 apoptotic process involved in development Any apoptotic process that is involved in anatomical structure development. GOC:TermGenie GOC:mtg_apoptosis GOC:pg GO_REF:0000060 apoptotic cell death involved in anatomical structure development GOC:TermGenie apoptotic cell death involved in development of an anatomical structure GOC:TermGenie apoptotic process involved in development of an anatomical structure GOC:TermGenie apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of apoptosis involved in development of an anatomical structure GOC:TermGenie apoptosis involved in anatomical structure development GOC:TermGenie apoptosis involved in development of an anatomical structure GOC:TermGenie apoptosis signaling involved in anatomical structure development GOC:TermGenie apoptosis signaling involved in development of an anatomical structure GOC:TermGenie apoptotic program involved in anatomical structure development GOC:TermGenie apoptotic program involved in development of an anatomical structure GOC:TermGenie type I programmed cell death involved in anatomical structure development GOC:TermGenie type I programmed cell death involved in development of an anatomical structure GOC:TermGenie apoptosis activator activity involved in anatomical structure development GOC:TermGenie apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie commitment to apoptosis involved in anatomical structure development GOC:TermGenie commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie induction of apoptosis involved in anatomical structure development GOC:TermGenie induction of apoptosis involved in development of an anatomical structure GOC:TermGenie signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that activates or increases the frequency, rate or extent of chondrocyte development. mr 2014-03-07T17:45:55Z up regulation of chondrocyte development up-regulation of chondrocyte development upregulation of chondrocyte development activation of chondrocyte development biological_process GO:1902761 positive regulation of chondrocyte development Any process that activates or increases the frequency, rate or extent of chondrocyte development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:16575901 up regulation of chondrocyte development GOC:TermGenie up-regulation of chondrocyte development GOC:TermGenie upregulation of chondrocyte development GOC:TermGenie activation of chondrocyte development GOC:TermGenie Any process that modulates the frequency, rate or extent of skeletal muscle fiber differentiation. mr 2014-03-26T21:18:26Z biological_process GO:1902809 regulation of skeletal muscle fiber differentiation Any process that modulates the frequency, rate or extent of skeletal muscle fiber differentiation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:17879321 Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle fiber differentiation. mr 2014-03-26T21:18:32Z down regulation of skeletal muscle fiber differentiation down-regulation of skeletal muscle fiber differentiation downregulation of skeletal muscle fiber differentiation inhibition of skeletal muscle fiber differentiation biological_process GO:1902810 negative regulation of skeletal muscle fiber differentiation Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle fiber differentiation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:17879321 down regulation of skeletal muscle fiber differentiation GOC:TermGenie down-regulation of skeletal muscle fiber differentiation GOC:TermGenie downregulation of skeletal muscle fiber differentiation GOC:TermGenie inhibition of skeletal muscle fiber differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of skeletal muscle fiber differentiation. mr 2014-03-26T21:18:38Z up regulation of skeletal muscle fiber differentiation up-regulation of skeletal muscle fiber differentiation upregulation of skeletal muscle fiber differentiation activation of skeletal muscle fiber differentiation biological_process GO:1902811 positive regulation of skeletal muscle fiber differentiation Any process that activates or increases the frequency, rate or extent of skeletal muscle fiber differentiation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:17879321 up regulation of skeletal muscle fiber differentiation GOC:TermGenie up-regulation of skeletal muscle fiber differentiation GOC:TermGenie upregulation of skeletal muscle fiber differentiation GOC:TermGenie activation of skeletal muscle fiber differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to microtubule. tb 2014-03-27T22:07:12Z regulation of protein localisation to microtubule biological_process GO:1902816 regulation of protein localization to microtubule Any process that modulates the frequency, rate or extent of protein localization to microtubule. GOC:TermGenie GOC:vw GO_REF:0000058 PMID:23087209 regulation of protein localisation to microtubule GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to microtubule. tb 2014-03-27T22:07:18Z down regulation of protein localisation to microtubule down regulation of protein localization to microtubule down-regulation of protein localisation to microtubule down-regulation of protein localization to microtubule downregulation of protein localisation to microtubule downregulation of protein localization to microtubule negative regulation of protein localisation to microtubule inhibition of protein localisation to microtubule inhibition of protein localization to microtubule biological_process GO:1902817 negative regulation of protein localization to microtubule Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to microtubule. GOC:TermGenie GOC:vw GO_REF:0000058 PMID:23087209 down regulation of protein localisation to microtubule GOC:TermGenie down regulation of protein localization to microtubule GOC:TermGenie down-regulation of protein localisation to microtubule GOC:TermGenie down-regulation of protein localization to microtubule GOC:TermGenie downregulation of protein localisation to microtubule GOC:TermGenie downregulation of protein localization to microtubule GOC:TermGenie negative regulation of protein localisation to microtubule GOC:TermGenie inhibition of protein localisation to microtubule GOC:TermGenie inhibition of protein localization to microtubule GOC:TermGenie Any process that modulates the frequency, rate or extent of nuclear migration along microtubule. vw 2014-04-01T13:50:23Z regulation of nuclear movement, microtubule-mediated regulation of nucleus migration regulation of microtubule cytoskeleton-dependent nuclear positioning regulation of microtubule cytoskeleton-dependent nucleus positioning regulation of microtubule-dependent nuclear positioning regulation of microtubule-dependent nucleus positioning regulation of microtubule-mediated nuclear migration regulation of nuclear migration, microtubule-mediated regulation of transport of nucleus by microtubules regulation of transport of nucleus, microtubule-mediated biological_process GO:1902838 regulation of nuclear migration along microtubule Any process that modulates the frequency, rate or extent of nuclear migration along microtubule. GOC:TermGenie GO_REF:0000058 PMID:23087209 regulation of nuclear movement, microtubule-mediated GOC:TermGenie regulation of nucleus migration GOC:TermGenie regulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie regulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie regulation of microtubule-dependent nuclear positioning GOC:TermGenie regulation of microtubule-dependent nucleus positioning GOC:TermGenie regulation of microtubule-mediated nuclear migration GOC:TermGenie regulation of nuclear migration, microtubule-mediated GOC:TermGenie regulation of transport of nucleus by microtubules GOC:TermGenie regulation of transport of nucleus, microtubule-mediated GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of nuclear migration along microtubule. vw 2014-04-01T13:50:29Z down regulation of microtubule cytoskeleton-dependent nuclear positioning down regulation of microtubule cytoskeleton-dependent nucleus positioning down regulation of microtubule-dependent nuclear positioning down regulation of microtubule-dependent nucleus positioning down regulation of microtubule-mediated nuclear migration down regulation of nuclear migration along microtubule down regulation of nuclear migration, microtubule-mediated down regulation of transport of nucleus by microtubules down regulation of transport of nucleus, microtubule-mediated down-regulation of microtubule cytoskeleton-dependent nuclear positioning down-regulation of microtubule cytoskeleton-dependent nucleus positioning down-regulation of microtubule-dependent nuclear positioning down-regulation of microtubule-dependent nucleus positioning down-regulation of microtubule-mediated nuclear migration down-regulation of nuclear migration along microtubule down-regulation of nuclear migration, microtubule-mediated down-regulation of transport of nucleus by microtubules down-regulation of transport of nucleus, microtubule-mediated downregulation of microtubule cytoskeleton-dependent nuclear positioning downregulation of microtubule cytoskeleton-dependent nucleus positioning downregulation of microtubule-dependent nuclear positioning downregulation of microtubule-dependent nucleus positioning downregulation of microtubule-mediated nuclear migration downregulation of nuclear migration along microtubule downregulation of nuclear migration, microtubule-mediated downregulation of transport of nucleus by microtubules downregulation of transport of nucleus, microtubule-mediated negative regulation of microtubule cytoskeleton-dependent nuclear positioning negative regulation of microtubule cytoskeleton-dependent nucleus positioning negative regulation of microtubule-dependent nuclear positioning negative regulation of microtubule-dependent nucleus positioning negative regulation of microtubule-mediated nuclear migration negative regulation of nuclear migration, microtubule-mediated negative regulation of transport of nucleus by microtubules negative regulation of transport of nucleus, microtubule-mediated inhibition of microtubule cytoskeleton-dependent nuclear positioning inhibition of microtubule cytoskeleton-dependent nucleus positioning inhibition of microtubule-dependent nuclear positioning inhibition of microtubule-dependent nucleus positioning inhibition of microtubule-mediated nuclear migration inhibition of nuclear migration along microtubule inhibition of nuclear migration, microtubule-mediated inhibition of transport of nucleus by microtubules inhibition of transport of nucleus, microtubule-mediated biological_process GO:1902839 negative regulation of nuclear migration along microtubule Any process that stops, prevents or reduces the frequency, rate or extent of nuclear migration along microtubule. GOC:TermGenie GO_REF:0000058 PMID:23087209 down regulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie down regulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie down regulation of microtubule-dependent nuclear positioning GOC:TermGenie down regulation of microtubule-dependent nucleus positioning GOC:TermGenie down regulation of microtubule-mediated nuclear migration GOC:TermGenie down regulation of nuclear migration along microtubule GOC:TermGenie down regulation of nuclear migration, microtubule-mediated GOC:TermGenie down regulation of transport of nucleus by microtubules GOC:TermGenie down regulation of transport of nucleus, microtubule-mediated GOC:TermGenie down-regulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie down-regulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie down-regulation of microtubule-dependent nuclear positioning GOC:TermGenie down-regulation of microtubule-dependent nucleus positioning GOC:TermGenie down-regulation of microtubule-mediated nuclear migration GOC:TermGenie down-regulation of nuclear migration along microtubule GOC:TermGenie down-regulation of nuclear migration, microtubule-mediated GOC:TermGenie down-regulation of transport of nucleus by microtubules GOC:TermGenie down-regulation of transport of nucleus, microtubule-mediated GOC:TermGenie downregulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie downregulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie downregulation of microtubule-dependent nuclear positioning GOC:TermGenie downregulation of microtubule-dependent nucleus positioning GOC:TermGenie downregulation of microtubule-mediated nuclear migration GOC:TermGenie downregulation of nuclear migration along microtubule GOC:TermGenie downregulation of nuclear migration, microtubule-mediated GOC:TermGenie downregulation of transport of nucleus by microtubules GOC:TermGenie downregulation of transport of nucleus, microtubule-mediated GOC:TermGenie negative regulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie negative regulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie negative regulation of microtubule-dependent nuclear positioning GOC:TermGenie negative regulation of microtubule-dependent nucleus positioning GOC:TermGenie negative regulation of microtubule-mediated nuclear migration GOC:TermGenie negative regulation of nuclear migration, microtubule-mediated GOC:TermGenie negative regulation of transport of nucleus by microtubules GOC:TermGenie negative regulation of transport of nucleus, microtubule-mediated GOC:TermGenie inhibition of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie inhibition of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie inhibition of microtubule-dependent nuclear positioning GOC:TermGenie inhibition of microtubule-dependent nucleus positioning GOC:TermGenie inhibition of microtubule-mediated nuclear migration GOC:TermGenie inhibition of nuclear migration along microtubule GOC:TermGenie inhibition of nuclear migration, microtubule-mediated GOC:TermGenie inhibition of transport of nucleus by microtubules GOC:TermGenie inhibition of transport of nucleus, microtubule-mediated GOC:TermGenie Any process that activates or increases the frequency, rate or extent of nuclear migration along microtubule. vw 2014-04-01T13:50:35Z positive regulation of microtubule cytoskeleton-dependent nuclear positioning positive regulation of microtubule cytoskeleton-dependent nucleus positioning positive regulation of microtubule-dependent nuclear positioning positive regulation of microtubule-dependent nucleus positioning positive regulation of microtubule-mediated nuclear migration positive regulation of nuclear migration, microtubule-mediated positive regulation of transport of nucleus by microtubules positive regulation of transport of nucleus, microtubule-mediated up regulation of microtubule cytoskeleton-dependent nuclear positioning up regulation of microtubule cytoskeleton-dependent nucleus positioning up regulation of microtubule-dependent nuclear positioning up regulation of microtubule-dependent nucleus positioning up regulation of microtubule-mediated nuclear migration up regulation of nuclear migration along microtubule up regulation of nuclear migration, microtubule-mediated up regulation of transport of nucleus by microtubules up regulation of transport of nucleus, microtubule-mediated up-regulation of microtubule cytoskeleton-dependent nuclear positioning up-regulation of microtubule cytoskeleton-dependent nucleus positioning up-regulation of microtubule-dependent nuclear positioning up-regulation of microtubule-dependent nucleus positioning up-regulation of microtubule-mediated nuclear migration up-regulation of nuclear migration along microtubule up-regulation of nuclear migration, microtubule-mediated up-regulation of transport of nucleus by microtubules up-regulation of transport of nucleus, microtubule-mediated upregulation of microtubule cytoskeleton-dependent nuclear positioning upregulation of microtubule cytoskeleton-dependent nucleus positioning upregulation of microtubule-dependent nuclear positioning upregulation of microtubule-dependent nucleus positioning upregulation of microtubule-mediated nuclear migration upregulation of nuclear migration along microtubule upregulation of nuclear migration, microtubule-mediated upregulation of transport of nucleus by microtubules upregulation of transport of nucleus, microtubule-mediated activation of microtubule cytoskeleton-dependent nuclear positioning activation of microtubule cytoskeleton-dependent nucleus positioning activation of microtubule-dependent nuclear positioning activation of microtubule-dependent nucleus positioning activation of microtubule-mediated nuclear migration activation of nuclear migration along microtubule activation of nuclear migration, microtubule-mediated activation of transport of nucleus by microtubules activation of transport of nucleus, microtubule-mediated biological_process GO:1902840 positive regulation of nuclear migration along microtubule Any process that activates or increases the frequency, rate or extent of nuclear migration along microtubule. GOC:TermGenie GO_REF:0000058 PMID:23087209 positive regulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie positive regulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie positive regulation of microtubule-dependent nuclear positioning GOC:TermGenie positive regulation of microtubule-dependent nucleus positioning GOC:TermGenie positive regulation of microtubule-mediated nuclear migration GOC:TermGenie positive regulation of nuclear migration, microtubule-mediated GOC:TermGenie positive regulation of transport of nucleus by microtubules GOC:TermGenie positive regulation of transport of nucleus, microtubule-mediated GOC:TermGenie up regulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie up regulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie up regulation of microtubule-dependent nuclear positioning GOC:TermGenie up regulation of microtubule-dependent nucleus positioning GOC:TermGenie up regulation of microtubule-mediated nuclear migration GOC:TermGenie up regulation of nuclear migration along microtubule GOC:TermGenie up regulation of nuclear migration, microtubule-mediated GOC:TermGenie up regulation of transport of nucleus by microtubules GOC:TermGenie up regulation of transport of nucleus, microtubule-mediated GOC:TermGenie up-regulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie up-regulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie up-regulation of microtubule-dependent nuclear positioning GOC:TermGenie up-regulation of microtubule-dependent nucleus positioning GOC:TermGenie up-regulation of microtubule-mediated nuclear migration GOC:TermGenie up-regulation of nuclear migration along microtubule GOC:TermGenie up-regulation of nuclear migration, microtubule-mediated GOC:TermGenie up-regulation of transport of nucleus by microtubules GOC:TermGenie up-regulation of transport of nucleus, microtubule-mediated GOC:TermGenie upregulation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie upregulation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie upregulation of microtubule-dependent nuclear positioning GOC:TermGenie upregulation of microtubule-dependent nucleus positioning GOC:TermGenie upregulation of microtubule-mediated nuclear migration GOC:TermGenie upregulation of nuclear migration along microtubule GOC:TermGenie upregulation of nuclear migration, microtubule-mediated GOC:TermGenie upregulation of transport of nucleus by microtubules GOC:TermGenie upregulation of transport of nucleus, microtubule-mediated GOC:TermGenie activation of microtubule cytoskeleton-dependent nuclear positioning GOC:TermGenie activation of microtubule cytoskeleton-dependent nucleus positioning GOC:TermGenie activation of microtubule-dependent nuclear positioning GOC:TermGenie activation of microtubule-dependent nucleus positioning GOC:TermGenie activation of microtubule-mediated nuclear migration GOC:TermGenie activation of nuclear migration along microtubule GOC:TermGenie activation of nuclear migration, microtubule-mediated GOC:TermGenie activation of transport of nucleus by microtubules GOC:TermGenie activation of transport of nucleus, microtubule-mediated GOC:TermGenie Any microtubule cytoskeleton organization that is involved in mitosis. vw 2014-04-02T14:19:38Z microtubule cytoskeleton organisation involved in mitosis microtubule dynamics involved in mitosis biological_process microtubule cytoskeleton organization and biogenesis involved in mitosis GO:1902850 microtubule cytoskeleton organization involved in mitosis Any microtubule cytoskeleton organization that is involved in mitosis. GOC:TermGenie GO_REF:0000060 PMID:18799626 microtubule cytoskeleton organisation involved in mitosis GOC:TermGenie microtubule dynamics involved in mitosis GOC:TermGenie microtubule cytoskeleton organization and biogenesis involved in mitosis GOC:TermGenie Any process that modulates the frequency, rate or extent of embryonic camera-type eye development. mr 2014-04-03T15:24:00Z regulation of embryonic eye development biological_process GO:1902863 regulation of embryonic camera-type eye development Any process that modulates the frequency, rate or extent of embryonic camera-type eye development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:16872597 regulation of embryonic eye development GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of embryonic camera-type eye development. mr 2014-04-03T15:24:06Z down regulation of embryonic camera-type eye development down regulation of embryonic eye development down-regulation of embryonic camera-type eye development down-regulation of embryonic eye development downregulation of embryonic camera-type eye development downregulation of embryonic eye development negative regulation of embryonic eye development inhibition of embryonic camera-type eye development inhibition of embryonic eye development biological_process GO:1902864 negative regulation of embryonic camera-type eye development Any process that stops, prevents or reduces the frequency, rate or extent of embryonic camera-type eye development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:16872597 down regulation of embryonic camera-type eye development GOC:TermGenie down regulation of embryonic eye development GOC:TermGenie down-regulation of embryonic camera-type eye development GOC:TermGenie down-regulation of embryonic eye development GOC:TermGenie downregulation of embryonic camera-type eye development GOC:TermGenie downregulation of embryonic eye development GOC:TermGenie negative regulation of embryonic eye development GOC:TermGenie inhibition of embryonic camera-type eye development GOC:TermGenie inhibition of embryonic eye development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of embryonic camera-type eye development. mr 2014-04-03T15:24:12Z positive regulation of embryonic eye development up regulation of embryonic camera-type eye development up regulation of embryonic eye development up-regulation of embryonic camera-type eye development up-regulation of embryonic eye development upregulation of embryonic camera-type eye development upregulation of embryonic eye development activation of embryonic camera-type eye development activation of embryonic eye development biological_process GO:1902865 positive regulation of embryonic camera-type eye development Any process that activates or increases the frequency, rate or extent of embryonic camera-type eye development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:16872597 positive regulation of embryonic eye development GOC:TermGenie up regulation of embryonic camera-type eye development GOC:TermGenie up regulation of embryonic eye development GOC:TermGenie up-regulation of embryonic camera-type eye development GOC:TermGenie up-regulation of embryonic eye development GOC:TermGenie upregulation of embryonic camera-type eye development GOC:TermGenie upregulation of embryonic eye development GOC:TermGenie activation of embryonic camera-type eye development GOC:TermGenie activation of embryonic eye development GOC:TermGenie Any process that modulates the frequency, rate or extent of retina development in camera-type eye. mr 2014-04-03T15:24:17Z regulation of retina development in camera-style eye biological_process regulation of retinal development GO:1902866 regulation of retina development in camera-type eye Any process that modulates the frequency, rate or extent of retina development in camera-type eye. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:16872597 regulation of retina development in camera-style eye GOC:TermGenie regulation of retinal development GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of retina development in camera-type eye. mr 2014-04-03T15:24:23Z down regulation of retina development in camera-style eye down regulation of retina development in camera-type eye down-regulation of retina development in camera-style eye down-regulation of retina development in camera-type eye downregulation of retina development in camera-style eye downregulation of retina development in camera-type eye negative regulation of retina development in camera-style eye inhibition of retina development in camera-style eye inhibition of retina development in camera-type eye biological_process down regulation of retinal development down-regulation of retinal development downregulation of retinal development inhibition of retinal development negative regulation of retinal development GO:1902867 negative regulation of retina development in camera-type eye Any process that stops, prevents or reduces the frequency, rate or extent of retina development in camera-type eye. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:16872597 down regulation of retina development in camera-style eye GOC:TermGenie down regulation of retina development in camera-type eye GOC:TermGenie down-regulation of retina development in camera-style eye GOC:TermGenie down-regulation of retina development in camera-type eye GOC:TermGenie downregulation of retina development in camera-style eye GOC:TermGenie downregulation of retina development in camera-type eye GOC:TermGenie negative regulation of retina development in camera-style eye GOC:TermGenie inhibition of retina development in camera-style eye GOC:TermGenie inhibition of retina development in camera-type eye GOC:TermGenie down regulation of retinal development GOC:TermGenie down-regulation of retinal development GOC:TermGenie downregulation of retinal development GOC:TermGenie inhibition of retinal development GOC:TermGenie negative regulation of retinal development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of retina development in camera-type eye. mr 2014-04-03T15:24:29Z positive regulation of retina development in camera-style eye up regulation of retina development in camera-style eye up regulation of retina development in camera-type eye up-regulation of retina development in camera-style eye up-regulation of retina development in camera-type eye upregulation of retina development in camera-style eye upregulation of retina development in camera-type eye activation of retina development in camera-style eye activation of retina development in camera-type eye biological_process activation of retinal development positive regulation of retinal development up regulation of retinal development up-regulation of retinal development upregulation of retinal development GO:1902868 positive regulation of retina development in camera-type eye Any process that activates or increases the frequency, rate or extent of retina development in camera-type eye. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:16872597 positive regulation of retina development in camera-style eye GOC:TermGenie up regulation of retina development in camera-style eye GOC:TermGenie up regulation of retina development in camera-type eye GOC:TermGenie up-regulation of retina development in camera-style eye GOC:TermGenie up-regulation of retina development in camera-type eye GOC:TermGenie upregulation of retina development in camera-style eye GOC:TermGenie upregulation of retina development in camera-type eye GOC:TermGenie activation of retina development in camera-style eye GOC:TermGenie activation of retina development in camera-type eye GOC:TermGenie activation of retinal development GOC:TermGenie positive regulation of retinal development GOC:TermGenie up regulation of retinal development GOC:TermGenie up-regulation of retinal development GOC:TermGenie upregulation of retinal development GOC:TermGenie Any process that modulates the frequency, rate or extent of supramolecular fiber organization. rl 2014-04-15T16:46:36Z biological_process regulation of fibril organisation GO:1902903 HSPA8, human, P11142 in PMID:23921388 inferred from direct assay to negatively regulate fibrillation of alpha-Syn in vitro regulation of supramolecular fiber organization Any process that modulates the frequency, rate or extent of supramolecular fiber organization. GOC:PARL GOC:TermGenie GOC:rl GO_REF:0000058 PMID:23921388 regulation of fibril organisation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of fibril organization. rl 2014-04-15T16:46:42Z inhibition of fibril organisation inhibition of fibril organization biological_process down regulation of fibril organisation down regulation of fibril organization down-regulation of fibril organisation down-regulation of fibril organization downregulation of fibril organisation downregulation of fibril organization negative regulation of fibril organisation GO:1902904 HSPA8, human, P11142 in PMID:23921388 inferred from direct assay to negatively regulate fibrillation of alpha-Syn in vitro negative regulation of supramolecular fiber organization Any process that stops, prevents or reduces the frequency, rate or extent of fibril organization. GOC:PARL GOC:TermGenie GOC:rl GO_REF:0000058 PMID:23921388 inhibition of fibril organisation GOC:TermGenie inhibition of fibril organization GOC:TermGenie down regulation of fibril organisation GOC:TermGenie down regulation of fibril organization GOC:TermGenie down-regulation of fibril organisation GOC:TermGenie down-regulation of fibril organization GOC:TermGenie downregulation of fibril organisation GOC:TermGenie downregulation of fibril organization GOC:TermGenie negative regulation of fibril organisation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of supramolecular fiber organization. rl 2014-04-15T16:46:48Z activation of fibril organisation activation of fibril organization biological_process positive regulation of fibril organisation up regulation of fibril organisation up regulation of fibril organization up-regulation of fibril organisation up-regulation of fibril organization upregulation of fibril organisation upregulation of fibril organization GO:1902905 HSPA8, human, P11142 in PMID:23921388 inferred from direct assay to negatively regulate fibrillation of alpha-Syn in vitro positive regulation of supramolecular fiber organization Any process that activates or increases the frequency, rate or extent of supramolecular fiber organization. GOC:PARL GOC:TermGenie GOC:rl GO_REF:0000058 PMID:23921388 activation of fibril organisation GOC:TermGenie activation of fibril organization GOC:TermGenie positive regulation of fibril organisation GOC:TermGenie up regulation of fibril organisation GOC:TermGenie up regulation of fibril organization GOC:TermGenie up-regulation of fibril organisation GOC:TermGenie up-regulation of fibril organization GOC:TermGenie upregulation of fibril organisation GOC:TermGenie upregulation of fibril organization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of neuroepithelial cell differentiation. mr 2014-04-18T21:06:42Z up regulation of neuroepithelial cell differentiation up-regulation of neuroepithelial cell differentiation upregulation of neuroepithelial cell differentiation activation of neuroepithelial cell differentiation biological_process GO:1902913 positive regulation of neuroepithelial cell differentiation Any process that activates or increases the frequency, rate or extent of neuroepithelial cell differentiation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:16916506 up regulation of neuroepithelial cell differentiation GOC:TermGenie up-regulation of neuroepithelial cell differentiation GOC:TermGenie upregulation of neuroepithelial cell differentiation GOC:TermGenie activation of neuroepithelial cell differentiation GOC:TermGenie The disaggregation of an organelle into its constituent components. jl 2014-05-13T12:36:03Z organelle degradation biological_process GO:1903008 organelle disassembly The disaggregation of an organelle into its constituent components. GOC:TermGenie GO_REF:0000079 Any process that modulates the frequency, rate or extent of bone development. mr 2014-05-13T22:41:53Z biological_process GO:1903010 regulation of bone development Any process that modulates the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 Any process that stops, prevents or reduces the frequency, rate or extent of bone development. mr 2014-05-13T22:42:00Z down regulation of bone development down-regulation of bone development downregulation of bone development inhibition of bone development biological_process GO:1903011 negative regulation of bone development Any process that stops, prevents or reduces the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 down regulation of bone development GOC:TermGenie down-regulation of bone development GOC:TermGenie downregulation of bone development GOC:TermGenie inhibition of bone development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bone development. mr 2014-05-13T22:42:06Z up regulation of bone development up-regulation of bone development upregulation of bone development activation of bone development biological_process GO:1903012 positive regulation of bone development Any process that activates or increases the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 up regulation of bone development GOC:TermGenie up-regulation of bone development GOC:TermGenie upregulation of bone development GOC:TermGenie activation of bone development GOC:TermGenie Any process that modulates the frequency, rate or extent of glycoprotein metabolic process. rl 2014-05-14T18:44:19Z regulation of glycoprotein metabolism biological_process GO:1903018 human serum amyloid P component (SAP) P02743 inhibits viral neuraminidase, NA (exo-alpha-sialidase activity) and thus the metabolism of glycoproteins, demonstrated in Figure 4A PMID:23544079, (IDA), the negative regulation term would be applied to this protein regulation of glycoprotein metabolic process Any process that modulates the frequency, rate or extent of glycoprotein metabolic process. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:23544079 regulation of glycoprotein metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of glycoprotein metabolic process. rl 2014-05-14T18:44:25Z down regulation of glycoprotein metabolic process down regulation of glycoprotein metabolism down-regulation of glycoprotein metabolic process down-regulation of glycoprotein metabolism downregulation of glycoprotein metabolic process downregulation of glycoprotein metabolism negative regulation of glycoprotein metabolism inhibition of glycoprotein metabolic process inhibition of glycoprotein metabolism biological_process GO:1903019 human serum amyloid P component (SAP) P02743 inhibits viral neuraminidase, NA (exo-alpha-sialidase activity) and thus the metabolism of glycoproteins, demonstrated in Figure 4A PMID:23544079, (IDA), the negative regulation term would be applied to this protein negative regulation of glycoprotein metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of glycoprotein metabolic process. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:23544079 down regulation of glycoprotein metabolic process GOC:TermGenie down regulation of glycoprotein metabolism GOC:TermGenie down-regulation of glycoprotein metabolic process GOC:TermGenie down-regulation of glycoprotein metabolism GOC:TermGenie downregulation of glycoprotein metabolic process GOC:TermGenie downregulation of glycoprotein metabolism GOC:TermGenie negative regulation of glycoprotein metabolism GOC:TermGenie inhibition of glycoprotein metabolic process GOC:TermGenie inhibition of glycoprotein metabolism GOC:TermGenie Any process that activates or increases the frequency, rate or extent of glycoprotein metabolic process. rl 2014-05-14T18:44:31Z positive regulation of glycoprotein metabolism up regulation of glycoprotein metabolic process up regulation of glycoprotein metabolism up-regulation of glycoprotein metabolic process up-regulation of glycoprotein metabolism upregulation of glycoprotein metabolic process upregulation of glycoprotein metabolism activation of glycoprotein metabolic process activation of glycoprotein metabolism biological_process GO:1903020 human serum amyloid P component (SAP) P02743 inhibits viral neuraminidase, NA (exo-alpha-sialidase activity) and thus the metabolism of glycoproteins, demonstrated in Figure 4A PMID:23544079, (IDA), the negative regulation term would be applied to this protein positive regulation of glycoprotein metabolic process Any process that activates or increases the frequency, rate or extent of glycoprotein metabolic process. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:23544079 positive regulation of glycoprotein metabolism GOC:TermGenie up regulation of glycoprotein metabolic process GOC:TermGenie up regulation of glycoprotein metabolism GOC:TermGenie up-regulation of glycoprotein metabolic process GOC:TermGenie up-regulation of glycoprotein metabolism GOC:TermGenie upregulation of glycoprotein metabolic process GOC:TermGenie upregulation of glycoprotein metabolism GOC:TermGenie activation of glycoprotein metabolic process GOC:TermGenie activation of glycoprotein metabolism GOC:TermGenie A process that is part of the meiotic cell cycle. jl 2014-05-22T14:22:28Z biological_process GO:1903046 meiotic cell cycle process A process that is part of the meiotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 A process that is part of the mitotic cell cycle. jl 2014-05-22T14:22:34Z biological_process GO:1903047 mitotic cell cycle process A process that is part of the mitotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 Any process that modulates the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:41Z regulation of extracellular matrix organisation biological_process regulation of extracellular matrix organization and biogenesis GO:1903053 regulation of extracellular matrix organization Any process that modulates the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 regulation of extracellular matrix organisation GOC:TermGenie regulation of extracellular matrix organization and biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:47Z down regulation of extracellular matrix organisation down regulation of extracellular matrix organization down-regulation of extracellular matrix organisation down-regulation of extracellular matrix organization downregulation of extracellular matrix organisation downregulation of extracellular matrix organization negative regulation of extracellular matrix organisation inhibition of extracellular matrix organisation inhibition of extracellular matrix organization biological_process down regulation of extracellular matrix organization and biogenesis down-regulation of extracellular matrix organization and biogenesis downregulation of extracellular matrix organization and biogenesis inhibition of extracellular matrix organization and biogenesis negative regulation of extracellular matrix organization and biogenesis GO:1903054 negative regulation of extracellular matrix organization Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 down regulation of extracellular matrix organisation GOC:TermGenie down regulation of extracellular matrix organization GOC:TermGenie down-regulation of extracellular matrix organisation GOC:TermGenie down-regulation of extracellular matrix organization GOC:TermGenie downregulation of extracellular matrix organisation GOC:TermGenie downregulation of extracellular matrix organization GOC:TermGenie negative regulation of extracellular matrix organisation GOC:TermGenie inhibition of extracellular matrix organisation GOC:TermGenie inhibition of extracellular matrix organization GOC:TermGenie down regulation of extracellular matrix organization and biogenesis GOC:TermGenie down-regulation of extracellular matrix organization and biogenesis GOC:TermGenie downregulation of extracellular matrix organization and biogenesis GOC:TermGenie inhibition of extracellular matrix organization and biogenesis GOC:TermGenie negative regulation of extracellular matrix organization and biogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:53Z positive regulation of extracellular matrix organisation up regulation of extracellular matrix organisation up regulation of extracellular matrix organization up-regulation of extracellular matrix organisation up-regulation of extracellular matrix organization upregulation of extracellular matrix organisation upregulation of extracellular matrix organization activation of extracellular matrix organisation activation of extracellular matrix organization biological_process activation of extracellular matrix organization and biogenesis positive regulation of extracellular matrix organization and biogenesis up regulation of extracellular matrix organization and biogenesis up-regulation of extracellular matrix organization and biogenesis upregulation of extracellular matrix organization and biogenesis GO:1903055 positive regulation of extracellular matrix organization Any process that activates or increases the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 positive regulation of extracellular matrix organisation GOC:TermGenie up regulation of extracellular matrix organisation GOC:TermGenie up regulation of extracellular matrix organization GOC:TermGenie up-regulation of extracellular matrix organisation GOC:TermGenie up-regulation of extracellular matrix organization GOC:TermGenie upregulation of extracellular matrix organisation GOC:TermGenie upregulation of extracellular matrix organization GOC:TermGenie activation of extracellular matrix organisation GOC:TermGenie activation of extracellular matrix organization GOC:TermGenie activation of extracellular matrix organization and biogenesis GOC:TermGenie positive regulation of extracellular matrix organization and biogenesis GOC:TermGenie up regulation of extracellular matrix organization and biogenesis GOC:TermGenie up-regulation of extracellular matrix organization and biogenesis GOC:TermGenie upregulation of extracellular matrix organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to plasma membrane. tb 2009-07-10T10:32:44Z GO:0090003 GO:1905963 regulation of protein localization in plasma membrane biological_process regulation of establishment of protein localisation in plasma membrane regulation of establishment of protein localization in plasma membrane regulation of establishment of protein localization to plasma membrane regulation of protein localisation in plasma membrane regulation of protein targeting to plasma membrane regulation of protein-plasma membrane targeting GO:1903076 regulation of protein localization to plasma membrane Any process that modulates the frequency, rate or extent of protein localization to plasma membrane. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:11602640 regulation of protein localization in plasma membrane GOC:TermGenie regulation of establishment of protein localisation in plasma membrane GOC:mah regulation of protein localisation in plasma membrane GOC:TermGenie regulation of protein-plasma membrane targeting GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane. tb 2014-05-29T17:10:16Z GO:0090005 GO:1905964 down regulation of protein localisation in plasma membrane down regulation of protein localization in plasma membrane down regulation of protein localization to plasma membrane down-regulation of protein localisation in plasma membrane down-regulation of protein localization in plasma membrane down-regulation of protein localization to plasma membrane downregulation of protein localisation in plasma membrane downregulation of protein localization in plasma membrane downregulation of protein localization to plasma membrane negative regulation of protein localization in plasma membrane inhibition of protein localisation in plasma membrane inhibition of protein localization in plasma membrane inhibition of protein localization to plasma membrane inhibition of protein targeting to plasma membrane inhibition of protein-plasma membrane targeting biological_process down regulation of protein targeting to plasma membrane down regulation of protein-plasma membrane targeting down-regulation of protein targeting to plasma membrane down-regulation of protein-plasma membrane targeting downregulation of protein targeting to plasma membrane downregulation of protein-plasma membrane targeting negative regulation of establishment of protein localisation in plasma membrane negative regulation of establishment of protein localization in plasma membrane negative regulation of establishment of protein localization to plasma membrane negative regulation of protein localisation in plasma membrane negative regulation of protein targeting to plasma membrane negative regulation of protein-plasma membrane targeting GO:1903077 negative regulation of protein localization to plasma membrane Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:11602640 down regulation of protein localisation in plasma membrane GOC:TermGenie down regulation of protein localization in plasma membrane GOC:TermGenie down regulation of protein localization to plasma membrane GOC:TermGenie down-regulation of protein localisation in plasma membrane GOC:TermGenie down-regulation of protein localization in plasma membrane GOC:TermGenie down-regulation of protein localization to plasma membrane GOC:TermGenie downregulation of protein localisation in plasma membrane GOC:TermGenie downregulation of protein localization in plasma membrane GOC:TermGenie downregulation of protein localization to plasma membrane GOC:TermGenie negative regulation of protein localization in plasma membrane GOC:TermGenie inhibition of protein localisation in plasma membrane GOC:TermGenie inhibition of protein localization in plasma membrane GOC:TermGenie inhibition of protein localization to plasma membrane GOC:TermGenie inhibition of protein targeting to plasma membrane GOC:TermGenie inhibition of protein-plasma membrane targeting GOC:TermGenie down regulation of protein targeting to plasma membrane GOC:TermGenie down regulation of protein-plasma membrane targeting GOC:TermGenie down-regulation of protein targeting to plasma membrane GOC:TermGenie down-regulation of protein-plasma membrane targeting GOC:TermGenie downregulation of protein targeting to plasma membrane GOC:TermGenie downregulation of protein-plasma membrane targeting GOC:TermGenie negative regulation of establishment of protein localisation in plasma membrane GOC:mah negative regulation of protein localisation in plasma membrane GOC:TermGenie negative regulation of protein-plasma membrane targeting GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to plasma membrane. tb 2009-07-10T10:34:17Z GO:0090004 GO:1905965 positive regulation of protein localisation in plasma membrane positive regulation of protein localization in plasma membrane up regulation of protein localisation in plasma membrane up regulation of protein localization in plasma membrane up regulation of protein localization to plasma membrane up-regulation of protein localisation in plasma membrane up-regulation of protein localization in plasma membrane up-regulation of protein localization to plasma membrane upregulation of protein localisation in plasma membrane upregulation of protein localization in plasma membrane upregulation of protein localization to plasma membrane activation of protein localisation in plasma membrane activation of protein localization in plasma membrane activation of protein localization to plasma membrane activation of protein targeting to plasma membrane activation of protein-plasma membrane targeting biological_process positive regulation of establishment of protein localisation in plasma membrane positive regulation of establishment of protein localization to plasma membrane positive regulation of protein targeting to plasma membrane positive regulation of protein-plasma membrane targeting up regulation of protein targeting to plasma membrane up regulation of protein-plasma membrane targeting up-regulation of protein targeting to plasma membrane up-regulation of protein-plasma membrane targeting upregulation of protein targeting to plasma membrane upregulation of protein-plasma membrane targeting GO:1903078 positive regulation of protein localization to plasma membrane Any process that activates or increases the frequency, rate or extent of protein localization to plasma membrane. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:11602640 positive regulation of protein localisation in plasma membrane GOC:TermGenie positive regulation of protein localization in plasma membrane GOC:TermGenie up regulation of protein localisation in plasma membrane GOC:TermGenie up regulation of protein localization in plasma membrane GOC:TermGenie up regulation of protein localization to plasma membrane GOC:TermGenie up-regulation of protein localisation in plasma membrane GOC:TermGenie up-regulation of protein localization in plasma membrane GOC:TermGenie up-regulation of protein localization to plasma membrane GOC:TermGenie upregulation of protein localisation in plasma membrane GOC:TermGenie upregulation of protein localization in plasma membrane GOC:TermGenie upregulation of protein localization to plasma membrane GOC:TermGenie activation of protein localisation in plasma membrane GOC:TermGenie activation of protein localization in plasma membrane GOC:TermGenie activation of protein localization to plasma membrane GOC:TermGenie activation of protein targeting to plasma membrane GOC:TermGenie activation of protein-plasma membrane targeting GOC:TermGenie positive regulation of establishment of protein localisation in plasma membrane GOC:mah positive regulation of protein-plasma membrane targeting GOC:TermGenie up regulation of protein targeting to plasma membrane GOC:TermGenie up regulation of protein-plasma membrane targeting GOC:TermGenie up-regulation of protein targeting to plasma membrane GOC:TermGenie up-regulation of protein-plasma membrane targeting GOC:TermGenie upregulation of protein targeting to plasma membrane GOC:TermGenie upregulation of protein-plasma membrane targeting GOC:TermGenie Any process that modulates the frequency, rate or extent of actin filament-based movement. al 2014-06-12T16:55:57Z biological_process GO:1903115 regulation of actin filament-based movement Any process that modulates the frequency, rate or extent of actin filament-based movement. GOC:TermGenie GO_REF:0000058 PMID:24798735 Any process that activates or increases the frequency, rate or extent of actin filament-based movement. al 2014-06-12T16:56:04Z up regulation of actin filament-based movement up-regulation of actin filament-based movement upregulation of actin filament-based movement activation of actin filament-based movement biological_process GO:1903116 positive regulation of actin filament-based movement Any process that activates or increases the frequency, rate or extent of actin filament-based movement. GOC:TermGenie GO_REF:0000058 PMID:24798735 up regulation of actin filament-based movement GOC:TermGenie up-regulation of actin filament-based movement GOC:TermGenie upregulation of actin filament-based movement GOC:TermGenie activation of actin filament-based movement GOC:TermGenie A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton. mah 2014-06-16T11:27:09Z protein localisation in actin cytoskeleton protein localisation to actin cytoskeleton protein localization in actin cytoskeleton biological_process GO:1903119 protein localization to actin cytoskeleton A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton. GOC:TermGenie GO_REF:0000087 PMID:24798735 protein localisation in actin cytoskeleton GOC:TermGenie protein localisation to actin cytoskeleton GOC:TermGenie protein localization in actin cytoskeleton GOC:TermGenie A process in which a protein is transported to, or maintained in, the location of an actin filament bundle. mah 2014-06-16T11:27:16Z protein localisation in actin filament bundle protein localisation to actin filament bundle protein localization in actin filament bundle biological_process protein localization to actin cable GO:1903120 protein localization to actin filament bundle A process in which a protein is transported to, or maintained in, the location of an actin filament bundle. GOC:TermGenie GO_REF:0000087 PMID:24798735 protein localisation in actin filament bundle GOC:TermGenie protein localisation to actin filament bundle GOC:TermGenie protein localization in actin filament bundle GOC:TermGenie protein localization to actin cable GOC:mah The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. cls 2014-06-25T15:47:09Z biological_process GO:1903131 mononuclear cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. CL:0000842 GOC:TermGenie GO_REF:0000086 PMID:24759906 Any process that modulates the frequency, rate or extent of endodermal cell differentiation. als 2014-07-29T13:22:35Z regulation of endoderm cell differentiation biological_process GO:1903224 regulation of endodermal cell differentiation Any process that modulates the frequency, rate or extent of endodermal cell differentiation. GOC:TermGenie GOC:als GO_REF:0000058 PMID:23154389 regulation of endoderm cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of endodermal cell differentiation. als 2014-07-29T13:22:41Z down regulation of endoderm cell differentiation down regulation of endodermal cell differentiation down-regulation of endoderm cell differentiation down-regulation of endodermal cell differentiation downregulation of endoderm cell differentiation downregulation of endodermal cell differentiation negative regulation of endoderm cell differentiation inhibition of endoderm cell differentiation inhibition of endodermal cell differentiation biological_process GO:1903225 negative regulation of endodermal cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of endodermal cell differentiation. GOC:TermGenie GOC:als GO_REF:0000058 PMID:23154389 down regulation of endoderm cell differentiation GOC:TermGenie down regulation of endodermal cell differentiation GOC:TermGenie down-regulation of endoderm cell differentiation GOC:TermGenie down-regulation of endodermal cell differentiation GOC:TermGenie downregulation of endoderm cell differentiation GOC:TermGenie downregulation of endodermal cell differentiation GOC:TermGenie negative regulation of endoderm cell differentiation GOC:TermGenie inhibition of endoderm cell differentiation GOC:TermGenie inhibition of endodermal cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of endodermal cell differentiation. als 2014-07-29T13:22:47Z positive regulation of endoderm cell differentiation up regulation of endoderm cell differentiation up regulation of endodermal cell differentiation up-regulation of endoderm cell differentiation up-regulation of endodermal cell differentiation upregulation of endoderm cell differentiation upregulation of endodermal cell differentiation activation of endoderm cell differentiation activation of endodermal cell differentiation biological_process GO:1903226 positive regulation of endodermal cell differentiation Any process that activates or increases the frequency, rate or extent of endodermal cell differentiation. GOC:TermGenie GOC:als GO_REF:0000058 PMID:23154389 positive regulation of endoderm cell differentiation GOC:TermGenie up regulation of endoderm cell differentiation GOC:TermGenie up regulation of endodermal cell differentiation GOC:TermGenie up-regulation of endoderm cell differentiation GOC:TermGenie up-regulation of endodermal cell differentiation GOC:TermGenie upregulation of endoderm cell differentiation GOC:TermGenie upregulation of endodermal cell differentiation GOC:TermGenie activation of endoderm cell differentiation GOC:TermGenie activation of endodermal cell differentiation GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a Golgi membrane. mah 2014-08-12T14:22:31Z protein localisation in Golgi membrane protein localisation to Golgi membrane protein localization in Golgi membrane biological_process GO:1903292 protein localization to Golgi membrane A process in which a protein is transported to, or maintained in, a location within a Golgi membrane. GOC:TermGenie GO_REF:0000087 PMID:11378902 protein localisation in Golgi membrane GOC:TermGenie protein localisation to Golgi membrane GOC:TermGenie protein localization in Golgi membrane GOC:TermGenie Any process that modulates the frequency, rate or extent of vacuolar transport. vw 2014-08-18T13:16:04Z biological_process GO:1903335 regulation of vacuolar transport Any process that modulates the frequency, rate or extent of vacuolar transport. GOC:TermGenie GOC:vw GO_REF:0000058 Any process that stops, prevents or reduces the frequency, rate or extent of vacuolar transport. vw 2014-08-18T13:16:11Z down regulation of vacuolar transport down-regulation of vacuolar transport downregulation of vacuolar transport inhibition of vacuolar transport biological_process GO:1903336 negative regulation of vacuolar transport Any process that stops, prevents or reduces the frequency, rate or extent of vacuolar transport. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of vacuolar transport GOC:TermGenie down-regulation of vacuolar transport GOC:TermGenie downregulation of vacuolar transport GOC:TermGenie inhibition of vacuolar transport GOC:TermGenie Any process that activates or increases the frequency, rate or extent of vacuolar transport. vw 2014-08-18T13:16:19Z up regulation of vacuolar transport up-regulation of vacuolar transport upregulation of vacuolar transport activation of vacuolar transport biological_process GO:1903337 positive regulation of vacuolar transport Any process that activates or increases the frequency, rate or extent of vacuolar transport. GOC:TermGenie GOC:vw GO_REF:0000058 up regulation of vacuolar transport GOC:TermGenie up-regulation of vacuolar transport GOC:TermGenie upregulation of vacuolar transport GOC:TermGenie activation of vacuolar transport GOC:TermGenie Any process that modulates the frequency, rate or extent of nucleus organization. hjd 2014-08-20T19:36:16Z regulation of nuclear organisation regulation of nuclear organization biological_process regulation of nuclear morphology regulation of nuclear organization and biogenesis regulation of nucleus organization and biogenesis GO:1903353 regulation of nucleus organization Any process that modulates the frequency, rate or extent of nucleus organization. GOC:TermGenie GO_REF:0000058 PMID:16943282 regulation of nuclear organisation GOC:TermGenie regulation of nuclear organization GOC:TermGenie regulation of nuclear morphology GOC:TermGenie regulation of nuclear organization and biogenesis GOC:TermGenie regulation of nucleus organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of Golgi organization. als 2014-08-21T10:22:22Z regulation of Golgi organisation biological_process regulation of Golgi organization and biogenesis GO:1903358 regulation of Golgi organization Any process that modulates the frequency, rate or extent of Golgi organization. GOC:TermGenie GOC:als GO_REF:0000058 PMID:17562788 regulation of Golgi organisation GOC:TermGenie regulation of Golgi organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of mitotic chromosome condensation. al 2014-08-26T13:57:13Z biological_process GO:1903379 regulation of mitotic chromosome condensation Any process that modulates the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:9490640 Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation. al 2014-08-26T13:57:29Z up regulation of mitotic chromosome condensation up-regulation of mitotic chromosome condensation upregulation of mitotic chromosome condensation activation of mitotic chromosome condensation biological_process GO:1903380 positive regulation of mitotic chromosome condensation Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:9490640 up regulation of mitotic chromosome condensation GOC:TermGenie up-regulation of mitotic chromosome condensation GOC:TermGenie upregulation of mitotic chromosome condensation GOC:TermGenie activation of mitotic chromosome condensation GOC:TermGenie Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bile acid stimulus. rl 2014-09-03T12:45:43Z biological_process GO:1903412 response to bile acid Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bile acid stimulus. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000071 PMID:21757002 Any process that modulates the frequency, rate or extent of cell maturation. jl 2014-09-15T13:31:23Z biological_process regulation of functional differentiation GO:1903429 regulation of cell maturation Any process that modulates the frequency, rate or extent of cell maturation. GOC:TermGenie GO_REF:0000058 PMID:17459944 regulation of functional differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cell maturation. jl 2014-09-15T13:31:32Z down regulation of cell maturation down-regulation of cell maturation downregulation of cell maturation inhibition of cell maturation biological_process down regulation of functional differentiation down-regulation of functional differentiation downregulation of functional differentiation inhibition of functional differentiation negative regulation of functional differentiation GO:1903430 negative regulation of cell maturation Any process that stops, prevents or reduces the frequency, rate or extent of cell maturation. GOC:TermGenie GO_REF:0000058 PMID:17459944 down regulation of cell maturation GOC:TermGenie down-regulation of cell maturation GOC:TermGenie downregulation of cell maturation GOC:TermGenie inhibition of cell maturation GOC:TermGenie down regulation of functional differentiation GOC:TermGenie down-regulation of functional differentiation GOC:TermGenie downregulation of functional differentiation GOC:TermGenie inhibition of functional differentiation GOC:TermGenie negative regulation of functional differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cell maturation. jl 2014-09-15T13:31:41Z up regulation of cell maturation up-regulation of cell maturation upregulation of cell maturation activation of cell maturation biological_process activation of functional differentiation positive regulation of functional differentiation up regulation of functional differentiation up-regulation of functional differentiation upregulation of functional differentiation GO:1903431 positive regulation of cell maturation Any process that activates or increases the frequency, rate or extent of cell maturation. GOC:TermGenie GO_REF:0000058 PMID:17459944 up regulation of cell maturation GOC:TermGenie up-regulation of cell maturation GOC:TermGenie upregulation of cell maturation GOC:TermGenie activation of cell maturation GOC:TermGenie activation of functional differentiation GOC:TermGenie positive regulation of functional differentiation GOC:TermGenie up regulation of functional differentiation GOC:TermGenie up-regulation of functional differentiation GOC:TermGenie upregulation of functional differentiation GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a ciliary membrane. pr 2014-09-16T15:15:39Z protein localisation in ciliary membrane protein localisation to ciliary membrane protein localization in ciliary membrane biological_process GO:1903441 protein localization to ciliary membrane A process in which a protein is transported to, or maintained in, a location within a ciliary membrane. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000087 PMID:22139371 protein localisation in ciliary membrane GOC:TermGenie protein localisation to ciliary membrane GOC:TermGenie protein localization in ciliary membrane GOC:TermGenie The chemical reactions and pathways involving mucopolysaccharide. dph 2014-10-01T21:55:47Z mucopolysaccharide metabolism biological_process GO:1903510 mucopolysaccharide metabolic process The chemical reactions and pathways involving mucopolysaccharide. GOC:TermGenie GOC:dph GO_REF:0000068 PMID:4236091 mucopolysaccharide metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of blood circulation. mr 2014-10-06T18:38:56Z biological_process regulation of hemolymph circulation GO:1903522 regulation of blood circulation Any process that modulates the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 regulation of hemolymph circulation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation. mr 2014-10-06T18:39:05Z down regulation of blood circulation down-regulation of blood circulation downregulation of blood circulation inhibition of blood circulation biological_process down regulation of hemolymph circulation down-regulation of hemolymph circulation downregulation of hemolymph circulation inhibition of hemolymph circulation negative regulation of hemolymph circulation GO:1903523 negative regulation of blood circulation Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 down regulation of blood circulation GOC:TermGenie down-regulation of blood circulation GOC:TermGenie downregulation of blood circulation GOC:TermGenie inhibition of blood circulation GOC:TermGenie down regulation of hemolymph circulation GOC:TermGenie down-regulation of hemolymph circulation GOC:TermGenie downregulation of hemolymph circulation GOC:TermGenie inhibition of hemolymph circulation GOC:TermGenie negative regulation of hemolymph circulation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of blood circulation. mr 2014-10-06T18:39:13Z up regulation of blood circulation up-regulation of blood circulation upregulation of blood circulation activation of blood circulation biological_process activation of hemolymph circulation positive regulation of hemolymph circulation up regulation of hemolymph circulation up-regulation of hemolymph circulation upregulation of hemolymph circulation GO:1903524 positive regulation of blood circulation Any process that activates or increases the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 up regulation of blood circulation GOC:TermGenie up-regulation of blood circulation GOC:TermGenie upregulation of blood circulation GOC:TermGenie activation of blood circulation GOC:TermGenie activation of hemolymph circulation GOC:TermGenie positive regulation of hemolymph circulation GOC:TermGenie up regulation of hemolymph circulation GOC:TermGenie up-regulation of hemolymph circulation GOC:TermGenie upregulation of hemolymph circulation GOC:TermGenie Any process that modulates the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:24:59Z regulation of cellular secretion biological_process GO:1903530 regulation of secretion by cell Any process that modulates the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 regulation of cellular secretion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:25:08Z down regulation of cellular secretion down regulation of secretion by cell down-regulation of cellular secretion down-regulation of secretion by cell downregulation of cellular secretion downregulation of secretion by cell negative regulation of cellular secretion inhibition of cellular secretion inhibition of secretion by cell biological_process GO:1903531 negative regulation of secretion by cell Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 down regulation of cellular secretion GOC:TermGenie down regulation of secretion by cell GOC:TermGenie down-regulation of cellular secretion GOC:TermGenie down-regulation of secretion by cell GOC:TermGenie downregulation of cellular secretion GOC:TermGenie downregulation of secretion by cell GOC:TermGenie negative regulation of cellular secretion GOC:TermGenie inhibition of cellular secretion GOC:TermGenie inhibition of secretion by cell GOC:TermGenie Any process that activates or increases the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:25:17Z positive regulation of cellular secretion up regulation of cellular secretion up regulation of secretion by cell up-regulation of cellular secretion up-regulation of secretion by cell upregulation of cellular secretion upregulation of secretion by cell activation of cellular secretion activation of secretion by cell biological_process GO:1903532 positive regulation of secretion by cell Any process that activates or increases the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 positive regulation of cellular secretion GOC:TermGenie up regulation of cellular secretion GOC:TermGenie up regulation of secretion by cell GOC:TermGenie up-regulation of cellular secretion GOC:TermGenie up-regulation of secretion by cell GOC:TermGenie upregulation of cellular secretion GOC:TermGenie upregulation of secretion by cell GOC:TermGenie activation of cellular secretion GOC:TermGenie activation of secretion by cell GOC:TermGenie Any meiotic cell cycle process that is involved in oocyte maturation. pr 2014-10-09T10:46:14Z meiosis involved in oocyte maturation biological_process GO:1903537 meiotic cell cycle process involved in oocyte maturation Any meiotic cell cycle process that is involved in oocyte maturation. GOC:TermGenie GOC:jz GO_REF:0000060 PMID:25212395 Any process that modulates the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation. pr 2014-10-09T10:52:38Z regulation of meiosis involved in oocyte maturation biological_process GO:1903538 regulation of meiotic cell cycle process involved in oocyte maturation Any process that modulates the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation. GOC:TermGenie GOC:jz GO_REF:0000058 PMID:25212395 regulation of meiosis involved in oocyte maturation GOC:TermGenie Any process that modulates the frequency, rate or extent of exosomal secretion. pga 2014-10-14T11:38:52Z regulation of exosomal secretory pathway regulation of extracellular vesicular exosome secretion regulation of secretion of exosome regulation of exosomal protein secretion biological_process GO:1903541 regulation of exosomal secretion Any process that modulates the frequency, rate or extent of exosomal secretion. GOC:TermGenie GO_REF:0000058 PMID:24105262 regulation of exosomal secretory pathway GOC:TermGenie regulation of extracellular vesicular exosome secretion GOC:TermGenie regulation of secretion of exosome GOC:TermGenie regulation of exosomal protein secretion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of exosomal secretion. pga 2014-10-14T11:39:02Z down regulation of exosomal secretion down regulation of exosomal secretory pathway down regulation of extracellular vesicular exosome secretion down regulation of secretion of exosome down-regulation of exosomal secretion down-regulation of exosomal secretory pathway down-regulation of extracellular vesicular exosome secretion down-regulation of secretion of exosome downregulation of exosomal secretion downregulation of exosomal secretory pathway downregulation of extracellular vesicular exosome secretion downregulation of secretion of exosome negative regulation of exosomal secretory pathway negative regulation of extracellular vesicular exosome secretion negative regulation of secretion of exosome down regulation of exosomal protein secretion down-regulation of exosomal protein secretion downregulation of exosomal protein secretion inhibition of exosomal protein secretion inhibition of exosomal secretion inhibition of exosomal secretory pathway inhibition of extracellular vesicular exosome secretion inhibition of secretion of exosome negative regulation of exosomal protein secretion biological_process GO:1903542 negative regulation of exosomal secretion Any process that stops, prevents or reduces the frequency, rate or extent of exosomal secretion. GOC:TermGenie GO_REF:0000058 PMID:24105262 down regulation of exosomal secretion GOC:TermGenie down regulation of exosomal secretory pathway GOC:TermGenie down regulation of extracellular vesicular exosome secretion GOC:TermGenie down regulation of secretion of exosome GOC:TermGenie down-regulation of exosomal secretion GOC:TermGenie down-regulation of exosomal secretory pathway GOC:TermGenie down-regulation of extracellular vesicular exosome secretion GOC:TermGenie down-regulation of secretion of exosome GOC:TermGenie downregulation of exosomal secretion GOC:TermGenie downregulation of exosomal secretory pathway GOC:TermGenie downregulation of extracellular vesicular exosome secretion GOC:TermGenie downregulation of secretion of exosome GOC:TermGenie negative regulation of exosomal secretory pathway GOC:TermGenie negative regulation of extracellular vesicular exosome secretion GOC:TermGenie negative regulation of secretion of exosome GOC:TermGenie down regulation of exosomal protein secretion GOC:TermGenie down-regulation of exosomal protein secretion GOC:TermGenie downregulation of exosomal protein secretion GOC:TermGenie inhibition of exosomal protein secretion GOC:TermGenie inhibition of exosomal secretion GOC:TermGenie inhibition of exosomal secretory pathway GOC:TermGenie inhibition of extracellular vesicular exosome secretion GOC:TermGenie inhibition of secretion of exosome GOC:TermGenie negative regulation of exosomal protein secretion GOC:TermGenie Any process that activates or increases the frequency, rate or extent of exosomal secretion. pga 2014-10-14T11:39:10Z positive regulation of exosomal secretory pathway positive regulation of extracellular vesicular exosome secretion positive regulation of secretion of exosome up regulation of exosomal secretion up regulation of exosomal secretory pathway up regulation of extracellular vesicular exosome secretion up regulation of secretion of exosome up-regulation of exosomal secretion up-regulation of exosomal secretory pathway up-regulation of extracellular vesicular exosome secretion up-regulation of secretion of exosome upregulation of exosomal secretion upregulation of exosomal secretory pathway upregulation of extracellular vesicular exosome secretion upregulation of secretion of exosome activation of exosomal protein secretion activation of exosomal secretion activation of exosomal secretory pathway activation of extracellular vesicular exosome secretion activation of secretion of exosome positive regulation of exosomal protein secretion up regulation of exosomal protein secretion up-regulation of exosomal protein secretion upregulation of exosomal protein secretion biological_process GO:1903543 positive regulation of exosomal secretion Any process that activates or increases the frequency, rate or extent of exosomal secretion. GOC:TermGenie GO_REF:0000058 PMID:24105262 positive regulation of exosomal secretory pathway GOC:TermGenie positive regulation of extracellular vesicular exosome secretion GOC:TermGenie positive regulation of secretion of exosome GOC:TermGenie up regulation of exosomal secretion GOC:TermGenie up regulation of exosomal secretory pathway GOC:TermGenie up regulation of extracellular vesicular exosome secretion GOC:TermGenie up regulation of secretion of exosome GOC:TermGenie up-regulation of exosomal secretion GOC:TermGenie up-regulation of exosomal secretory pathway GOC:TermGenie up-regulation of extracellular vesicular exosome secretion GOC:TermGenie up-regulation of secretion of exosome GOC:TermGenie upregulation of exosomal secretion GOC:TermGenie upregulation of exosomal secretory pathway GOC:TermGenie upregulation of extracellular vesicular exosome secretion GOC:TermGenie upregulation of secretion of exosome GOC:TermGenie activation of exosomal protein secretion GOC:TermGenie activation of exosomal secretion GOC:TermGenie activation of exosomal secretory pathway GOC:TermGenie activation of extracellular vesicular exosome secretion GOC:TermGenie activation of secretion of exosome GOC:TermGenie positive regulation of exosomal protein secretion GOC:TermGenie up regulation of exosomal protein secretion GOC:TermGenie up-regulation of exosomal protein secretion GOC:TermGenie upregulation of exosomal protein secretion GOC:TermGenie Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:25Z regulation of extracellular vesicular exosome assembly biological_process GO:1903551 regulation of extracellular exosome assembly Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 regulation of extracellular vesicular exosome assembly GOC:vesicles Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:33Z down regulation of extracellular vesicular exosome assembly down-regulation of extracellular vesicular exosome assembly downregulation of extracellular vesicular exosome assembly negative regulation of extracellular vesicular exosome assembly inhibition of extracellular vesicular exosome assembly biological_process GO:1903552 negative regulation of extracellular exosome assembly Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 down regulation of extracellular vesicular exosome assembly GOC:TermGenie down-regulation of extracellular vesicular exosome assembly GOC:TermGenie downregulation of extracellular vesicular exosome assembly GOC:TermGenie negative regulation of extracellular vesicular exosome assembly GOC:vesicles inhibition of extracellular vesicular exosome assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:42Z up regulation of extracellular vesicular exosome assembly up-regulation of extracellular vesicular exosome assembly upregulation of extracellular vesicular exosome assembly activation of extracellular vesicular exosome assembly biological_process positive regulation of extracellular vesicular exosome assembly GO:1903553 positive regulation of extracellular exosome assembly Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 up regulation of extracellular vesicular exosome assembly GOC:TermGenie up-regulation of extracellular vesicular exosome assembly GOC:TermGenie upregulation of extracellular vesicular exosome assembly GOC:TermGenie activation of extracellular vesicular exosome assembly GOC:TermGenie positive regulation of extracellular vesicular exosome assembly GOC:vesicles Any vesicle that is part of the extracellular region. jl 2014-10-22T14:26:11Z cellular_component microparticle GO:1903561 extracellular vesicle Any vesicle that is part of the extracellular region. GOC:TermGenie GOC:pm GO_REF:0000064 PMID:24769233 microparticle GOC:vesicles Any process that modulates the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:11Z biological_process GO:1903564 regulation of protein localization to cilium Any process that modulates the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:20Z down regulation of protein localization to cilium down-regulation of protein localization to cilium downregulation of protein localization to cilium inhibition of protein localization to cilium biological_process GO:1903565 negative regulation of protein localization to cilium Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 down regulation of protein localization to cilium GOC:TermGenie down-regulation of protein localization to cilium GOC:TermGenie downregulation of protein localization to cilium GOC:TermGenie inhibition of protein localization to cilium GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:28Z up regulation of protein localization to cilium up-regulation of protein localization to cilium upregulation of protein localization to cilium activation of protein localization to cilium biological_process GO:1903566 positive regulation of protein localization to cilium Any process that activates or increases the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 up regulation of protein localization to cilium GOC:TermGenie up-regulation of protein localization to cilium GOC:TermGenie upregulation of protein localization to cilium GOC:TermGenie activation of protein localization to cilium GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to ciliary membrane. krc 2014-10-24T21:32:51Z regulation of protein localisation in ciliary membrane regulation of protein localisation to ciliary membrane regulation of protein localization in ciliary membrane biological_process GO:1903567 regulation of protein localization to ciliary membrane Any process that modulates the frequency, rate or extent of protein localization to ciliary membrane. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 regulation of protein localisation in ciliary membrane GOC:TermGenie regulation of protein localisation to ciliary membrane GOC:TermGenie regulation of protein localization in ciliary membrane GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to ciliary membrane. krc 2014-10-24T21:32:59Z down regulation of protein localisation in ciliary membrane down regulation of protein localisation to ciliary membrane down regulation of protein localization in ciliary membrane down regulation of protein localization to ciliary membrane down-regulation of protein localisation in ciliary membrane down-regulation of protein localisation to ciliary membrane down-regulation of protein localization in ciliary membrane down-regulation of protein localization to ciliary membrane downregulation of protein localisation in ciliary membrane downregulation of protein localisation to ciliary membrane downregulation of protein localization in ciliary membrane downregulation of protein localization to ciliary membrane negative regulation of protein localisation in ciliary membrane negative regulation of protein localisation to ciliary membrane negative regulation of protein localization in ciliary membrane inhibition of protein localisation in ciliary membrane inhibition of protein localisation to ciliary membrane inhibition of protein localization in ciliary membrane inhibition of protein localization to ciliary membrane biological_process GO:1903568 negative regulation of protein localization to ciliary membrane Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to ciliary membrane. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 down regulation of protein localisation in ciliary membrane GOC:TermGenie down regulation of protein localisation to ciliary membrane GOC:TermGenie down regulation of protein localization in ciliary membrane GOC:TermGenie down regulation of protein localization to ciliary membrane GOC:TermGenie down-regulation of protein localisation in ciliary membrane GOC:TermGenie down-regulation of protein localisation to ciliary membrane GOC:TermGenie down-regulation of protein localization in ciliary membrane GOC:TermGenie down-regulation of protein localization to ciliary membrane GOC:TermGenie downregulation of protein localisation in ciliary membrane GOC:TermGenie downregulation of protein localisation to ciliary membrane GOC:TermGenie downregulation of protein localization in ciliary membrane GOC:TermGenie downregulation of protein localization to ciliary membrane GOC:TermGenie negative regulation of protein localisation in ciliary membrane GOC:TermGenie negative regulation of protein localisation to ciliary membrane GOC:TermGenie negative regulation of protein localization in ciliary membrane GOC:TermGenie inhibition of protein localisation in ciliary membrane GOC:TermGenie inhibition of protein localisation to ciliary membrane GOC:TermGenie inhibition of protein localization in ciliary membrane GOC:TermGenie inhibition of protein localization to ciliary membrane GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to ciliary membrane. krc 2014-10-24T21:33:08Z positive regulation of protein localisation in ciliary membrane positive regulation of protein localisation to ciliary membrane positive regulation of protein localization in ciliary membrane up regulation of protein localisation in ciliary membrane up regulation of protein localisation to ciliary membrane up regulation of protein localization in ciliary membrane up regulation of protein localization to ciliary membrane up-regulation of protein localisation in ciliary membrane up-regulation of protein localisation to ciliary membrane up-regulation of protein localization in ciliary membrane up-regulation of protein localization to ciliary membrane upregulation of protein localisation in ciliary membrane upregulation of protein localisation to ciliary membrane upregulation of protein localization in ciliary membrane upregulation of protein localization to ciliary membrane activation of protein localisation in ciliary membrane activation of protein localisation to ciliary membrane activation of protein localization in ciliary membrane activation of protein localization to ciliary membrane biological_process GO:1903569 positive regulation of protein localization to ciliary membrane Any process that activates or increases the frequency, rate or extent of protein localization to ciliary membrane. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 positive regulation of protein localisation in ciliary membrane GOC:TermGenie positive regulation of protein localisation to ciliary membrane GOC:TermGenie positive regulation of protein localization in ciliary membrane GOC:TermGenie up regulation of protein localisation in ciliary membrane GOC:TermGenie up regulation of protein localisation to ciliary membrane GOC:TermGenie up regulation of protein localization in ciliary membrane GOC:TermGenie up regulation of protein localization to ciliary membrane GOC:TermGenie up-regulation of protein localisation in ciliary membrane GOC:TermGenie up-regulation of protein localisation to ciliary membrane GOC:TermGenie up-regulation of protein localization in ciliary membrane GOC:TermGenie up-regulation of protein localization to ciliary membrane GOC:TermGenie upregulation of protein localisation in ciliary membrane GOC:TermGenie upregulation of protein localisation to ciliary membrane GOC:TermGenie upregulation of protein localization in ciliary membrane GOC:TermGenie upregulation of protein localization to ciliary membrane GOC:TermGenie activation of protein localisation in ciliary membrane GOC:TermGenie activation of protein localisation to ciliary membrane GOC:TermGenie activation of protein localization in ciliary membrane GOC:TermGenie activation of protein localization to ciliary membrane GOC:TermGenie Any process that modulates the frequency, rate or extent of DNA catabolic process. sl 2014-11-19T22:36:35Z regulation of DNA breakdown regulation of DNA catabolism regulation of DNA degradation biological_process GO:1903624 regulation of DNA catabolic process Any process that modulates the frequency, rate or extent of DNA catabolic process. GOC:TermGenie GO_REF:0000058 PMID:2001740 regulation of DNA breakdown GOC:TermGenie regulation of DNA catabolism GOC:TermGenie regulation of DNA degradation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process. sl 2014-11-19T22:36:43Z down regulation of DNA breakdown down regulation of DNA catabolic process down regulation of DNA catabolism down regulation of DNA degradation down-regulation of DNA breakdown down-regulation of DNA catabolic process down-regulation of DNA catabolism down-regulation of DNA degradation downregulation of DNA breakdown downregulation of DNA catabolic process downregulation of DNA catabolism downregulation of DNA degradation negative regulation of DNA breakdown negative regulation of DNA catabolism negative regulation of DNA degradation inhibition of DNA breakdown inhibition of DNA catabolic process inhibition of DNA catabolism inhibition of DNA degradation biological_process GO:1903625 negative regulation of DNA catabolic process Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process. GOC:TermGenie GO_REF:0000058 PMID:2001740 down regulation of DNA breakdown GOC:TermGenie down regulation of DNA catabolic process GOC:TermGenie down regulation of DNA catabolism GOC:TermGenie down regulation of DNA degradation GOC:TermGenie down-regulation of DNA breakdown GOC:TermGenie down-regulation of DNA catabolic process GOC:TermGenie down-regulation of DNA catabolism GOC:TermGenie down-regulation of DNA degradation GOC:TermGenie downregulation of DNA breakdown GOC:TermGenie downregulation of DNA catabolic process GOC:TermGenie downregulation of DNA catabolism GOC:TermGenie downregulation of DNA degradation GOC:TermGenie negative regulation of DNA breakdown GOC:TermGenie negative regulation of DNA catabolism GOC:TermGenie negative regulation of DNA degradation GOC:TermGenie inhibition of DNA breakdown GOC:TermGenie inhibition of DNA catabolic process GOC:TermGenie inhibition of DNA catabolism GOC:TermGenie inhibition of DNA degradation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of DNA catabolic process. sl 2014-11-19T22:36:51Z positive regulation of DNA breakdown positive regulation of DNA catabolism positive regulation of DNA degradation up regulation of DNA breakdown up regulation of DNA catabolic process up regulation of DNA catabolism up regulation of DNA degradation up-regulation of DNA breakdown up-regulation of DNA catabolic process up-regulation of DNA catabolism up-regulation of DNA degradation upregulation of DNA breakdown upregulation of DNA catabolic process upregulation of DNA catabolism upregulation of DNA degradation activation of DNA breakdown activation of DNA catabolic process activation of DNA catabolism activation of DNA degradation biological_process GO:1903626 positive regulation of DNA catabolic process Any process that activates or increases the frequency, rate or extent of DNA catabolic process. GOC:TermGenie GO_REF:0000058 PMID:2001740 positive regulation of DNA breakdown GOC:TermGenie positive regulation of DNA catabolism GOC:TermGenie positive regulation of DNA degradation GOC:TermGenie up regulation of DNA breakdown GOC:TermGenie up regulation of DNA catabolic process GOC:TermGenie up regulation of DNA catabolism GOC:TermGenie up regulation of DNA degradation GOC:TermGenie up-regulation of DNA breakdown GOC:TermGenie up-regulation of DNA catabolic process GOC:TermGenie up-regulation of DNA catabolism GOC:TermGenie up-regulation of DNA degradation GOC:TermGenie upregulation of DNA breakdown GOC:TermGenie upregulation of DNA catabolic process GOC:TermGenie upregulation of DNA catabolism GOC:TermGenie upregulation of DNA degradation GOC:TermGenie activation of DNA breakdown GOC:TermGenie activation of DNA catabolic process GOC:TermGenie activation of DNA catabolism GOC:TermGenie activation of DNA degradation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of microvillus assembly. als 2014-12-03T11:45:08Z down regulation of microvillus assembly down-regulation of microvillus assembly downregulation of microvillus assembly inhibition of microvillus assembly biological_process down regulation of microvillus biogenesis down-regulation of microvillus biogenesis downregulation of microvillus biogenesis inhibition of microvillus biogenesis negative regulation of microvillus biogenesis GO:1903697 negative regulation of microvillus assembly Any process that stops, prevents or reduces the frequency, rate or extent of microvillus assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:22797597 down regulation of microvillus assembly GOC:TermGenie down-regulation of microvillus assembly GOC:TermGenie downregulation of microvillus assembly GOC:TermGenie inhibition of microvillus assembly GOC:TermGenie down regulation of microvillus biogenesis GOC:TermGenie down-regulation of microvillus biogenesis GOC:TermGenie downregulation of microvillus biogenesis GOC:TermGenie inhibition of microvillus biogenesis GOC:TermGenie negative regulation of microvillus biogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of microvillus assembly. als 2014-12-03T11:45:17Z up regulation of microvillus assembly up-regulation of microvillus assembly upregulation of microvillus assembly activation of microvillus assembly biological_process activation of microvillus biogenesis positive regulation of microvillus biogenesis up regulation of microvillus biogenesis up-regulation of microvillus biogenesis upregulation of microvillus biogenesis GO:1903698 positive regulation of microvillus assembly Any process that activates or increases the frequency, rate or extent of microvillus assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:22797597 up regulation of microvillus assembly GOC:TermGenie up-regulation of microvillus assembly GOC:TermGenie upregulation of microvillus assembly GOC:TermGenie activation of microvillus assembly GOC:TermGenie activation of microvillus biogenesis GOC:TermGenie positive regulation of microvillus biogenesis GOC:TermGenie up regulation of microvillus biogenesis GOC:TermGenie up-regulation of microvillus biogenesis GOC:TermGenie upregulation of microvillus biogenesis GOC:TermGenie The process whose specific outcome is the progression of a substantia propria of cornea over time, from its formation to the mature structure. cls 2014-12-03T13:12:09Z corneal stroma development stroma of cornea development biological_process substantia propria development GO:1903701 substantia propria of cornea development The process whose specific outcome is the progression of a substantia propria of cornea over time, from its formation to the mature structure. GOC:TermGenie GO_REF:0000094 PMID:12556382 corneal stroma development GOC:TermGenie stroma of cornea development GOC:TermGenie substantia propria development GOC:TermGenie The process whose specific outcome is the progression of an esophagus over time, from its formation to the mature structure. cls 2014-12-03T14:41:30Z esophageal development gullet development oesophagus development biological_process GO:1903702 esophagus development The process whose specific outcome is the progression of an esophagus over time, from its formation to the mature structure. GOC:TermGenie GO_REF:0000094 ISBN:0-683-40008-8 esophageal development MGI:csmith gullet development GOC:TermGenie oesophagus development GOC:TermGenie Any process that modulates the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:13Z regulation of blood cell biosynthesis regulation of blood cell formation regulation of haemopoiesis regulation of hematopoiesis biological_process GO:1903706 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. regulation of hemopoiesis Any process that modulates the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 regulation of blood cell biosynthesis GOC:TermGenie regulation of blood cell formation GOC:TermGenie regulation of haemopoiesis GOC:TermGenie regulation of hematopoiesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:21Z down regulation of blood cell biosynthesis down regulation of blood cell formation down regulation of haemopoiesis down regulation of hematopoiesis down regulation of hemopoiesis down-regulation of blood cell biosynthesis down-regulation of blood cell formation down-regulation of haemopoiesis down-regulation of hematopoiesis down-regulation of hemopoiesis downregulation of blood cell biosynthesis downregulation of blood cell formation downregulation of haemopoiesis downregulation of hematopoiesis downregulation of hemopoiesis negative regulation of blood cell biosynthesis negative regulation of blood cell formation negative regulation of haemopoiesis negative regulation of hematopoiesis inhibition of blood cell biosynthesis inhibition of blood cell formation inhibition of haemopoiesis inhibition of hematopoiesis inhibition of hemopoiesis biological_process GO:1903707 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. negative regulation of hemopoiesis Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 down regulation of blood cell biosynthesis GOC:TermGenie down regulation of blood cell formation GOC:TermGenie down regulation of haemopoiesis GOC:TermGenie down regulation of hematopoiesis GOC:TermGenie down regulation of hemopoiesis GOC:TermGenie down-regulation of blood cell biosynthesis GOC:TermGenie down-regulation of blood cell formation GOC:TermGenie down-regulation of haemopoiesis GOC:TermGenie down-regulation of hematopoiesis GOC:TermGenie down-regulation of hemopoiesis GOC:TermGenie downregulation of blood cell biosynthesis GOC:TermGenie downregulation of blood cell formation GOC:TermGenie downregulation of haemopoiesis GOC:TermGenie downregulation of hematopoiesis GOC:TermGenie downregulation of hemopoiesis GOC:TermGenie negative regulation of blood cell biosynthesis GOC:TermGenie negative regulation of blood cell formation GOC:TermGenie negative regulation of haemopoiesis GOC:TermGenie negative regulation of hematopoiesis GOC:TermGenie inhibition of blood cell biosynthesis GOC:TermGenie inhibition of blood cell formation GOC:TermGenie inhibition of haemopoiesis GOC:TermGenie inhibition of hematopoiesis GOC:TermGenie inhibition of hemopoiesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:30Z positive regulation of blood cell biosynthesis positive regulation of blood cell formation positive regulation of haemopoiesis positive regulation of hematopoiesis up regulation of blood cell biosynthesis up regulation of blood cell formation up regulation of haemopoiesis up regulation of hematopoiesis up regulation of hemopoiesis up-regulation of blood cell biosynthesis up-regulation of blood cell formation up-regulation of haemopoiesis up-regulation of hematopoiesis up-regulation of hemopoiesis upregulation of blood cell biosynthesis upregulation of blood cell formation upregulation of haemopoiesis upregulation of hematopoiesis upregulation of hemopoiesis activation of blood cell biosynthesis activation of blood cell formation activation of haemopoiesis activation of hematopoiesis activation of hemopoiesis biological_process GO:1903708 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. positive regulation of hemopoiesis Any process that activates or increases the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 positive regulation of blood cell biosynthesis GOC:TermGenie positive regulation of blood cell formation GOC:TermGenie positive regulation of haemopoiesis GOC:TermGenie positive regulation of hematopoiesis GOC:TermGenie up regulation of blood cell biosynthesis GOC:TermGenie up regulation of blood cell formation GOC:TermGenie up regulation of haemopoiesis GOC:TermGenie up regulation of hematopoiesis GOC:TermGenie up regulation of hemopoiesis GOC:TermGenie up-regulation of blood cell biosynthesis GOC:TermGenie up-regulation of blood cell formation GOC:TermGenie up-regulation of haemopoiesis GOC:TermGenie up-regulation of hematopoiesis GOC:TermGenie up-regulation of hemopoiesis GOC:TermGenie upregulation of blood cell biosynthesis GOC:TermGenie upregulation of blood cell formation GOC:TermGenie upregulation of haemopoiesis GOC:TermGenie upregulation of hematopoiesis GOC:TermGenie upregulation of hemopoiesis GOC:TermGenie activation of blood cell biosynthesis GOC:TermGenie activation of blood cell formation GOC:TermGenie activation of haemopoiesis GOC:TermGenie activation of hematopoiesis GOC:TermGenie activation of hemopoiesis GOC:TermGenie Any process that modulates the frequency, rate or extent of plasma membrane organization. al 2014-12-10T18:59:44Z regulation of plasma membrane organisation biological_process regulation of plasma membrane organization and biogenesis GO:1903729 regulation of plasma membrane organization Any process that modulates the frequency, rate or extent of plasma membrane organization. GOC:TermGenie GO_REF:0000058 PMID:24514900 regulation of plasma membrane organisation GOC:TermGenie regulation of plasma membrane organization and biogenesis GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane. mah 2015-01-07T13:15:54Z protein localisation in vacuolar membrane protein localisation to vacuolar membrane protein localization in vacuolar membrane biological_process GO:1903778 protein localization to vacuolar membrane A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane. GOC:TermGenie GO_REF:0000087 PMID:25378562 protein localisation in vacuolar membrane GOC:TermGenie protein localisation to vacuolar membrane GOC:TermGenie protein localization in vacuolar membrane GOC:TermGenie Any process that modulates the frequency, rate or extent of cardiac conduction. rph 2015-01-07T13:20:11Z biological_process GO:1903779 regulation of cardiac conduction Any process that modulates the frequency, rate or extent of cardiac conduction. GOC:BHF GOC:TermGenie GOC:mtg_cardiac_conduct_nov11 GOC:rph GO_REF:0000058 PMID:12967627 Any process that stops, prevents or reduces the frequency, rate or extent of cardiac conduction. rph 2015-01-07T13:20:20Z down regulation of cardiac conduction down-regulation of cardiac conduction downregulation of cardiac conduction inhibition of cardiac conduction biological_process GO:1903780 negative regulation of cardiac conduction Any process that stops, prevents or reduces the frequency, rate or extent of cardiac conduction. GOC:BHF GOC:TermGenie GOC:mtg_cardiac_conduct_nov11 GOC:rph GO_REF:0000058 PMID:12967627 down regulation of cardiac conduction GOC:TermGenie down-regulation of cardiac conduction GOC:TermGenie downregulation of cardiac conduction GOC:TermGenie inhibition of cardiac conduction GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cardiac conduction. rph 2015-01-07T13:20:28Z up regulation of cardiac conduction up-regulation of cardiac conduction upregulation of cardiac conduction activation of cardiac conduction biological_process GO:1903781 positive regulation of cardiac conduction Any process that activates or increases the frequency, rate or extent of cardiac conduction. GOC:BHF GOC:TermGenie GOC:mtg_cardiac_conduct_nov11 GOC:rph GO_REF:0000058 PMID:12967627 up regulation of cardiac conduction GOC:TermGenie up-regulation of cardiac conduction GOC:TermGenie upregulation of cardiac conduction GOC:TermGenie activation of cardiac conduction GOC:TermGenie Any process that modulates the frequency, rate or extent of amino acid transmembrane transport. al 2015-01-08T17:42:18Z regulation of amino acid membrane transport biological_process GO:1903789 regulation of amino acid transmembrane transport Any process that modulates the frequency, rate or extent of amino acid transmembrane transport. GOC:TermGenie GO_REF:0000058 PMID:16115814 regulation of amino acid membrane transport GOC:TermGenie Any process that modulates the frequency, rate or extent of inorganic anion transmembrane transport. sl 2015-01-14T21:44:49Z regulation of inorganic anion membrane transport regulation of transmembrane inorganic anion transport biological_process GO:1903795 regulation of inorganic anion transmembrane transport Any process that modulates the frequency, rate or extent of inorganic anion transmembrane transport. GOC:TermGenie GO_REF:0000058 PMID:11336802 regulation of inorganic anion membrane transport GOC:TermGenie regulation of transmembrane inorganic anion transport GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of inorganic anion transmembrane transport. sl 2015-01-14T21:44:59Z down regulation of inorganic anion membrane transport down regulation of inorganic anion transmembrane transport down regulation of transmembrane inorganic anion transport down-regulation of inorganic anion membrane transport down-regulation of inorganic anion transmembrane transport down-regulation of transmembrane inorganic anion transport downregulation of inorganic anion membrane transport downregulation of inorganic anion transmembrane transport downregulation of transmembrane inorganic anion transport negative regulation of inorganic anion membrane transport negative regulation of transmembrane inorganic anion transport inhibition of inorganic anion membrane transport inhibition of inorganic anion transmembrane transport inhibition of transmembrane inorganic anion transport biological_process GO:1903796 negative regulation of inorganic anion transmembrane transport Any process that stops, prevents or reduces the frequency, rate or extent of inorganic anion transmembrane transport. GOC:TermGenie GO_REF:0000058 PMID:11336802 down regulation of inorganic anion membrane transport GOC:TermGenie down regulation of inorganic anion transmembrane transport GOC:TermGenie down regulation of transmembrane inorganic anion transport GOC:TermGenie down-regulation of inorganic anion membrane transport GOC:TermGenie down-regulation of inorganic anion transmembrane transport GOC:TermGenie down-regulation of transmembrane inorganic anion transport GOC:TermGenie downregulation of inorganic anion membrane transport GOC:TermGenie downregulation of inorganic anion transmembrane transport GOC:TermGenie downregulation of transmembrane inorganic anion transport GOC:TermGenie negative regulation of inorganic anion membrane transport GOC:TermGenie negative regulation of transmembrane inorganic anion transport GOC:TermGenie inhibition of inorganic anion membrane transport GOC:TermGenie inhibition of inorganic anion transmembrane transport GOC:TermGenie inhibition of transmembrane inorganic anion transport GOC:TermGenie Any process that activates or increases the frequency, rate or extent of inorganic anion transmembrane transport. sl 2015-01-14T21:45:08Z positive regulation of inorganic anion membrane transport positive regulation of transmembrane inorganic anion transport up regulation of inorganic anion membrane transport up regulation of inorganic anion transmembrane transport up regulation of transmembrane inorganic anion transport up-regulation of inorganic anion membrane transport up-regulation of inorganic anion transmembrane transport up-regulation of transmembrane inorganic anion transport upregulation of inorganic anion membrane transport upregulation of inorganic anion transmembrane transport upregulation of transmembrane inorganic anion transport activation of inorganic anion membrane transport activation of inorganic anion transmembrane transport activation of transmembrane inorganic anion transport biological_process GO:1903797 positive regulation of inorganic anion transmembrane transport Any process that activates or increases the frequency, rate or extent of inorganic anion transmembrane transport. GOC:TermGenie GO_REF:0000058 PMID:11336802 positive regulation of inorganic anion membrane transport GOC:TermGenie positive regulation of transmembrane inorganic anion transport GOC:TermGenie up regulation of inorganic anion membrane transport GOC:TermGenie up regulation of inorganic anion transmembrane transport GOC:TermGenie up regulation of transmembrane inorganic anion transport GOC:TermGenie up-regulation of inorganic anion membrane transport GOC:TermGenie up-regulation of inorganic anion transmembrane transport GOC:TermGenie up-regulation of transmembrane inorganic anion transport GOC:TermGenie upregulation of inorganic anion membrane transport GOC:TermGenie upregulation of inorganic anion transmembrane transport GOC:TermGenie upregulation of transmembrane inorganic anion transport GOC:TermGenie activation of inorganic anion membrane transport GOC:TermGenie activation of inorganic anion transmembrane transport GOC:TermGenie activation of transmembrane inorganic anion transport GOC:TermGenie The process in which an organic acid is transported across a membrane. vw 2015-01-20T10:20:58Z biological_process GO:1903825 organic acid transmembrane transport The process in which an organic acid is transported across a membrane. GOC:TermGenie GO_REF:0000069 Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:24Z down regulation of cellular protein localisation down regulation of cellular protein localization down-regulation of cellular protein localisation down-regulation of cellular protein localization downregulation of cellular protein localisation downregulation of cellular protein localization negative regulation of cellular protein localisation negative regulation of cellular protein localization inhibition of cellular protein localisation inhibition of cellular protein localization biological_process GO:1903828 negative regulation of protein localization Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of cellular protein localisation GOC:TermGenie down regulation of cellular protein localization GOC:TermGenie down-regulation of cellular protein localisation GOC:TermGenie down-regulation of cellular protein localization GOC:TermGenie downregulation of cellular protein localisation GOC:TermGenie downregulation of cellular protein localization GOC:TermGenie negative regulation of cellular protein localisation GOC:TermGenie inhibition of cellular protein localisation GOC:TermGenie inhibition of cellular protein localization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of a protein localization. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:33Z positive regulation of cellular protein localisation positive regulation of cellular protein localization up regulation of cellular protein localisation up regulation of cellular protein localization up-regulation of cellular protein localisation up-regulation of cellular protein localization upregulation of cellular protein localisation upregulation of cellular protein localization biological_process GO:1903829 positive regulation of protein localization Any process that activates or increases the frequency, rate or extent of a protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 positive regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localization GOC:TermGenie up-regulation of cellular protein localisation GOC:TermGenie up-regulation of cellular protein localization GOC:TermGenie upregulation of cellular protein localisation GOC:TermGenie upregulation of cellular protein localization GOC:TermGenie Any process that modulates the frequency, rate or extent of aorta morphogenesis. rph 2015-01-23T14:00:51Z biological_process GO:1903847 regulation of aorta morphogenesis Any process that modulates the frequency, rate or extent of aorta morphogenesis. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:22269326 Any process that stops, prevents or reduces the frequency, rate or extent of aorta morphogenesis. rph 2015-01-23T14:01:01Z down regulation of aorta morphogenesis down-regulation of aorta morphogenesis downregulation of aorta morphogenesis inhibition of aorta morphogenesis biological_process GO:1903848 negative regulation of aorta morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of aorta morphogenesis. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:22269326 down regulation of aorta morphogenesis GOC:TermGenie down-regulation of aorta morphogenesis GOC:TermGenie downregulation of aorta morphogenesis GOC:TermGenie inhibition of aorta morphogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of aorta morphogenesis. rph 2015-01-23T14:01:09Z up regulation of aorta morphogenesis up-regulation of aorta morphogenesis upregulation of aorta morphogenesis activation of aorta morphogenesis biological_process GO:1903849 positive regulation of aorta morphogenesis Any process that activates or increases the frequency, rate or extent of aorta morphogenesis. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:22269326 up regulation of aorta morphogenesis GOC:TermGenie up-regulation of aorta morphogenesis GOC:TermGenie upregulation of aorta morphogenesis GOC:TermGenie activation of aorta morphogenesis GOC:TermGenie The process whose specific outcome is the progression of an extraembryonic membrane over time, from its formation to the mature structure. cjm 2015-02-05T00:42:16Z biological_process GO:1903867 extraembryonic membrane development The process whose specific outcome is the progression of an extraembryonic membrane over time, from its formation to the mature structure. GOC:TermGenie GO_REF:0000094 ISBN:0073040584 Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange. sl 2015-02-17T20:26:24Z down regulation of respiratory gaseous exchange down-regulation of respiratory gaseous exchange downregulation of respiratory gaseous exchange inhibition of respiratory gaseous exchange biological_process GO:1903941 negative regulation of respiratory gaseous exchange Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange. GOC:TermGenie GO_REF:0000058 PMID:22819705 down regulation of respiratory gaseous exchange GOC:TermGenie down-regulation of respiratory gaseous exchange GOC:TermGenie downregulation of respiratory gaseous exchange GOC:TermGenie inhibition of respiratory gaseous exchange GOC:TermGenie Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange. sl 2015-02-17T20:26:35Z up regulation of respiratory gaseous exchange up-regulation of respiratory gaseous exchange upregulation of respiratory gaseous exchange activation of respiratory gaseous exchange biological_process GO:1903942 positive regulation of respiratory gaseous exchange Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange. GOC:TermGenie GO_REF:0000058 PMID:22819705 up regulation of respiratory gaseous exchange GOC:TermGenie up-regulation of respiratory gaseous exchange GOC:TermGenie upregulation of respiratory gaseous exchange GOC:TermGenie activation of respiratory gaseous exchange GOC:TermGenie Any process that modulates the frequency, rate or extent of hepatocyte apoptotic process. sl 2015-02-19T12:54:40Z regulation of hepatocyte apoptosis biological_process GO:1903943 regulation of hepatocyte apoptotic process Any process that modulates the frequency, rate or extent of hepatocyte apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:8649852 regulation of hepatocyte apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hepatocyte apoptotic process. sl 2015-02-19T12:54:50Z down regulation of hepatocyte apoptotic process down-regulation of hepatocyte apoptotic process downregulation of hepatocyte apoptotic process down regulation of hepatocyte apoptosis down-regulation of hepatocyte apoptosis downregulation of hepatocyte apoptosis inhibition of hepatocyte apoptosis inhibition of hepatocyte apoptotic process negative regulation of hepatocyte apoptosis biological_process GO:1903944 negative regulation of hepatocyte apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of hepatocyte apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:8649852 down regulation of hepatocyte apoptotic process GOC:TermGenie down-regulation of hepatocyte apoptotic process GOC:TermGenie downregulation of hepatocyte apoptotic process GOC:TermGenie down regulation of hepatocyte apoptosis GOC:TermGenie down-regulation of hepatocyte apoptosis GOC:TermGenie downregulation of hepatocyte apoptosis GOC:TermGenie inhibition of hepatocyte apoptosis GOC:TermGenie inhibition of hepatocyte apoptotic process GOC:TermGenie negative regulation of hepatocyte apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hepatocyte apoptotic process. sl 2015-02-19T12:54:59Z up regulation of hepatocyte apoptotic process up-regulation of hepatocyte apoptotic process upregulation of hepatocyte apoptotic process activation of hepatocyte apoptosis activation of hepatocyte apoptotic process positive regulation of hepatocyte apoptosis up regulation of hepatocyte apoptosis up-regulation of hepatocyte apoptosis upregulation of hepatocyte apoptosis biological_process GO:1903945 positive regulation of hepatocyte apoptotic process Any process that activates or increases the frequency, rate or extent of hepatocyte apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:8649852 up regulation of hepatocyte apoptotic process GOC:TermGenie up-regulation of hepatocyte apoptotic process GOC:TermGenie upregulation of hepatocyte apoptotic process GOC:TermGenie activation of hepatocyte apoptosis GOC:TermGenie activation of hepatocyte apoptotic process GOC:TermGenie positive regulation of hepatocyte apoptosis GOC:TermGenie up regulation of hepatocyte apoptosis GOC:TermGenie up-regulation of hepatocyte apoptosis GOC:TermGenie upregulation of hepatocyte apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of AV node cell action potential. nc 2015-02-20T14:59:41Z down regulation of AV node cardiac muscle cell action potential down regulation of AV node cell action potential down regulation of atrioventricular node cardiac muscle cell action potential down-regulation of AV node cardiac muscle cell action potential down-regulation of AV node cell action potential down-regulation of atrioventricular node cardiac muscle cell action potential downregulation of AV node cardiac muscle cell action potential downregulation of AV node cell action potential downregulation of atrioventricular node cardiac muscle cell action potential negative regulation of AV node cardiac muscle cell action potential negative regulation of atrioventricular node cardiac muscle cell action potential inhibition of AV node cardiac muscle cell action potential inhibition of AV node cell action potential inhibition of atrioventricular node cardiac muscle cell action potential biological_process GO:1903950 negative regulation of AV node cell action potential Any process that stops, prevents or reduces the frequency, rate or extent of AV node cell action potential. GOC:BHF GOC:TermGenie GOC:mtg_cardiac_conduct_nov11 GOC:nc GO_REF:0000058 PMID:25281747 down regulation of AV node cardiac muscle cell action potential GOC:TermGenie down regulation of AV node cell action potential GOC:TermGenie down regulation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie down-regulation of AV node cardiac muscle cell action potential GOC:TermGenie down-regulation of AV node cell action potential GOC:TermGenie down-regulation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie downregulation of AV node cardiac muscle cell action potential GOC:TermGenie downregulation of AV node cell action potential GOC:TermGenie downregulation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie negative regulation of AV node cardiac muscle cell action potential GOC:TermGenie negative regulation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie inhibition of AV node cardiac muscle cell action potential GOC:TermGenie inhibition of AV node cell action potential GOC:TermGenie inhibition of atrioventricular node cardiac muscle cell action potential GOC:TermGenie Any process that activates or increases the frequency, rate or extent of AV node cell action potential. nc 2015-02-20T14:59:50Z positive regulation of AV node cardiac muscle cell action potential positive regulation of atrioventricular node cardiac muscle cell action potential up regulation of AV node cardiac muscle cell action potential up regulation of AV node cell action potential up regulation of atrioventricular node cardiac muscle cell action potential up-regulation of AV node cardiac muscle cell action potential up-regulation of AV node cell action potential up-regulation of atrioventricular node cardiac muscle cell action potential upregulation of AV node cardiac muscle cell action potential upregulation of AV node cell action potential upregulation of atrioventricular node cardiac muscle cell action potential activation of AV node cardiac muscle cell action potential activation of AV node cell action potential activation of atrioventricular node cardiac muscle cell action potential biological_process GO:1903951 positive regulation of AV node cell action potential Any process that activates or increases the frequency, rate or extent of AV node cell action potential. GOC:BHF GOC:TermGenie GOC:mtg_cardiac_conduct_nov11 GOC:nc GO_REF:0000058 PMID:25281747 positive regulation of AV node cardiac muscle cell action potential GOC:TermGenie positive regulation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie up regulation of AV node cardiac muscle cell action potential GOC:TermGenie up regulation of AV node cell action potential GOC:TermGenie up regulation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie up-regulation of AV node cardiac muscle cell action potential GOC:TermGenie up-regulation of AV node cell action potential GOC:TermGenie up-regulation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie upregulation of AV node cardiac muscle cell action potential GOC:TermGenie upregulation of AV node cell action potential GOC:TermGenie upregulation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie activation of AV node cardiac muscle cell action potential GOC:TermGenie activation of AV node cell action potential GOC:TermGenie activation of atrioventricular node cardiac muscle cell action potential GOC:TermGenie Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a serotonin stimulus. sl 2015-03-06T19:33:54Z biological_process GO:1904014 response to serotonin Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a serotonin stimulus. GOC:TermGenie GO_REF:0000071 PMID:1505525 Any process that activates or increases the frequency, rate or extent of vasculature development. sl 2015-03-06T22:17:04Z up regulation of vasculature development up-regulation of vasculature development upregulation of vasculature development activation of vasculature development biological_process activation of vascular system development positive regulation of vascular system development up regulation of vascular system development up-regulation of vascular system development upregulation of vascular system development GO:1904018 positive regulation of vasculature development Any process that activates or increases the frequency, rate or extent of vasculature development. GOC:TermGenie GO_REF:0000058 PMID:21472453 up regulation of vasculature development GOC:TermGenie up-regulation of vasculature development GOC:TermGenie upregulation of vasculature development GOC:TermGenie activation of vasculature development GOC:TermGenie activation of vascular system development GOC:TermGenie positive regulation of vascular system development GOC:TermGenie up regulation of vascular system development GOC:TermGenie up-regulation of vascular system development GOC:TermGenie upregulation of vascular system development GOC:TermGenie Any apoptotic process in an epithelial cell. sl 2015-03-06T22:27:17Z epitheliocyte apoptotic process epithelial cell apoptosis epitheliocyte apoptosis biological_process GO:1904019 epithelial cell apoptotic process Any apoptotic process in an epithelial cell. GOC:TermGenie GO_REF:0000085 PMID:19137015 epitheliocyte apoptotic process GOC:TermGenie epithelial cell apoptosis GOC:TermGenie epitheliocyte apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of collagen fibril organization. ae 2015-03-12T12:36:52Z regulation of collagen fibril organisation regulation of fibrillar collagen organization biological_process regulation of collagen fibrillogenesis GO:1904026 regulation of collagen fibril organization Any process that modulates the frequency, rate or extent of collagen fibril organization. GOC:TermGenie GO_REF:0000058 PMID:25451920 regulation of collagen fibril organisation GOC:TermGenie regulation of fibrillar collagen organization GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of collagen fibril organization. ae 2015-03-12T12:36:59Z down regulation of collagen fibril organisation down regulation of collagen fibril organization down regulation of fibrillar collagen organization down-regulation of collagen fibril organisation down-regulation of collagen fibril organization down-regulation of fibrillar collagen organization downregulation of collagen fibril organisation downregulation of collagen fibril organization downregulation of fibrillar collagen organization negative regulation of collagen fibril organisation negative regulation of fibrillar collagen organization inhibition of collagen fibril organisation inhibition of collagen fibril organization inhibition of fibrillar collagen organization biological_process GO:1904027 negative regulation of collagen fibril organization Any process that stops, prevents or reduces the frequency, rate or extent of collagen fibril organization. GOC:TermGenie GO_REF:0000058 PMID:25451920 down regulation of collagen fibril organisation GOC:TermGenie down regulation of collagen fibril organization GOC:TermGenie down regulation of fibrillar collagen organization GOC:TermGenie down-regulation of collagen fibril organisation GOC:TermGenie down-regulation of collagen fibril organization GOC:TermGenie down-regulation of fibrillar collagen organization GOC:TermGenie downregulation of collagen fibril organisation GOC:TermGenie downregulation of collagen fibril organization GOC:TermGenie downregulation of fibrillar collagen organization GOC:TermGenie negative regulation of collagen fibril organisation GOC:TermGenie negative regulation of fibrillar collagen organization GOC:TermGenie inhibition of collagen fibril organisation GOC:TermGenie inhibition of collagen fibril organization GOC:TermGenie inhibition of fibrillar collagen organization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of collagen fibril organization. ae 2015-03-12T12:37:06Z positive regulation of collagen fibril organisation positive regulation of fibrillar collagen organization up regulation of collagen fibril organisation up regulation of collagen fibril organization up regulation of fibrillar collagen organization up-regulation of collagen fibril organisation up-regulation of collagen fibril organization up-regulation of fibrillar collagen organization upregulation of collagen fibril organisation upregulation of collagen fibril organization upregulation of fibrillar collagen organization activation of collagen fibril organisation activation of collagen fibril organization activation of fibrillar collagen organization biological_process GO:1904028 positive regulation of collagen fibril organization Any process that activates or increases the frequency, rate or extent of collagen fibril organization. GOC:TermGenie GO_REF:0000058 PMID:25451920 positive regulation of collagen fibril organisation GOC:TermGenie positive regulation of fibrillar collagen organization GOC:TermGenie up regulation of collagen fibril organisation GOC:TermGenie up regulation of collagen fibril organization GOC:TermGenie up regulation of fibrillar collagen organization GOC:TermGenie up-regulation of collagen fibril organisation GOC:TermGenie up-regulation of collagen fibril organization GOC:TermGenie up-regulation of fibrillar collagen organization GOC:TermGenie upregulation of collagen fibril organisation GOC:TermGenie upregulation of collagen fibril organization GOC:TermGenie upregulation of fibrillar collagen organization GOC:TermGenie activation of collagen fibril organisation GOC:TermGenie activation of collagen fibril organization GOC:TermGenie activation of fibrillar collagen organization GOC:TermGenie Any process that modulates the frequency, rate or extent of epithelial cell apoptotic process. sl 2015-03-13T22:05:41Z regulation of epitheliocyte apoptotic process regulation of epithelial cell apoptosis regulation of epitheliocyte apoptosis biological_process GO:1904035 regulation of epithelial cell apoptotic process Any process that modulates the frequency, rate or extent of epithelial cell apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:19137015 regulation of epitheliocyte apoptotic process GOC:TermGenie regulation of epithelial cell apoptosis GOC:TermGenie regulation of epitheliocyte apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell apoptotic process. sl 2015-03-13T22:05:47Z down regulation of epithelial cell apoptotic process down regulation of epitheliocyte apoptotic process down-regulation of epithelial cell apoptotic process down-regulation of epitheliocyte apoptotic process downregulation of epithelial cell apoptotic process downregulation of epitheliocyte apoptotic process negative regulation of epitheliocyte apoptotic process down regulation of epithelial cell apoptosis down regulation of epitheliocyte apoptosis down-regulation of epithelial cell apoptosis down-regulation of epitheliocyte apoptosis downregulation of epithelial cell apoptosis downregulation of epitheliocyte apoptosis inhibition of epithelial cell apoptosis inhibition of epithelial cell apoptotic process inhibition of epitheliocyte apoptosis inhibition of epitheliocyte apoptotic process negative regulation of epithelial cell apoptosis negative regulation of epitheliocyte apoptosis biological_process GO:1904036 negative regulation of epithelial cell apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:19137015 down regulation of epithelial cell apoptotic process GOC:TermGenie down regulation of epitheliocyte apoptotic process GOC:TermGenie down-regulation of epithelial cell apoptotic process GOC:TermGenie down-regulation of epitheliocyte apoptotic process GOC:TermGenie downregulation of epithelial cell apoptotic process GOC:TermGenie downregulation of epitheliocyte apoptotic process GOC:TermGenie negative regulation of epitheliocyte apoptotic process GOC:TermGenie down regulation of epithelial cell apoptosis GOC:TermGenie down regulation of epitheliocyte apoptosis GOC:TermGenie down-regulation of epithelial cell apoptosis GOC:TermGenie down-regulation of epitheliocyte apoptosis GOC:TermGenie downregulation of epithelial cell apoptosis GOC:TermGenie downregulation of epitheliocyte apoptosis GOC:TermGenie inhibition of epithelial cell apoptosis GOC:TermGenie inhibition of epithelial cell apoptotic process GOC:TermGenie inhibition of epitheliocyte apoptosis GOC:TermGenie inhibition of epitheliocyte apoptotic process GOC:TermGenie negative regulation of epithelial cell apoptosis GOC:TermGenie negative regulation of epitheliocyte apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of epithelial cell apoptotic process. sl 2015-03-13T22:05:53Z positive regulation of epitheliocyte apoptotic process up regulation of epithelial cell apoptotic process up regulation of epitheliocyte apoptotic process up-regulation of epithelial cell apoptotic process up-regulation of epitheliocyte apoptotic process upregulation of epithelial cell apoptotic process upregulation of epitheliocyte apoptotic process activation of epithelial cell apoptosis activation of epithelial cell apoptotic process activation of epitheliocyte apoptosis activation of epitheliocyte apoptotic process positive regulation of epithelial cell apoptosis positive regulation of epitheliocyte apoptosis up regulation of epithelial cell apoptosis up regulation of epitheliocyte apoptosis up-regulation of epithelial cell apoptosis up-regulation of epitheliocyte apoptosis upregulation of epithelial cell apoptosis upregulation of epitheliocyte apoptosis biological_process GO:1904037 positive regulation of epithelial cell apoptotic process Any process that activates or increases the frequency, rate or extent of epithelial cell apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:19137015 positive regulation of epitheliocyte apoptotic process GOC:TermGenie up regulation of epithelial cell apoptotic process GOC:TermGenie up regulation of epitheliocyte apoptotic process GOC:TermGenie up-regulation of epithelial cell apoptotic process GOC:TermGenie up-regulation of epitheliocyte apoptotic process GOC:TermGenie upregulation of epithelial cell apoptotic process GOC:TermGenie upregulation of epitheliocyte apoptotic process GOC:TermGenie activation of epithelial cell apoptosis GOC:TermGenie activation of epithelial cell apoptotic process GOC:TermGenie activation of epitheliocyte apoptosis GOC:TermGenie activation of epitheliocyte apoptotic process GOC:TermGenie positive regulation of epithelial cell apoptosis GOC:TermGenie positive regulation of epitheliocyte apoptosis GOC:TermGenie up regulation of epithelial cell apoptosis GOC:TermGenie up regulation of epitheliocyte apoptosis GOC:TermGenie up-regulation of epithelial cell apoptosis GOC:TermGenie up-regulation of epitheliocyte apoptosis GOC:TermGenie upregulation of epithelial cell apoptosis GOC:TermGenie upregulation of epitheliocyte apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of cholangiocyte proliferation. sl 2015-03-18T17:56:14Z regulation of hepatoblast proliferation biological_process GO:1904054 regulation of cholangiocyte proliferation Any process that modulates the frequency, rate or extent of cholangiocyte proliferation. GOC:TermGenie GO_REF:0000058 PMID:24434010 regulation of hepatoblast proliferation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte proliferation. sl 2015-03-18T17:56:20Z down regulation of cholangiocyte proliferation down regulation of hepatoblast proliferation down-regulation of cholangiocyte proliferation down-regulation of hepatoblast proliferation downregulation of cholangiocyte proliferation downregulation of hepatoblast proliferation negative regulation of hepatoblast proliferation inhibition of cholangiocyte proliferation inhibition of hepatoblast proliferation biological_process GO:1904055 negative regulation of cholangiocyte proliferation Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte proliferation. GOC:TermGenie GO_REF:0000058 PMID:24434010 down regulation of cholangiocyte proliferation GOC:TermGenie down regulation of hepatoblast proliferation GOC:TermGenie down-regulation of cholangiocyte proliferation GOC:TermGenie down-regulation of hepatoblast proliferation GOC:TermGenie downregulation of cholangiocyte proliferation GOC:TermGenie downregulation of hepatoblast proliferation GOC:TermGenie negative regulation of hepatoblast proliferation GOC:TermGenie inhibition of cholangiocyte proliferation GOC:TermGenie inhibition of hepatoblast proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cholangiocyte proliferation. sl 2015-03-18T17:56:26Z positive regulation of hepatoblast proliferation up regulation of cholangiocyte proliferation up regulation of hepatoblast proliferation up-regulation of cholangiocyte proliferation up-regulation of hepatoblast proliferation upregulation of cholangiocyte proliferation upregulation of hepatoblast proliferation activation of cholangiocyte proliferation activation of hepatoblast proliferation biological_process GO:1904056 positive regulation of cholangiocyte proliferation Any process that activates or increases the frequency, rate or extent of cholangiocyte proliferation. GOC:TermGenie GO_REF:0000058 PMID:24434010 positive regulation of hepatoblast proliferation GOC:TermGenie up regulation of cholangiocyte proliferation GOC:TermGenie up regulation of hepatoblast proliferation GOC:TermGenie up-regulation of cholangiocyte proliferation GOC:TermGenie up-regulation of hepatoblast proliferation GOC:TermGenie upregulation of cholangiocyte proliferation GOC:TermGenie upregulation of hepatoblast proliferation GOC:TermGenie activation of cholangiocyte proliferation GOC:TermGenie activation of hepatoblast proliferation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of sensory perception of pain. sl 2015-03-18T20:33:57Z down regulation of nociception down regulation of sensory perception of pain down-regulation of nociception down-regulation of sensory perception of pain downregulation of nociception downregulation of sensory perception of pain negative regulation of nociception down regulation of perception of physiological pain down-regulation of perception of physiological pain downregulation of perception of physiological pain inhibition of nociception inhibition of perception of physiological pain inhibition of sensory perception of pain negative regulation of perception of physiological pain biological_process GO:1904057 negative regulation of sensory perception of pain Any process that stops, prevents or reduces the frequency, rate or extent of sensory perception of pain. GOC:TermGenie GO_REF:0000058 PMID:17167094 down regulation of nociception GOC:TermGenie down regulation of sensory perception of pain GOC:TermGenie down-regulation of nociception GOC:TermGenie down-regulation of sensory perception of pain GOC:TermGenie downregulation of nociception GOC:TermGenie downregulation of sensory perception of pain GOC:TermGenie negative regulation of nociception GOC:TermGenie down regulation of perception of physiological pain GOC:TermGenie down-regulation of perception of physiological pain GOC:TermGenie downregulation of perception of physiological pain GOC:TermGenie inhibition of nociception GOC:TermGenie inhibition of perception of physiological pain GOC:TermGenie inhibition of sensory perception of pain GOC:TermGenie negative regulation of perception of physiological pain GOC:TermGenie Any process that activates or increases the frequency, rate or extent of sensory perception of pain. sl 2015-03-18T20:34:03Z positive regulation of nociception up regulation of nociception up regulation of sensory perception of pain up-regulation of nociception up-regulation of sensory perception of pain upregulation of nociception upregulation of sensory perception of pain activation of nociception activation of perception of physiological pain activation of sensory perception of pain positive regulation of perception of physiological pain up regulation of perception of physiological pain up-regulation of perception of physiological pain upregulation of perception of physiological pain biological_process GO:1904058 positive regulation of sensory perception of pain Any process that activates or increases the frequency, rate or extent of sensory perception of pain. GOC:TermGenie GO_REF:0000058 PMID:17167094 positive regulation of nociception GOC:TermGenie up regulation of nociception GOC:TermGenie up regulation of sensory perception of pain GOC:TermGenie up-regulation of nociception GOC:TermGenie up-regulation of sensory perception of pain GOC:TermGenie upregulation of nociception GOC:TermGenie upregulation of sensory perception of pain GOC:TermGenie activation of nociception GOC:TermGenie activation of perception of physiological pain GOC:TermGenie activation of sensory perception of pain GOC:TermGenie positive regulation of perception of physiological pain GOC:TermGenie up regulation of perception of physiological pain GOC:TermGenie up-regulation of perception of physiological pain GOC:TermGenie upregulation of perception of physiological pain GOC:TermGenie Any process that modulates the frequency, rate or extent of cation transmembrane transport. sl 2015-03-18T21:11:43Z regulation of cation transmembrane transport biological_process GO:1904062 regulation of monoatomic cation transmembrane transport Any process that modulates the frequency, rate or extent of cation transmembrane transport. GOC:TermGenie GO_REF:0000058 PMID:15304482 Any process that stops, prevents or reduces the frequency, rate or extent of cation transmembrane transport. sl 2015-03-18T21:11:50Z down regulation of cation transmembrane transport down-regulation of cation transmembrane transport downregulation of cation transmembrane transport inhibition of cation transmembrane transport biological_process GO:1904063 negative regulation of cation transmembrane transport Any process that stops, prevents or reduces the frequency, rate or extent of cation transmembrane transport. GOC:TermGenie GO_REF:0000058 PMID:15304482 down regulation of cation transmembrane transport GOC:TermGenie down-regulation of cation transmembrane transport GOC:TermGenie downregulation of cation transmembrane transport GOC:TermGenie inhibition of cation transmembrane transport GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cation transmembrane transport. sl 2015-03-18T21:11:55Z up regulation of cation transmembrane transport up-regulation of cation transmembrane transport upregulation of cation transmembrane transport activation of cation transmembrane transport biological_process GO:1904064 positive regulation of cation transmembrane transport Any process that activates or increases the frequency, rate or extent of cation transmembrane transport. GOC:TermGenie GO_REF:0000058 PMID:15304482 up regulation of cation transmembrane transport GOC:TermGenie up-regulation of cation transmembrane transport GOC:TermGenie upregulation of cation transmembrane transport GOC:TermGenie activation of cation transmembrane transport GOC:TermGenie Any process that modulates the frequency, rate or extent of trophectodermal cell proliferation. tb 2015-03-20T16:55:56Z regulation of trophectoderm cell proliferation biological_process GO:1904073 regulation of trophectodermal cell proliferation Any process that modulates the frequency, rate or extent of trophectodermal cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:24508636 regulation of trophectoderm cell proliferation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of trophectodermal cell proliferation. tb 2015-03-20T16:56:02Z down regulation of trophectoderm cell proliferation down regulation of trophectodermal cell proliferation down-regulation of trophectoderm cell proliferation down-regulation of trophectodermal cell proliferation downregulation of trophectoderm cell proliferation downregulation of trophectodermal cell proliferation negative regulation of trophectoderm cell proliferation inhibition of trophectoderm cell proliferation inhibition of trophectodermal cell proliferation biological_process GO:1904074 negative regulation of trophectodermal cell proliferation Any process that stops, prevents or reduces the frequency, rate or extent of trophectodermal cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:24508636 down regulation of trophectoderm cell proliferation GOC:TermGenie down regulation of trophectodermal cell proliferation GOC:TermGenie down-regulation of trophectoderm cell proliferation GOC:TermGenie down-regulation of trophectodermal cell proliferation GOC:TermGenie downregulation of trophectoderm cell proliferation GOC:TermGenie downregulation of trophectodermal cell proliferation GOC:TermGenie negative regulation of trophectoderm cell proliferation GOC:TermGenie inhibition of trophectoderm cell proliferation GOC:TermGenie inhibition of trophectodermal cell proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of trophectodermal cell proliferation. tb 2015-03-20T16:56:08Z positive regulation of trophectoderm cell proliferation up regulation of trophectoderm cell proliferation up regulation of trophectodermal cell proliferation up-regulation of trophectoderm cell proliferation up-regulation of trophectodermal cell proliferation upregulation of trophectoderm cell proliferation upregulation of trophectodermal cell proliferation activation of trophectoderm cell proliferation activation of trophectodermal cell proliferation biological_process GO:1904075 positive regulation of trophectodermal cell proliferation Any process that activates or increases the frequency, rate or extent of trophectodermal cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:24508636 positive regulation of trophectoderm cell proliferation GOC:TermGenie up regulation of trophectoderm cell proliferation GOC:TermGenie up regulation of trophectodermal cell proliferation GOC:TermGenie up-regulation of trophectoderm cell proliferation GOC:TermGenie up-regulation of trophectodermal cell proliferation GOC:TermGenie upregulation of trophectoderm cell proliferation GOC:TermGenie upregulation of trophectodermal cell proliferation GOC:TermGenie activation of trophectoderm cell proliferation GOC:TermGenie activation of trophectodermal cell proliferation GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a microvillus. kmv 2015-04-01T18:14:41Z protein localisation in microvillus protein localisation to microvillus protein localization in microvillus biological_process GO:1904106 protein localization to microvillus A process in which a protein is transported to, or maintained in, a location within a microvillus. GOC:TermGenie GOC:kmv GO_REF:0000087 PMID:25335890 protein localisation in microvillus GOC:TermGenie protein localisation to microvillus GOC:TermGenie protein localization in microvillus GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation. tb 2015-04-14T15:59:22Z down regulation of meiotic cell cycle process involved in oocyte maturation down-regulation of meiotic cell cycle process involved in oocyte maturation downregulation of meiotic cell cycle process involved in oocyte maturation inhibition of meiotic cell cycle process involved in oocyte maturation biological_process GO:1904145 negative regulation of meiotic cell cycle process involved in oocyte maturation Any process that stops, prevents or reduces the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation. GOC:TermGenie GO_REF:0000058 PMID:22674394 down regulation of meiotic cell cycle process involved in oocyte maturation GOC:TermGenie down-regulation of meiotic cell cycle process involved in oocyte maturation GOC:TermGenie downregulation of meiotic cell cycle process involved in oocyte maturation GOC:TermGenie inhibition of meiotic cell cycle process involved in oocyte maturation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation. tb 2015-04-14T15:59:28Z up regulation of meiotic cell cycle process involved in oocyte maturation up-regulation of meiotic cell cycle process involved in oocyte maturation upregulation of meiotic cell cycle process involved in oocyte maturation activation of meiotic cell cycle process involved in oocyte maturation biological_process GO:1904146 positive regulation of meiotic cell cycle process involved in oocyte maturation Any process that activates or increases the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation. GOC:TermGenie GO_REF:0000058 PMID:22674394 up regulation of meiotic cell cycle process involved in oocyte maturation GOC:TermGenie up-regulation of meiotic cell cycle process involved in oocyte maturation GOC:TermGenie upregulation of meiotic cell cycle process involved in oocyte maturation GOC:TermGenie activation of meiotic cell cycle process involved in oocyte maturation GOC:TermGenie Any process that modulates the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:19Z regulation of cell blebbing biological_process GO:1904170 regulation of bleb assembly Any process that modulates the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 regulation of cell blebbing GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:25Z down regulation of bleb assembly down regulation of cell blebbing down-regulation of bleb assembly down-regulation of cell blebbing downregulation of bleb assembly downregulation of cell blebbing negative regulation of cell blebbing inhibition of bleb assembly inhibition of cell blebbing biological_process GO:1904171 negative regulation of bleb assembly Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 down regulation of bleb assembly GOC:TermGenie down regulation of cell blebbing GOC:TermGenie down-regulation of bleb assembly GOC:TermGenie down-regulation of cell blebbing GOC:TermGenie downregulation of bleb assembly GOC:TermGenie downregulation of cell blebbing GOC:TermGenie negative regulation of cell blebbing GOC:TermGenie inhibition of bleb assembly GOC:TermGenie inhibition of cell blebbing GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:31Z positive regulation of cell blebbing up regulation of bleb assembly up regulation of cell blebbing up-regulation of bleb assembly up-regulation of cell blebbing upregulation of bleb assembly upregulation of cell blebbing activation of bleb assembly activation of cell blebbing biological_process GO:1904172 positive regulation of bleb assembly Any process that activates or increases the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 positive regulation of cell blebbing GOC:TermGenie up regulation of bleb assembly GOC:TermGenie up regulation of cell blebbing GOC:TermGenie up-regulation of bleb assembly GOC:TermGenie up-regulation of cell blebbing GOC:TermGenie upregulation of bleb assembly GOC:TermGenie upregulation of cell blebbing GOC:TermGenie activation of bleb assembly GOC:TermGenie activation of cell blebbing GOC:TermGenie Any process that modulates the frequency, rate or extent of adipose tissue development. sl 2015-04-29T20:01:01Z biological_process regulation of adipogenesis GO:1904177 regulation of adipose tissue development Any process that modulates the frequency, rate or extent of adipose tissue development. GOC:TermGenie GO_REF:0000058 PMID:23081848 regulation of adipogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of adipose tissue development. sl 2015-04-29T20:01:07Z down regulation of adipose tissue development down-regulation of adipose tissue development downregulation of adipose tissue development inhibition of adipose tissue development biological_process down regulation of adipogenesis down-regulation of adipogenesis downregulation of adipogenesis inhibition of adipogenesis negative regulation of adipogenesis GO:1904178 negative regulation of adipose tissue development Any process that stops, prevents or reduces the frequency, rate or extent of adipose tissue development. GOC:TermGenie GO_REF:0000058 PMID:23081848 down regulation of adipose tissue development GOC:TermGenie down-regulation of adipose tissue development GOC:TermGenie downregulation of adipose tissue development GOC:TermGenie inhibition of adipose tissue development GOC:TermGenie down regulation of adipogenesis GOC:TermGenie down-regulation of adipogenesis GOC:TermGenie downregulation of adipogenesis GOC:TermGenie inhibition of adipogenesis GOC:TermGenie negative regulation of adipogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of adipose tissue development. sl 2015-04-29T20:01:13Z up regulation of adipose tissue development up-regulation of adipose tissue development upregulation of adipose tissue development activation of adipose tissue development biological_process activation of adipogenesis positive regulation of adipogenesis up regulation of adipogenesis up-regulation of adipogenesis upregulation of adipogenesis GO:1904179 positive regulation of adipose tissue development Any process that activates or increases the frequency, rate or extent of adipose tissue development. GOC:TermGenie GO_REF:0000058 PMID:23081848 up regulation of adipose tissue development GOC:TermGenie up-regulation of adipose tissue development GOC:TermGenie upregulation of adipose tissue development GOC:TermGenie activation of adipose tissue development GOC:TermGenie activation of adipogenesis GOC:TermGenie positive regulation of adipogenesis GOC:TermGenie up regulation of adipogenesis GOC:TermGenie up-regulation of adipogenesis GOC:TermGenie upregulation of adipogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of cholangiocyte apoptotic process. sl 2015-05-06T15:25:48Z regulation of epithelial cell of bile duct apoptotic process regulation of cholangiocyte apoptosis regulation of epithelial cell of bile duct apoptosis biological_process GO:1904192 regulation of cholangiocyte apoptotic process Any process that modulates the frequency, rate or extent of cholangiocyte apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:24498161 regulation of epithelial cell of bile duct apoptotic process GOC:TermGenie regulation of cholangiocyte apoptosis GOC:TermGenie regulation of epithelial cell of bile duct apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte apoptotic process. sl 2015-05-06T15:25:55Z down regulation of cholangiocyte apoptotic process down regulation of epithelial cell of bile duct apoptotic process down-regulation of cholangiocyte apoptotic process down-regulation of epithelial cell of bile duct apoptotic process downregulation of cholangiocyte apoptotic process downregulation of epithelial cell of bile duct apoptotic process negative regulation of epithelial cell of bile duct apoptotic process down regulation of cholangiocyte apoptosis down regulation of epithelial cell of bile duct apoptosis down-regulation of cholangiocyte apoptosis down-regulation of epithelial cell of bile duct apoptosis downregulation of cholangiocyte apoptosis downregulation of epithelial cell of bile duct apoptosis inhibition of cholangiocyte apoptosis inhibition of cholangiocyte apoptotic process inhibition of epithelial cell of bile duct apoptosis inhibition of epithelial cell of bile duct apoptotic process negative regulation of cholangiocyte apoptosis negative regulation of epithelial cell of bile duct apoptosis biological_process GO:1904193 negative regulation of cholangiocyte apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:24498161 down regulation of cholangiocyte apoptotic process GOC:TermGenie down regulation of epithelial cell of bile duct apoptotic process GOC:TermGenie down-regulation of cholangiocyte apoptotic process GOC:TermGenie down-regulation of epithelial cell of bile duct apoptotic process GOC:TermGenie downregulation of cholangiocyte apoptotic process GOC:TermGenie downregulation of epithelial cell of bile duct apoptotic process GOC:TermGenie negative regulation of epithelial cell of bile duct apoptotic process GOC:TermGenie down regulation of cholangiocyte apoptosis GOC:TermGenie down regulation of epithelial cell of bile duct apoptosis GOC:TermGenie down-regulation of cholangiocyte apoptosis GOC:TermGenie down-regulation of epithelial cell of bile duct apoptosis GOC:TermGenie downregulation of cholangiocyte apoptosis GOC:TermGenie downregulation of epithelial cell of bile duct apoptosis GOC:TermGenie inhibition of cholangiocyte apoptosis GOC:TermGenie inhibition of cholangiocyte apoptotic process GOC:TermGenie inhibition of epithelial cell of bile duct apoptosis GOC:TermGenie inhibition of epithelial cell of bile duct apoptotic process GOC:TermGenie negative regulation of cholangiocyte apoptosis GOC:TermGenie negative regulation of epithelial cell of bile duct apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cholangiocyte apoptotic process. sl 2015-05-06T15:26:00Z positive regulation of epithelial cell of bile duct apoptotic process up regulation of cholangiocyte apoptotic process up regulation of epithelial cell of bile duct apoptotic process up-regulation of cholangiocyte apoptotic process up-regulation of epithelial cell of bile duct apoptotic process upregulation of cholangiocyte apoptotic process upregulation of epithelial cell of bile duct apoptotic process activation of cholangiocyte apoptosis activation of cholangiocyte apoptotic process activation of epithelial cell of bile duct apoptosis activation of epithelial cell of bile duct apoptotic process positive regulation of cholangiocyte apoptosis positive regulation of epithelial cell of bile duct apoptosis up regulation of cholangiocyte apoptosis up regulation of epithelial cell of bile duct apoptosis up-regulation of cholangiocyte apoptosis up-regulation of epithelial cell of bile duct apoptosis upregulation of cholangiocyte apoptosis upregulation of epithelial cell of bile duct apoptosis biological_process GO:1904194 positive regulation of cholangiocyte apoptotic process Any process that activates or increases the frequency, rate or extent of cholangiocyte apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:24498161 positive regulation of epithelial cell of bile duct apoptotic process GOC:TermGenie up regulation of cholangiocyte apoptotic process GOC:TermGenie up regulation of epithelial cell of bile duct apoptotic process GOC:TermGenie up-regulation of cholangiocyte apoptotic process GOC:TermGenie up-regulation of epithelial cell of bile duct apoptotic process GOC:TermGenie upregulation of cholangiocyte apoptotic process GOC:TermGenie upregulation of epithelial cell of bile duct apoptotic process GOC:TermGenie activation of cholangiocyte apoptosis GOC:TermGenie activation of cholangiocyte apoptotic process GOC:TermGenie activation of epithelial cell of bile duct apoptosis GOC:TermGenie activation of epithelial cell of bile duct apoptotic process GOC:TermGenie positive regulation of cholangiocyte apoptosis GOC:TermGenie positive regulation of epithelial cell of bile duct apoptosis GOC:TermGenie up regulation of cholangiocyte apoptosis GOC:TermGenie up regulation of epithelial cell of bile duct apoptosis GOC:TermGenie up-regulation of cholangiocyte apoptosis GOC:TermGenie up-regulation of epithelial cell of bile duct apoptosis GOC:TermGenie upregulation of cholangiocyte apoptosis GOC:TermGenie upregulation of epithelial cell of bile duct apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of skeletal muscle hypertrophy. sl 2015-05-08T17:38:13Z biological_process GO:1904204 regulation of skeletal muscle hypertrophy Any process that modulates the frequency, rate or extent of skeletal muscle hypertrophy. GOC:TermGenie GO_REF:0000058 PMID:23470307 Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle hypertrophy. sl 2015-05-08T17:38:19Z down regulation of skeletal muscle hypertrophy down-regulation of skeletal muscle hypertrophy downregulation of skeletal muscle hypertrophy inhibition of skeletal muscle hypertrophy biological_process GO:1904205 negative regulation of skeletal muscle hypertrophy Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle hypertrophy. GOC:TermGenie GO_REF:0000058 PMID:23470307 down regulation of skeletal muscle hypertrophy GOC:TermGenie down-regulation of skeletal muscle hypertrophy GOC:TermGenie downregulation of skeletal muscle hypertrophy GOC:TermGenie inhibition of skeletal muscle hypertrophy GOC:TermGenie Any process that activates or increases the frequency, rate or extent of skeletal muscle hypertrophy. sl 2015-05-08T17:38:25Z up regulation of skeletal muscle hypertrophy up-regulation of skeletal muscle hypertrophy upregulation of skeletal muscle hypertrophy activation of skeletal muscle hypertrophy biological_process GO:1904206 positive regulation of skeletal muscle hypertrophy Any process that activates or increases the frequency, rate or extent of skeletal muscle hypertrophy. GOC:TermGenie GO_REF:0000058 PMID:23470307 up regulation of skeletal muscle hypertrophy GOC:TermGenie up-regulation of skeletal muscle hypertrophy GOC:TermGenie upregulation of skeletal muscle hypertrophy GOC:TermGenie activation of skeletal muscle hypertrophy GOC:TermGenie Any process that modulates the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:28Z regulation of bile acid metabolism biological_process GO:1904251 regulation of bile acid metabolic process Any process that modulates the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 regulation of bile acid metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:35Z down regulation of bile acid metabolic process down regulation of bile acid metabolism down-regulation of bile acid metabolic process down-regulation of bile acid metabolism downregulation of bile acid metabolic process downregulation of bile acid metabolism negative regulation of bile acid metabolism inhibition of bile acid metabolic process inhibition of bile acid metabolism biological_process GO:1904252 negative regulation of bile acid metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 down regulation of bile acid metabolic process GOC:TermGenie down regulation of bile acid metabolism GOC:TermGenie down-regulation of bile acid metabolic process GOC:TermGenie down-regulation of bile acid metabolism GOC:TermGenie downregulation of bile acid metabolic process GOC:TermGenie downregulation of bile acid metabolism GOC:TermGenie negative regulation of bile acid metabolism GOC:TermGenie inhibition of bile acid metabolic process GOC:TermGenie inhibition of bile acid metabolism GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:40Z positive regulation of bile acid metabolism up regulation of bile acid metabolic process up regulation of bile acid metabolism up-regulation of bile acid metabolic process up-regulation of bile acid metabolism upregulation of bile acid metabolic process upregulation of bile acid metabolism activation of bile acid metabolic process activation of bile acid metabolism biological_process GO:1904253 positive regulation of bile acid metabolic process Any process that activates or increases the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 positive regulation of bile acid metabolism GOC:TermGenie up regulation of bile acid metabolic process GOC:TermGenie up regulation of bile acid metabolism GOC:TermGenie up-regulation of bile acid metabolic process GOC:TermGenie up-regulation of bile acid metabolism GOC:TermGenie upregulation of bile acid metabolic process GOC:TermGenie upregulation of bile acid metabolism GOC:TermGenie activation of bile acid metabolic process GOC:TermGenie activation of bile acid metabolism GOC:TermGenie The cell cortex of the leading edge of a cell. kmv 2015-05-28T19:16:03Z cell cortex of cell leading edge cell cortex of front of cell cell cortex of leading edge of cell cellular_component cell periphery of cell leading edge cell periphery of front of cell cell periphery of leading edge of cell peripheral cytoplasm of cell leading edge peripheral cytoplasm of front of cell peripheral cytoplasm of leading edge of cell GO:1904269 cell leading edge cell cortex The cell cortex of the leading edge of a cell. GOC:TermGenie GOC:kmv GO_REF:0000064 PMID:25843030 cell cortex of cell leading edge GOC:TermGenie cell cortex of front of cell GOC:TermGenie cell cortex of leading edge of cell GOC:TermGenie cell periphery of cell leading edge GOC:TermGenie cell periphery of front of cell GOC:TermGenie cell periphery of leading edge of cell GOC:TermGenie peripheral cytoplasm of cell leading edge GOC:TermGenie peripheral cytoplasm of front of cell GOC:TermGenie peripheral cytoplasm of leading edge of cell GOC:TermGenie Any process that modulates the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. sl 2015-06-09T23:18:42Z biological_process GO:1904304 regulation of gastro-intestinal system smooth muscle contraction Any process that modulates the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:10821044 Any process that stops, prevents or reduces the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. sl 2015-06-09T23:18:48Z down regulation of gastro-intestinal system smooth muscle contraction down-regulation of gastro-intestinal system smooth muscle contraction downregulation of gastro-intestinal system smooth muscle contraction inhibition of gastro-intestinal system smooth muscle contraction biological_process GO:1904305 negative regulation of gastro-intestinal system smooth muscle contraction Any process that stops, prevents or reduces the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:10821044 down regulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie down-regulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie downregulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie inhibition of gastro-intestinal system smooth muscle contraction GOC:TermGenie Any process that activates or increases the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. sl 2015-06-09T23:18:54Z up regulation of gastro-intestinal system smooth muscle contraction up-regulation of gastro-intestinal system smooth muscle contraction upregulation of gastro-intestinal system smooth muscle contraction activation of gastro-intestinal system smooth muscle contraction biological_process GO:1904306 positive regulation of gastro-intestinal system smooth muscle contraction Any process that activates or increases the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:10821044 up regulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie up-regulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie upregulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie activation of gastro-intestinal system smooth muscle contraction GOC:TermGenie Any process that modulates the frequency, rate or extent of colon smooth muscle contraction. sl 2015-06-11T21:16:58Z biological_process GO:1904341 regulation of colon smooth muscle contraction Any process that modulates the frequency, rate or extent of colon smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:24170253 Any process that stops, prevents or reduces the frequency, rate or extent of colon smooth muscle contraction. sl 2015-06-11T21:17:05Z down regulation of colon smooth muscle contraction down-regulation of colon smooth muscle contraction downregulation of colon smooth muscle contraction inhibition of colon smooth muscle contraction biological_process GO:1904342 negative regulation of colon smooth muscle contraction Any process that stops, prevents or reduces the frequency, rate or extent of colon smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:24170253 down regulation of colon smooth muscle contraction GOC:TermGenie down-regulation of colon smooth muscle contraction GOC:TermGenie downregulation of colon smooth muscle contraction GOC:TermGenie inhibition of colon smooth muscle contraction GOC:TermGenie Any process that activates or increases the frequency, rate or extent of colon smooth muscle contraction. sl 2015-06-11T21:17:11Z up regulation of colon smooth muscle contraction up-regulation of colon smooth muscle contraction upregulation of colon smooth muscle contraction activation of colon smooth muscle contraction biological_process GO:1904343 positive regulation of colon smooth muscle contraction Any process that activates or increases the frequency, rate or extent of colon smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:24170253 up regulation of colon smooth muscle contraction GOC:TermGenie up-regulation of colon smooth muscle contraction GOC:TermGenie upregulation of colon smooth muscle contraction GOC:TermGenie activation of colon smooth muscle contraction GOC:TermGenie Any process that modulates the frequency, rate or extent of gastric mucosal blood circulation. sl 2015-06-11T21:20:31Z regulation of stomach mucosal blood circulation biological_process GO:1904344 regulation of gastric mucosal blood circulation Any process that modulates the frequency, rate or extent of gastric mucosal blood circulation. GOC:TermGenie GO_REF:0000058 PMID:10807413 regulation of stomach mucosal blood circulation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of gastric mucosal blood circulation. sl 2015-06-11T21:20:44Z down regulation of gastric mucosal blood circulation down regulation of stomach mucosal blood circulation down-regulation of gastric mucosal blood circulation down-regulation of stomach mucosal blood circulation downregulation of gastric mucosal blood circulation downregulation of stomach mucosal blood circulation negative regulation of stomach mucosal blood circulation inhibition of gastric mucosal blood circulation inhibition of stomach mucosal blood circulation biological_process GO:1904345 negative regulation of gastric mucosal blood circulation Any process that stops, prevents or reduces the frequency, rate or extent of gastric mucosal blood circulation. GOC:TermGenie GO_REF:0000058 PMID:10807413 down regulation of gastric mucosal blood circulation GOC:TermGenie down regulation of stomach mucosal blood circulation GOC:TermGenie down-regulation of gastric mucosal blood circulation GOC:TermGenie down-regulation of stomach mucosal blood circulation GOC:TermGenie downregulation of gastric mucosal blood circulation GOC:TermGenie downregulation of stomach mucosal blood circulation GOC:TermGenie negative regulation of stomach mucosal blood circulation GOC:TermGenie inhibition of gastric mucosal blood circulation GOC:TermGenie inhibition of stomach mucosal blood circulation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of gastric mucosal blood circulation. sl 2015-06-11T21:20:50Z positive regulation of stomach mucosal blood circulation up regulation of gastric mucosal blood circulation up regulation of stomach mucosal blood circulation up-regulation of gastric mucosal blood circulation up-regulation of stomach mucosal blood circulation upregulation of gastric mucosal blood circulation upregulation of stomach mucosal blood circulation activation of gastric mucosal blood circulation activation of stomach mucosal blood circulation biological_process GO:1904346 positive regulation of gastric mucosal blood circulation Any process that activates or increases the frequency, rate or extent of gastric mucosal blood circulation. GOC:TermGenie GO_REF:0000058 PMID:10807413 positive regulation of stomach mucosal blood circulation GOC:TermGenie up regulation of gastric mucosal blood circulation GOC:TermGenie up regulation of stomach mucosal blood circulation GOC:TermGenie up-regulation of gastric mucosal blood circulation GOC:TermGenie up-regulation of stomach mucosal blood circulation GOC:TermGenie upregulation of gastric mucosal blood circulation GOC:TermGenie upregulation of stomach mucosal blood circulation GOC:TermGenie activation of gastric mucosal blood circulation GOC:TermGenie activation of stomach mucosal blood circulation GOC:TermGenie Any process that modulates the frequency, rate or extent of small intestine smooth muscle contraction. sl 2015-06-11T21:37:34Z biological_process GO:1904347 regulation of small intestine smooth muscle contraction Any process that modulates the frequency, rate or extent of small intestine smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:11991626 Any process that stops, prevents or reduces the frequency, rate or extent of small intestine smooth muscle contraction. sl 2015-06-11T21:37:40Z down regulation of small intestine smooth muscle contraction down-regulation of small intestine smooth muscle contraction downregulation of small intestine smooth muscle contraction inhibition of small intestine smooth muscle contraction biological_process GO:1904348 negative regulation of small intestine smooth muscle contraction Any process that stops, prevents or reduces the frequency, rate or extent of small intestine smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:11991626 down regulation of small intestine smooth muscle contraction GOC:TermGenie down-regulation of small intestine smooth muscle contraction GOC:TermGenie downregulation of small intestine smooth muscle contraction GOC:TermGenie inhibition of small intestine smooth muscle contraction GOC:TermGenie Any process that activates or increases the frequency, rate or extent of small intestine smooth muscle contraction. sl 2015-06-11T21:37:46Z up regulation of small intestine smooth muscle contraction up-regulation of small intestine smooth muscle contraction upregulation of small intestine smooth muscle contraction activation of small intestine smooth muscle contraction biological_process GO:1904349 positive regulation of small intestine smooth muscle contraction Any process that activates or increases the frequency, rate or extent of small intestine smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:11991626 up regulation of small intestine smooth muscle contraction GOC:TermGenie up-regulation of small intestine smooth muscle contraction GOC:TermGenie upregulation of small intestine smooth muscle contraction GOC:TermGenie activation of small intestine smooth muscle contraction GOC:TermGenie Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole. rl 2015-06-12T09:10:36Z biological_process regulation of vacuolar protein breakdown regulation of vacuolar protein catabolic process regulation of vacuolar protein catabolism regulation of vacuolar protein degradation GO:1904350 regulation of protein catabolic process in the vacuole Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:25635054 regulation of vacuolar protein breakdown GOC:TermGenie regulation of vacuolar protein catabolic process GOC:TermGenie regulation of vacuolar protein catabolism GOC:TermGenie regulation of vacuolar protein degradation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole. rl 2015-06-12T09:10:42Z down regulation of protein catabolic process in the vacuole down-regulation of protein catabolic process in the vacuole downregulation of protein catabolic process in the vacuole inhibition of protein catabolic process in the vacuole biological_process down regulation of vacuolar protein breakdown down regulation of vacuolar protein catabolic process down regulation of vacuolar protein catabolism down regulation of vacuolar protein degradation down-regulation of vacuolar protein breakdown down-regulation of vacuolar protein catabolic process down-regulation of vacuolar protein catabolism down-regulation of vacuolar protein degradation downregulation of vacuolar protein breakdown downregulation of vacuolar protein catabolic process downregulation of vacuolar protein catabolism downregulation of vacuolar protein degradation inhibition of vacuolar protein breakdown inhibition of vacuolar protein catabolic process inhibition of vacuolar protein catabolism inhibition of vacuolar protein degradation negative regulation of vacuolar protein breakdown negative regulation of vacuolar protein catabolic process negative regulation of vacuolar protein catabolism negative regulation of vacuolar protein degradation GO:1904351 negative regulation of protein catabolic process in the vacuole Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:25635054 down regulation of protein catabolic process in the vacuole GOC:TermGenie down-regulation of protein catabolic process in the vacuole GOC:TermGenie downregulation of protein catabolic process in the vacuole GOC:TermGenie inhibition of protein catabolic process in the vacuole GOC:TermGenie down regulation of vacuolar protein breakdown GOC:TermGenie down regulation of vacuolar protein catabolic process GOC:TermGenie down regulation of vacuolar protein catabolism GOC:TermGenie down regulation of vacuolar protein degradation GOC:TermGenie down-regulation of vacuolar protein breakdown GOC:TermGenie down-regulation of vacuolar protein catabolic process GOC:TermGenie down-regulation of vacuolar protein catabolism GOC:TermGenie down-regulation of vacuolar protein degradation GOC:TermGenie downregulation of vacuolar protein breakdown GOC:TermGenie downregulation of vacuolar protein catabolic process GOC:TermGenie downregulation of vacuolar protein catabolism GOC:TermGenie downregulation of vacuolar protein degradation GOC:TermGenie inhibition of vacuolar protein breakdown GOC:TermGenie inhibition of vacuolar protein catabolic process GOC:TermGenie inhibition of vacuolar protein catabolism GOC:TermGenie inhibition of vacuolar protein degradation GOC:TermGenie negative regulation of vacuolar protein breakdown GOC:TermGenie negative regulation of vacuolar protein catabolic process GOC:TermGenie negative regulation of vacuolar protein catabolism GOC:TermGenie negative regulation of vacuolar protein degradation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole. rl 2015-06-12T09:10:49Z up regulation of protein catabolic process in the vacuole up-regulation of protein catabolic process in the vacuole upregulation of protein catabolic process in the vacuole activation of protein catabolic process in the vacuole biological_process activation of vacuolar protein breakdown activation of vacuolar protein catabolic process activation of vacuolar protein catabolism activation of vacuolar protein degradation positive regulation of vacuolar protein breakdown positive regulation of vacuolar protein catabolic process positive regulation of vacuolar protein catabolism positive regulation of vacuolar protein degradation up regulation of vacuolar protein breakdown up regulation of vacuolar protein catabolic process up regulation of vacuolar protein catabolism up regulation of vacuolar protein degradation up-regulation of vacuolar protein breakdown up-regulation of vacuolar protein catabolic process up-regulation of vacuolar protein catabolism up-regulation of vacuolar protein degradation upregulation of vacuolar protein breakdown upregulation of vacuolar protein catabolic process upregulation of vacuolar protein catabolism upregulation of vacuolar protein degradation GO:1904352 positive regulation of protein catabolic process in the vacuole Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:25635054 up regulation of protein catabolic process in the vacuole GOC:TermGenie up-regulation of protein catabolic process in the vacuole GOC:TermGenie upregulation of protein catabolic process in the vacuole GOC:TermGenie activation of protein catabolic process in the vacuole GOC:TermGenie activation of vacuolar protein breakdown GOC:TermGenie activation of vacuolar protein catabolic process GOC:TermGenie activation of vacuolar protein catabolism GOC:TermGenie activation of vacuolar protein degradation GOC:TermGenie positive regulation of vacuolar protein breakdown GOC:TermGenie positive regulation of vacuolar protein catabolic process GOC:TermGenie positive regulation of vacuolar protein catabolism GOC:TermGenie positive regulation of vacuolar protein degradation GOC:TermGenie up regulation of vacuolar protein breakdown GOC:TermGenie up regulation of vacuolar protein catabolic process GOC:TermGenie up regulation of vacuolar protein catabolism GOC:TermGenie up regulation of vacuolar protein degradation GOC:TermGenie up-regulation of vacuolar protein breakdown GOC:TermGenie up-regulation of vacuolar protein catabolic process GOC:TermGenie up-regulation of vacuolar protein catabolism GOC:TermGenie up-regulation of vacuolar protein degradation GOC:TermGenie upregulation of vacuolar protein breakdown GOC:TermGenie upregulation of vacuolar protein catabolic process GOC:TermGenie upregulation of vacuolar protein catabolism GOC:TermGenie upregulation of vacuolar protein degradation GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to cell periphery. sl 2015-06-22T22:09:25Z biological_process GO:1904375 regulation of protein localization to cell periphery Any process that modulates the frequency, rate or extent of protein localization to cell periphery. GOC:TermGenie GO_REF:0000058 PMID:18216290 Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell periphery. sl 2015-06-22T22:09:32Z down regulation of protein localization to cell periphery down-regulation of protein localization to cell periphery downregulation of protein localization to cell periphery inhibition of protein localization to cell periphery biological_process GO:1904376 negative regulation of protein localization to cell periphery Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell periphery. GOC:TermGenie GO_REF:0000058 PMID:18216290 down regulation of protein localization to cell periphery GOC:TermGenie down-regulation of protein localization to cell periphery GOC:TermGenie downregulation of protein localization to cell periphery GOC:TermGenie inhibition of protein localization to cell periphery GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to cell periphery. sl 2015-06-22T22:09:37Z up regulation of protein localization to cell periphery up-regulation of protein localization to cell periphery upregulation of protein localization to cell periphery activation of protein localization to cell periphery biological_process GO:1904377 positive regulation of protein localization to cell periphery Any process that activates or increases the frequency, rate or extent of protein localization to cell periphery. GOC:TermGenie GO_REF:0000058 PMID:18216290 up regulation of protein localization to cell periphery GOC:TermGenie up-regulation of protein localization to cell periphery GOC:TermGenie upregulation of protein localization to cell periphery GOC:TermGenie activation of protein localization to cell periphery GOC:TermGenie Any process that modulates the frequency, rate or extent of neuromuscular junction development. sl 2015-06-23T19:23:42Z regulation of neuromuscular junction organization biological_process regulation of NMJ stability regulation of neuromuscular junction stability GO:1904396 regulation of neuromuscular junction development Any process that modulates the frequency, rate or extent of neuromuscular junction development. GOC:TermGenie GO_REF:0000058 PMID:7722643 regulation of neuromuscular junction organization GOC:TermGenie regulation of NMJ stability GOC:TermGenie regulation of neuromuscular junction stability GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular junction development. sl 2015-06-23T19:23:48Z down regulation of neuromuscular junction development down regulation of neuromuscular junction organization down-regulation of neuromuscular junction development down-regulation of neuromuscular junction organization downregulation of neuromuscular junction development downregulation of neuromuscular junction organization negative regulation of neuromuscular junction organization inhibition of neuromuscular junction development inhibition of neuromuscular junction organization biological_process down regulation of NMJ stability down regulation of neuromuscular junction stability down-regulation of NMJ stability down-regulation of neuromuscular junction stability downregulation of NMJ stability downregulation of neuromuscular junction stability inhibition of NMJ stability inhibition of neuromuscular junction stability negative regulation of NMJ stability negative regulation of neuromuscular junction stability GO:1904397 negative regulation of neuromuscular junction development Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular junction development. GOC:TermGenie GO_REF:0000058 PMID:7722643 down regulation of neuromuscular junction development GOC:TermGenie down regulation of neuromuscular junction organization GOC:TermGenie down-regulation of neuromuscular junction development GOC:TermGenie down-regulation of neuromuscular junction organization GOC:TermGenie downregulation of neuromuscular junction development GOC:TermGenie downregulation of neuromuscular junction organization GOC:TermGenie negative regulation of neuromuscular junction organization GOC:TermGenie inhibition of neuromuscular junction development GOC:TermGenie inhibition of neuromuscular junction organization GOC:TermGenie down regulation of NMJ stability GOC:TermGenie down regulation of neuromuscular junction stability GOC:TermGenie down-regulation of NMJ stability GOC:TermGenie down-regulation of neuromuscular junction stability GOC:TermGenie downregulation of NMJ stability GOC:TermGenie downregulation of neuromuscular junction stability GOC:TermGenie inhibition of NMJ stability GOC:TermGenie inhibition of neuromuscular junction stability GOC:TermGenie negative regulation of NMJ stability GOC:TermGenie negative regulation of neuromuscular junction stability GOC:TermGenie Any process that activates or increases the frequency, rate or extent of neuromuscular junction development. sl 2015-06-23T19:23:54Z positive regulation of neuromuscular junction organization up regulation of neuromuscular junction development up regulation of neuromuscular junction organization up-regulation of neuromuscular junction development up-regulation of neuromuscular junction organization upregulation of neuromuscular junction development upregulation of neuromuscular junction organization activation of neuromuscular junction development activation of neuromuscular junction organization biological_process activation of NMJ stability activation of neuromuscular junction stability positive regulation of NMJ stability positive regulation of neuromuscular junction stability up regulation of NMJ stability up regulation of neuromuscular junction stability up-regulation of NMJ stability up-regulation of neuromuscular junction stability upregulation of NMJ stability upregulation of neuromuscular junction stability GO:1904398 positive regulation of neuromuscular junction development Any process that activates or increases the frequency, rate or extent of neuromuscular junction development. GOC:TermGenie GO_REF:0000058 PMID:7722643 positive regulation of neuromuscular junction organization GOC:TermGenie up regulation of neuromuscular junction development GOC:TermGenie up regulation of neuromuscular junction organization GOC:TermGenie up-regulation of neuromuscular junction development GOC:TermGenie up-regulation of neuromuscular junction organization GOC:TermGenie upregulation of neuromuscular junction development GOC:TermGenie upregulation of neuromuscular junction organization GOC:TermGenie activation of neuromuscular junction development GOC:TermGenie activation of neuromuscular junction organization GOC:TermGenie activation of NMJ stability GOC:TermGenie activation of neuromuscular junction stability GOC:TermGenie positive regulation of NMJ stability GOC:TermGenie positive regulation of neuromuscular junction stability GOC:TermGenie up regulation of NMJ stability GOC:TermGenie up regulation of neuromuscular junction stability GOC:TermGenie up-regulation of NMJ stability GOC:TermGenie up-regulation of neuromuscular junction stability GOC:TermGenie upregulation of NMJ stability GOC:TermGenie upregulation of neuromuscular junction stability GOC:TermGenie Any process that modulates the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:42Z regulation of secretory granule organisation biological_process regulation of secretory granule organization and biogenesis GO:1904409 regulation of secretory granule organization Any process that modulates the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 regulation of secretory granule organisation GOC:TermGenie regulation of secretory granule organization and biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:49Z down regulation of secretory granule organisation down regulation of secretory granule organization down-regulation of secretory granule organisation down-regulation of secretory granule organization downregulation of secretory granule organisation downregulation of secretory granule organization negative regulation of secretory granule organisation inhibition of secretory granule organisation inhibition of secretory granule organization biological_process down regulation of secretory granule organization and biogenesis down-regulation of secretory granule organization and biogenesis downregulation of secretory granule organization and biogenesis inhibition of secretory granule organization and biogenesis negative regulation of secretory granule organization and biogenesis GO:1904410 negative regulation of secretory granule organization Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 down regulation of secretory granule organisation GOC:TermGenie down regulation of secretory granule organization GOC:TermGenie down-regulation of secretory granule organisation GOC:TermGenie down-regulation of secretory granule organization GOC:TermGenie downregulation of secretory granule organisation GOC:TermGenie downregulation of secretory granule organization GOC:TermGenie negative regulation of secretory granule organisation GOC:TermGenie inhibition of secretory granule organisation GOC:TermGenie inhibition of secretory granule organization GOC:TermGenie down regulation of secretory granule organization and biogenesis GOC:TermGenie down-regulation of secretory granule organization and biogenesis GOC:TermGenie downregulation of secretory granule organization and biogenesis GOC:TermGenie inhibition of secretory granule organization and biogenesis GOC:TermGenie negative regulation of secretory granule organization and biogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:55Z positive regulation of secretory granule organisation up regulation of secretory granule organisation up regulation of secretory granule organization up-regulation of secretory granule organisation up-regulation of secretory granule organization upregulation of secretory granule organisation upregulation of secretory granule organization activation of secretory granule organisation activation of secretory granule organization biological_process activation of secretory granule organization and biogenesis positive regulation of secretory granule organization and biogenesis up regulation of secretory granule organization and biogenesis up-regulation of secretory granule organization and biogenesis upregulation of secretory granule organization and biogenesis GO:1904411 positive regulation of secretory granule organization Any process that activates or increases the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 positive regulation of secretory granule organisation GOC:TermGenie up regulation of secretory granule organisation GOC:TermGenie up regulation of secretory granule organization GOC:TermGenie up-regulation of secretory granule organisation GOC:TermGenie up-regulation of secretory granule organization GOC:TermGenie upregulation of secretory granule organisation GOC:TermGenie upregulation of secretory granule organization GOC:TermGenie activation of secretory granule organisation GOC:TermGenie activation of secretory granule organization GOC:TermGenie activation of secretory granule organization and biogenesis GOC:TermGenie positive regulation of secretory granule organization and biogenesis GOC:TermGenie up regulation of secretory granule organization and biogenesis GOC:TermGenie up-regulation of secretory granule organization and biogenesis GOC:TermGenie upregulation of secretory granule organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of cardiac ventricle development. sl 2015-06-25T19:52:15Z biological_process GO:1904412 regulation of cardiac ventricle development Any process that modulates the frequency, rate or extent of cardiac ventricle development. GOC:TermGenie GO_REF:0000058 PMID:19590510 Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle development. sl 2015-06-25T19:52:21Z down regulation of cardiac ventricle development down-regulation of cardiac ventricle development downregulation of cardiac ventricle development inhibition of cardiac ventricle development biological_process GO:1904413 negative regulation of cardiac ventricle development Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle development. GOC:TermGenie GO_REF:0000058 PMID:19590510 down regulation of cardiac ventricle development GOC:TermGenie down-regulation of cardiac ventricle development GOC:TermGenie downregulation of cardiac ventricle development GOC:TermGenie inhibition of cardiac ventricle development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cardiac ventricle development. sl 2015-06-25T19:52:27Z up regulation of cardiac ventricle development up-regulation of cardiac ventricle development upregulation of cardiac ventricle development activation of cardiac ventricle development biological_process GO:1904414 positive regulation of cardiac ventricle development Any process that activates or increases the frequency, rate or extent of cardiac ventricle development. GOC:TermGenie GO_REF:0000058 PMID:19590510 up regulation of cardiac ventricle development GOC:TermGenie up-regulation of cardiac ventricle development GOC:TermGenie upregulation of cardiac ventricle development GOC:TermGenie activation of cardiac ventricle development GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of neuronal action potential. sl 2015-07-09T18:02:40Z down regulation of neuronal action potential down-regulation of neuronal action potential downregulation of neuronal action potential inhibition of neuronal action potential biological_process down regulation of generation of action potential down-regulation of generation of action potential downregulation of generation of action potential inhibition of generation of action potential negative regulation of generation of action potential GO:1904456 negative regulation of neuronal action potential Any process that stops, prevents or reduces the frequency, rate or extent of neuronal action potential. GOC:TermGenie GO_REF:0000058 PMID:25126967 down regulation of neuronal action potential GOC:TermGenie down-regulation of neuronal action potential GOC:TermGenie downregulation of neuronal action potential GOC:TermGenie inhibition of neuronal action potential GOC:TermGenie down regulation of generation of action potential GOC:TermGenie down-regulation of generation of action potential GOC:TermGenie downregulation of generation of action potential GOC:TermGenie inhibition of generation of action potential GOC:TermGenie negative regulation of generation of action potential GOC:TermGenie Any process that activates or increases the frequency, rate or extent of neuronal action potential. sl 2015-07-09T18:02:46Z up regulation of neuronal action potential up-regulation of neuronal action potential upregulation of neuronal action potential activation of neuronal action potential biological_process activation of generation of action potential positive regulation of generation of action potential up regulation of generation of action potential up-regulation of generation of action potential upregulation of generation of action potential GO:1904457 positive regulation of neuronal action potential Any process that activates or increases the frequency, rate or extent of neuronal action potential. GOC:TermGenie GO_REF:0000058 PMID:25126967 up regulation of neuronal action potential GOC:TermGenie up-regulation of neuronal action potential GOC:TermGenie upregulation of neuronal action potential GOC:TermGenie activation of neuronal action potential GOC:TermGenie activation of generation of action potential GOC:TermGenie positive regulation of generation of action potential GOC:TermGenie up regulation of generation of action potential GOC:TermGenie up-regulation of generation of action potential GOC:TermGenie upregulation of generation of action potential GOC:TermGenie The process whose specific outcome is the progression of a cloacal gland over time, from its formation to the mature structure. mr 2015-07-15T22:14:39Z biological_process GO:1904484 cloacal gland development The process whose specific outcome is the progression of a cloacal gland over time, from its formation to the mature structure. GOC:TermGenie GOC:mr GO_REF:0000094 PMID:18805421 A process in which a protein is transported to, or maintained in, a location within a ciliary transition zone. kmv 2015-07-17T20:43:21Z protein localisation in ciliary transition zone protein localisation to ciliary transition zone protein localization in ciliary transition zone biological_process GO:1904491 protein localization to ciliary transition zone A process in which a protein is transported to, or maintained in, a location within a ciliary transition zone. GOC:TermGenie GOC:kmv GO_REF:0000087 PMID:21422230 protein localisation in ciliary transition zone GOC:TermGenie protein localisation to ciliary transition zone GOC:TermGenie protein localization in ciliary transition zone GOC:TermGenie Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycoprotein stimulus. sl 2015-08-20T16:46:24Z response to glycoproteins biological_process GO:1904587 response to glycoprotein Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycoprotein stimulus. GOC:TermGenie GO_REF:0000071 PMID:14597422 Any apoptotic process in a fat cell. sl 2015-08-27T18:13:06Z adipocyte apoptotic process adipose cell apoptotic process adipocyte apoptosis adipose cell apoptosis fat cell apoptosis biological_process GO:1904606 fat cell apoptotic process Any apoptotic process in a fat cell. GOC:TermGenie GO_REF:0000085 PMID:17024416 adipocyte apoptotic process GOC:TermGenie adipose cell apoptotic process GOC:TermGenie adipocyte apoptosis GOC:TermGenie adipose cell apoptosis GOC:TermGenie fat cell apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of fat cell apoptotic process. sl 2015-08-31T20:59:28Z regulation of adipocyte apoptotic process regulation of adipose cell apoptotic process regulation of adipocyte apoptosis regulation of adipose cell apoptosis regulation of fat cell apoptosis biological_process GO:1904649 regulation of fat cell apoptotic process Any process that modulates the frequency, rate or extent of fat cell apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:17024416 regulation of adipocyte apoptotic process GOC:TermGenie regulation of adipose cell apoptotic process GOC:TermGenie regulation of adipocyte apoptosis GOC:TermGenie regulation of adipose cell apoptosis GOC:TermGenie regulation of fat cell apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of fat cell apoptotic process. sl 2015-08-31T20:59:34Z down regulation of adipocyte apoptotic process down regulation of adipose cell apoptotic process down regulation of fat cell apoptotic process down-regulation of adipocyte apoptotic process down-regulation of adipose cell apoptotic process down-regulation of fat cell apoptotic process downregulation of adipocyte apoptotic process downregulation of adipose cell apoptotic process downregulation of fat cell apoptotic process negative regulation of adipocyte apoptotic process negative regulation of adipose cell apoptotic process down regulation of adipocyte apoptosis down regulation of adipose cell apoptosis down regulation of fat cell apoptosis down-regulation of adipocyte apoptosis down-regulation of adipose cell apoptosis down-regulation of fat cell apoptosis downregulation of adipocyte apoptosis downregulation of adipose cell apoptosis downregulation of fat cell apoptosis inhibition of adipocyte apoptosis inhibition of adipocyte apoptotic process inhibition of adipose cell apoptosis inhibition of adipose cell apoptotic process inhibition of fat cell apoptosis inhibition of fat cell apoptotic process negative regulation of adipocyte apoptosis negative regulation of adipose cell apoptosis negative regulation of fat cell apoptosis biological_process GO:1904650 negative regulation of fat cell apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of fat cell apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:17024416 down regulation of adipocyte apoptotic process GOC:TermGenie down regulation of adipose cell apoptotic process GOC:TermGenie down regulation of fat cell apoptotic process GOC:TermGenie down-regulation of adipocyte apoptotic process GOC:TermGenie down-regulation of adipose cell apoptotic process GOC:TermGenie down-regulation of fat cell apoptotic process GOC:TermGenie downregulation of adipocyte apoptotic process GOC:TermGenie downregulation of adipose cell apoptotic process GOC:TermGenie downregulation of fat cell apoptotic process GOC:TermGenie negative regulation of adipocyte apoptotic process GOC:TermGenie negative regulation of adipose cell apoptotic process GOC:TermGenie down regulation of adipocyte apoptosis GOC:TermGenie down regulation of adipose cell apoptosis GOC:TermGenie down regulation of fat cell apoptosis GOC:TermGenie down-regulation of adipocyte apoptosis GOC:TermGenie down-regulation of adipose cell apoptosis GOC:TermGenie down-regulation of fat cell apoptosis GOC:TermGenie downregulation of adipocyte apoptosis GOC:TermGenie downregulation of adipose cell apoptosis GOC:TermGenie downregulation of fat cell apoptosis GOC:TermGenie inhibition of adipocyte apoptosis GOC:TermGenie inhibition of adipocyte apoptotic process GOC:TermGenie inhibition of adipose cell apoptosis GOC:TermGenie inhibition of adipose cell apoptotic process GOC:TermGenie inhibition of fat cell apoptosis GOC:TermGenie inhibition of fat cell apoptotic process GOC:TermGenie negative regulation of adipocyte apoptosis GOC:TermGenie negative regulation of adipose cell apoptosis GOC:TermGenie negative regulation of fat cell apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of fat cell apoptotic process. sl 2015-08-31T20:59:40Z positive regulation of adipocyte apoptotic process positive regulation of adipose cell apoptotic process up regulation of adipocyte apoptotic process up regulation of adipose cell apoptotic process up regulation of fat cell apoptotic process up-regulation of adipocyte apoptotic process up-regulation of adipose cell apoptotic process up-regulation of fat cell apoptotic process upregulation of adipocyte apoptotic process upregulation of adipose cell apoptotic process upregulation of fat cell apoptotic process activation of adipocyte apoptosis activation of adipocyte apoptotic process activation of adipose cell apoptosis activation of adipose cell apoptotic process activation of fat cell apoptosis activation of fat cell apoptotic process positive regulation of adipocyte apoptosis positive regulation of adipose cell apoptosis positive regulation of fat cell apoptosis up regulation of adipocyte apoptosis up regulation of adipose cell apoptosis up regulation of fat cell apoptosis up-regulation of adipocyte apoptosis up-regulation of adipose cell apoptosis up-regulation of fat cell apoptosis upregulation of adipocyte apoptosis upregulation of adipose cell apoptosis upregulation of fat cell apoptosis biological_process GO:1904651 positive regulation of fat cell apoptotic process Any process that activates or increases the frequency, rate or extent of fat cell apoptotic process. GOC:TermGenie GO_REF:0000058 PMID:17024416 positive regulation of adipocyte apoptotic process GOC:TermGenie positive regulation of adipose cell apoptotic process GOC:TermGenie up regulation of adipocyte apoptotic process GOC:TermGenie up regulation of adipose cell apoptotic process GOC:TermGenie up regulation of fat cell apoptotic process GOC:TermGenie up-regulation of adipocyte apoptotic process GOC:TermGenie up-regulation of adipose cell apoptotic process GOC:TermGenie up-regulation of fat cell apoptotic process GOC:TermGenie upregulation of adipocyte apoptotic process GOC:TermGenie upregulation of adipose cell apoptotic process GOC:TermGenie upregulation of fat cell apoptotic process GOC:TermGenie activation of adipocyte apoptosis GOC:TermGenie activation of adipocyte apoptotic process GOC:TermGenie activation of adipose cell apoptosis GOC:TermGenie activation of adipose cell apoptotic process GOC:TermGenie activation of fat cell apoptosis GOC:TermGenie activation of fat cell apoptotic process GOC:TermGenie positive regulation of adipocyte apoptosis GOC:TermGenie positive regulation of adipose cell apoptosis GOC:TermGenie positive regulation of fat cell apoptosis GOC:TermGenie up regulation of adipocyte apoptosis GOC:TermGenie up regulation of adipose cell apoptosis GOC:TermGenie up regulation of fat cell apoptosis GOC:TermGenie up-regulation of adipocyte apoptosis GOC:TermGenie up-regulation of adipose cell apoptosis GOC:TermGenie up-regulation of fat cell apoptosis GOC:TermGenie upregulation of adipocyte apoptosis GOC:TermGenie upregulation of adipose cell apoptosis GOC:TermGenie upregulation of fat cell apoptosis GOC:TermGenie The process in which glucose is transported across a membrane. vw 2015-09-04T17:20:16Z GO:0015758 biological_process glucose transport GO:1904659 glucose transmembrane transport The process in which glucose is transported across a membrane. GOC:TermGenie GO_REF:0000069 PMID:9090050 Any process that modulates the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:22Z regulation of somatic stem cell renewal biological_process GO:1904675 regulation of somatic stem cell division Any process that modulates the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 regulation of somatic stem cell renewal GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:28Z down regulation of somatic stem cell division down regulation of somatic stem cell renewal down-regulation of somatic stem cell division down-regulation of somatic stem cell renewal downregulation of somatic stem cell division downregulation of somatic stem cell renewal negative regulation of somatic stem cell renewal inhibition of somatic stem cell division inhibition of somatic stem cell renewal biological_process GO:1904676 negative regulation of somatic stem cell division Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 down regulation of somatic stem cell division GOC:TermGenie down regulation of somatic stem cell renewal GOC:TermGenie down-regulation of somatic stem cell division GOC:TermGenie down-regulation of somatic stem cell renewal GOC:TermGenie downregulation of somatic stem cell division GOC:TermGenie downregulation of somatic stem cell renewal GOC:TermGenie negative regulation of somatic stem cell renewal GOC:TermGenie inhibition of somatic stem cell division GOC:TermGenie inhibition of somatic stem cell renewal GOC:TermGenie Any process that activates or increases the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:34Z positive regulation of somatic stem cell renewal up regulation of somatic stem cell division up regulation of somatic stem cell renewal up-regulation of somatic stem cell division up-regulation of somatic stem cell renewal upregulation of somatic stem cell division upregulation of somatic stem cell renewal activation of somatic stem cell division activation of somatic stem cell renewal biological_process GO:1904677 positive regulation of somatic stem cell division Any process that activates or increases the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 positive regulation of somatic stem cell renewal GOC:TermGenie up regulation of somatic stem cell division GOC:TermGenie up regulation of somatic stem cell renewal GOC:TermGenie up-regulation of somatic stem cell division GOC:TermGenie up-regulation of somatic stem cell renewal GOC:TermGenie upregulation of somatic stem cell division GOC:TermGenie upregulation of somatic stem cell renewal GOC:TermGenie activation of somatic stem cell division GOC:TermGenie activation of somatic stem cell renewal GOC:TermGenie Enables the transfer of a peptide from one side of a membrane to the other. tb 2015-09-22T18:50:41Z GO:0015197 GO:0015637 Reactome:R-HSA-1500817 molecular_function peptide transporter activity peptide uptake permease activity GO:1904680 peptide transmembrane transporter activity Enables the transfer of a peptide from one side of a membrane to the other. GOC:TermGenie GOC:vw GO_REF:0000070 Reactome:R-HSA-1500817 Glutathione is taken up by the bacterium Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell proliferation. sl 2015-09-25T15:23:38Z down regulation of pancreatic B cell proliferation down regulation of pancreatic beta cell proliferation down regulation of type B pancreatic cell proliferation down-regulation of pancreatic B cell proliferation down-regulation of pancreatic beta cell proliferation down-regulation of type B pancreatic cell proliferation downregulation of pancreatic B cell proliferation downregulation of pancreatic beta cell proliferation downregulation of type B pancreatic cell proliferation negative regulation of pancreatic B cell proliferation negative regulation of pancreatic beta cell proliferation inhibition of pancreatic B cell proliferation inhibition of pancreatic beta cell proliferation inhibition of type B pancreatic cell proliferation biological_process GO:1904691 negative regulation of type B pancreatic cell proliferation Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:24055447 down regulation of pancreatic B cell proliferation GOC:TermGenie down regulation of pancreatic beta cell proliferation GOC:TermGenie down regulation of type B pancreatic cell proliferation GOC:TermGenie down-regulation of pancreatic B cell proliferation GOC:TermGenie down-regulation of pancreatic beta cell proliferation GOC:TermGenie down-regulation of type B pancreatic cell proliferation GOC:TermGenie downregulation of pancreatic B cell proliferation GOC:TermGenie downregulation of pancreatic beta cell proliferation GOC:TermGenie downregulation of type B pancreatic cell proliferation GOC:TermGenie negative regulation of pancreatic B cell proliferation GOC:TermGenie negative regulation of pancreatic beta cell proliferation GOC:TermGenie inhibition of pancreatic B cell proliferation GOC:TermGenie inhibition of pancreatic beta cell proliferation GOC:TermGenie inhibition of type B pancreatic cell proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of type B pancreatic cell proliferation. sl 2015-09-25T15:23:44Z positive regulation of pancreatic B cell proliferation positive regulation of pancreatic beta cell proliferation up regulation of pancreatic B cell proliferation up regulation of pancreatic beta cell proliferation up regulation of type B pancreatic cell proliferation up-regulation of pancreatic B cell proliferation up-regulation of pancreatic beta cell proliferation up-regulation of type B pancreatic cell proliferation upregulation of pancreatic B cell proliferation upregulation of pancreatic beta cell proliferation upregulation of type B pancreatic cell proliferation activation of pancreatic B cell proliferation activation of pancreatic beta cell proliferation activation of type B pancreatic cell proliferation biological_process GO:1904692 positive regulation of type B pancreatic cell proliferation Any process that activates or increases the frequency, rate or extent of type B pancreatic cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:24055447 positive regulation of pancreatic B cell proliferation GOC:TermGenie positive regulation of pancreatic beta cell proliferation GOC:TermGenie up regulation of pancreatic B cell proliferation GOC:TermGenie up regulation of pancreatic beta cell proliferation GOC:TermGenie up regulation of type B pancreatic cell proliferation GOC:TermGenie up-regulation of pancreatic B cell proliferation GOC:TermGenie up-regulation of pancreatic beta cell proliferation GOC:TermGenie up-regulation of type B pancreatic cell proliferation GOC:TermGenie upregulation of pancreatic B cell proliferation GOC:TermGenie upregulation of pancreatic beta cell proliferation GOC:TermGenie upregulation of type B pancreatic cell proliferation GOC:TermGenie activation of pancreatic B cell proliferation GOC:TermGenie activation of pancreatic beta cell proliferation GOC:TermGenie activation of type B pancreatic cell proliferation GOC:TermGenie The developmental process by which a midbrain is generated and organized. bf 2015-09-29T09:15:28Z MB morphogenesis biological_process mesencephalon morphogenesis GO:1904693 midbrain morphogenesis The developmental process by which a midbrain is generated and organized. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000083 PMID:21347250 MB morphogenesis GOC:TermGenie mesencephalon morphogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of acinar cell proliferation. sl 2015-09-30T15:19:50Z regulation of acinic cell proliferation regulation of acinous cell proliferation biological_process GO:1904697 regulation of acinar cell proliferation Any process that modulates the frequency, rate or extent of acinar cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:9788538 regulation of acinic cell proliferation GOC:TermGenie regulation of acinous cell proliferation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of acinar cell proliferation. sl 2015-09-30T15:19:57Z down regulation of acinar cell proliferation down regulation of acinic cell proliferation down regulation of acinous cell proliferation down-regulation of acinar cell proliferation down-regulation of acinic cell proliferation down-regulation of acinous cell proliferation downregulation of acinar cell proliferation downregulation of acinic cell proliferation downregulation of acinous cell proliferation negative regulation of acinic cell proliferation negative regulation of acinous cell proliferation inhibition of acinar cell proliferation inhibition of acinic cell proliferation inhibition of acinous cell proliferation biological_process GO:1904698 negative regulation of acinar cell proliferation Any process that stops, prevents or reduces the frequency, rate or extent of acinar cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:9788538 down regulation of acinar cell proliferation GOC:TermGenie down regulation of acinic cell proliferation GOC:TermGenie down regulation of acinous cell proliferation GOC:TermGenie down-regulation of acinar cell proliferation GOC:TermGenie down-regulation of acinic cell proliferation GOC:TermGenie down-regulation of acinous cell proliferation GOC:TermGenie downregulation of acinar cell proliferation GOC:TermGenie downregulation of acinic cell proliferation GOC:TermGenie downregulation of acinous cell proliferation GOC:TermGenie negative regulation of acinic cell proliferation GOC:TermGenie negative regulation of acinous cell proliferation GOC:TermGenie inhibition of acinar cell proliferation GOC:TermGenie inhibition of acinic cell proliferation GOC:TermGenie inhibition of acinous cell proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of acinar cell proliferation. sl 2015-09-30T15:20:03Z positive regulation of acinic cell proliferation positive regulation of acinous cell proliferation up regulation of acinar cell proliferation up regulation of acinic cell proliferation up regulation of acinous cell proliferation up-regulation of acinar cell proliferation up-regulation of acinic cell proliferation up-regulation of acinous cell proliferation upregulation of acinar cell proliferation upregulation of acinic cell proliferation upregulation of acinous cell proliferation activation of acinar cell proliferation activation of acinic cell proliferation activation of acinous cell proliferation biological_process GO:1904699 positive regulation of acinar cell proliferation Any process that activates or increases the frequency, rate or extent of acinar cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:9788538 positive regulation of acinic cell proliferation GOC:TermGenie positive regulation of acinous cell proliferation GOC:TermGenie up regulation of acinar cell proliferation GOC:TermGenie up regulation of acinic cell proliferation GOC:TermGenie up regulation of acinous cell proliferation GOC:TermGenie up-regulation of acinar cell proliferation GOC:TermGenie up-regulation of acinic cell proliferation GOC:TermGenie up-regulation of acinous cell proliferation GOC:TermGenie upregulation of acinar cell proliferation GOC:TermGenie upregulation of acinic cell proliferation GOC:TermGenie upregulation of acinous cell proliferation GOC:TermGenie activation of acinar cell proliferation GOC:TermGenie activation of acinic cell proliferation GOC:TermGenie activation of acinous cell proliferation GOC:TermGenie Any process that modulates the frequency, rate or extent of vascular smooth muscle cell proliferation. sl 2015-10-01T16:05:20Z regulation of VSMC proliferation regulation of vascular smooth muscle cell proliferation biological_process GO:1904705 regulation of vascular associated smooth muscle cell proliferation Any process that modulates the frequency, rate or extent of vascular smooth muscle cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:23246467 regulation of VSMC proliferation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell proliferation. sl 2015-10-01T16:05:26Z down regulation of VSMC proliferation down regulation of vascular smooth muscle cell proliferation down-regulation of VSMC proliferation down-regulation of vascular smooth muscle cell proliferation downregulation of VSMC proliferation downregulation of vascular smooth muscle cell proliferation negative regulation of VSMC proliferation negative regulation of vascular smooth muscle cell proliferation inhibition of VSMC proliferation inhibition of vascular smooth muscle cell proliferation biological_process GO:1904706 negative regulation of vascular associated smooth muscle cell proliferation Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:23246467 down regulation of VSMC proliferation GOC:TermGenie down regulation of vascular smooth muscle cell proliferation GOC:TermGenie down-regulation of VSMC proliferation GOC:TermGenie down-regulation of vascular smooth muscle cell proliferation GOC:TermGenie downregulation of VSMC proliferation GOC:TermGenie downregulation of vascular smooth muscle cell proliferation GOC:TermGenie negative regulation of VSMC proliferation GOC:TermGenie inhibition of VSMC proliferation GOC:TermGenie inhibition of vascular smooth muscle cell proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell proliferation. sl 2015-10-01T16:05:32Z positive regulation of VSMC proliferation positive regulation of vascular smooth muscle cell proliferation up regulation of VSMC proliferation up regulation of vascular smooth muscle cell proliferation up-regulation of VSMC proliferation up-regulation of vascular smooth muscle cell proliferation upregulation of VSMC proliferation upregulation of vascular smooth muscle cell proliferation activation of VSMC proliferation activation of vascular smooth muscle cell proliferation biological_process GO:1904707 positive regulation of vascular associated smooth muscle cell proliferation Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:23246467 positive regulation of VSMC proliferation GOC:TermGenie up regulation of VSMC proliferation GOC:TermGenie up regulation of vascular smooth muscle cell proliferation GOC:TermGenie up-regulation of VSMC proliferation GOC:TermGenie up-regulation of vascular smooth muscle cell proliferation GOC:TermGenie upregulation of VSMC proliferation GOC:TermGenie upregulation of vascular smooth muscle cell proliferation GOC:TermGenie activation of VSMC proliferation GOC:TermGenie activation of vascular smooth muscle cell proliferation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T14:12:27Z down regulation of apoptotic cell death involved in anatomical structure development down regulation of apoptotic cell death involved in development of an anatomical structure down regulation of apoptotic process involved in anatomical structure development down regulation of apoptotic process involved in development down regulation of apoptotic process involved in development of an anatomical structure down regulation of apoptotic programmed cell death involved in anatomical structure development down regulation of apoptotic programmed cell death involved in development of an anatomical structure down regulation of programmed cell death by apoptosis involved in anatomical structure development down regulation of programmed cell death by apoptosis involved in development of an anatomical structure down-regulation of apoptotic cell death involved in anatomical structure development down-regulation of apoptotic cell death involved in development of an anatomical structure down-regulation of apoptotic process involved in anatomical structure development down-regulation of apoptotic process involved in development down-regulation of apoptotic process involved in development of an anatomical structure down-regulation of apoptotic programmed cell death involved in anatomical structure development down-regulation of apoptotic programmed cell death involved in development of an anatomical structure down-regulation of programmed cell death by apoptosis involved in anatomical structure development down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure downregulation of apoptotic cell death involved in anatomical structure development downregulation of apoptotic cell death involved in development of an anatomical structure downregulation of apoptotic process involved in anatomical structure development downregulation of apoptotic process involved in development downregulation of apoptotic process involved in development of an anatomical structure downregulation of apoptotic programmed cell death involved in anatomical structure development downregulation of apoptotic programmed cell death involved in development of an anatomical structure downregulation of programmed cell death by apoptosis involved in anatomical structure development downregulation of programmed cell death by apoptosis involved in development of an anatomical structure negative regulation of apoptotic cell death involved in anatomical structure development negative regulation of apoptotic cell death involved in development of an anatomical structure negative regulation of apoptotic process involved in anatomical structure development negative regulation of apoptotic process involved in development of an anatomical structure negative regulation of apoptotic programmed cell death involved in anatomical structure development negative regulation of apoptotic programmed cell death involved in development of an anatomical structure negative regulation of programmed cell death by apoptosis involved in anatomical structure development negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure down regulation of activation of apoptosis involved in anatomical structure development down regulation of activation of apoptosis involved in development of an anatomical structure down regulation of apoptosis involved in anatomical structure development down regulation of apoptosis involved in development of an anatomical structure down regulation of apoptosis signaling involved in anatomical structure development down regulation of apoptosis signaling involved in development of an anatomical structure down regulation of apoptotic program involved in anatomical structure development down regulation of apoptotic program involved in development of an anatomical structure down regulation of type I programmed cell death involved in anatomical structure development down regulation of type I programmed cell death involved in development of an anatomical structure down-regulation of activation of apoptosis involved in anatomical structure development down-regulation of activation of apoptosis involved in development of an anatomical structure down-regulation of apoptosis involved in anatomical structure development down-regulation of apoptosis involved in development of an anatomical structure down-regulation of apoptosis signaling involved in anatomical structure development down-regulation of apoptosis signaling involved in development of an anatomical structure down-regulation of apoptotic program involved in anatomical structure development down-regulation of apoptotic program involved in development of an anatomical structure down-regulation of type I programmed cell death involved in anatomical structure development down-regulation of type I programmed cell death involved in development of an anatomical structure downregulation of activation of apoptosis involved in anatomical structure development downregulation of activation of apoptosis involved in development of an anatomical structure downregulation of apoptosis involved in anatomical structure development downregulation of apoptosis involved in development of an anatomical structure downregulation of apoptosis signaling involved in anatomical structure development downregulation of apoptosis signaling involved in development of an anatomical structure downregulation of apoptotic program involved in anatomical structure development downregulation of apoptotic program involved in development of an anatomical structure downregulation of type I programmed cell death involved in anatomical structure development downregulation of type I programmed cell death involved in development of an anatomical structure inhibition of activation of apoptosis involved in anatomical structure development inhibition of activation of apoptosis involved in development of an anatomical structure inhibition of apoptosis involved in anatomical structure development inhibition of apoptosis involved in development of an anatomical structure inhibition of apoptosis signaling involved in anatomical structure development inhibition of apoptosis signaling involved in development of an anatomical structure inhibition of apoptotic cell death involved in anatomical structure development inhibition of apoptotic cell death involved in development of an anatomical structure inhibition of apoptotic process involved in anatomical structure development inhibition of apoptotic process involved in development inhibition of apoptotic process involved in development of an anatomical structure inhibition of apoptotic program involved in anatomical structure development inhibition of apoptotic program involved in development of an anatomical structure inhibition of apoptotic programmed cell death involved in anatomical structure development inhibition of apoptotic programmed cell death involved in development of an anatomical structure inhibition of programmed cell death by apoptosis involved in anatomical structure development inhibition of programmed cell death by apoptosis involved in development of an anatomical structure inhibition of type I programmed cell death involved in anatomical structure development inhibition of type I programmed cell death involved in development of an anatomical structure negative regulation of activation of apoptosis involved in anatomical structure development negative regulation of activation of apoptosis involved in development of an anatomical structure negative regulation of apoptosis involved in anatomical structure development negative regulation of apoptosis involved in development of an anatomical structure negative regulation of apoptosis signaling involved in anatomical structure development negative regulation of apoptosis signaling involved in development of an anatomical structure negative regulation of apoptotic program involved in anatomical structure development negative regulation of apoptotic program involved in development of an anatomical structure negative regulation of type I programmed cell death involved in anatomical structure development negative regulation of type I programmed cell death involved in development of an anatomical structure biological_process down regulation of apoptosis activator activity involved in anatomical structure development down regulation of apoptosis activator activity involved in development of an anatomical structure down regulation of commitment to apoptosis involved in anatomical structure development down regulation of commitment to apoptosis involved in development of an anatomical structure down regulation of induction of apoptosis by p53 involved in anatomical structure development down regulation of induction of apoptosis by p53 involved in development of an anatomical structure down regulation of induction of apoptosis involved in anatomical structure development down regulation of induction of apoptosis involved in development of an anatomical structure down regulation of signaling (initiator) caspase activity involved in anatomical structure development down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure down-regulation of apoptosis activator activity involved in anatomical structure development down-regulation of apoptosis activator activity involved in development of an anatomical structure down-regulation of commitment to apoptosis involved in anatomical structure development down-regulation of commitment to apoptosis involved in development of an anatomical structure down-regulation of induction of apoptosis by p53 involved in anatomical structure development down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure down-regulation of induction of apoptosis involved in anatomical structure development down-regulation of induction of apoptosis involved in development of an anatomical structure down-regulation of signaling (initiator) caspase activity involved in anatomical structure development down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure downregulation of apoptosis activator activity involved in anatomical structure development downregulation of apoptosis activator activity involved in development of an anatomical structure downregulation of commitment to apoptosis involved in anatomical structure development downregulation of commitment to apoptosis involved in development of an anatomical structure downregulation of induction of apoptosis by p53 involved in anatomical structure development downregulation of induction of apoptosis by p53 involved in development of an anatomical structure downregulation of induction of apoptosis involved in anatomical structure development downregulation of induction of apoptosis involved in development of an anatomical structure downregulation of signaling (initiator) caspase activity involved in anatomical structure development downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure inhibition of apoptosis activator activity involved in anatomical structure development inhibition of apoptosis activator activity involved in development of an anatomical structure inhibition of commitment to apoptosis involved in anatomical structure development inhibition of commitment to apoptosis involved in development of an anatomical structure inhibition of induction of apoptosis by p53 involved in anatomical structure development inhibition of induction of apoptosis by p53 involved in development of an anatomical structure inhibition of induction of apoptosis involved in anatomical structure development inhibition of induction of apoptosis involved in development of an anatomical structure inhibition of signaling (initiator) caspase activity involved in anatomical structure development inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure negative regulation of apoptosis activator activity involved in anatomical structure development negative regulation of apoptosis activator activity involved in development of an anatomical structure negative regulation of commitment to apoptosis involved in anatomical structure development negative regulation of commitment to apoptosis involved in development of an anatomical structure negative regulation of induction of apoptosis by p53 involved in anatomical structure development negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure negative regulation of induction of apoptosis involved in anatomical structure development negative regulation of induction of apoptosis involved in development of an anatomical structure negative regulation of signaling (initiator) caspase activity involved in anatomical structure development negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904746 U4PR86 in PMID:22801495 inferred from mutant phenotype negative regulation of apoptotic process involved in development Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 down regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie down regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic process involved in anatomical structure development GOC:TermGenie down regulation of apoptotic process involved in development GOC:TermGenie down regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie down regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie down regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie down regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic process involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic process involved in development GOC:TermGenie down-regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie downregulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic process involved in anatomical structure development GOC:TermGenie downregulation of apoptotic process involved in development GOC:TermGenie downregulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie downregulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie downregulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie downregulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic process involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie down regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic program involved in anatomical structure development GOC:TermGenie down regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie down regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie down regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic program involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie down-regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie down-regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie downregulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie downregulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic program involved in anatomical structure development GOC:TermGenie downregulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie downregulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie downregulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie inhibition of activation of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis signaling involved in anatomical structure development GOC:TermGenie inhibition of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic cell death involved in anatomical structure development GOC:TermGenie inhibition of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic process involved in anatomical structure development GOC:TermGenie inhibition of apoptotic process involved in development GOC:TermGenie inhibition of apoptotic process involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic program involved in anatomical structure development GOC:TermGenie inhibition of apoptotic program involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie inhibition of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie inhibition of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie inhibition of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of type I programmed cell death involved in anatomical structure development GOC:TermGenie inhibition of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic program involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie negative regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie negative regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie down regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie down regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie down regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie down regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie down regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie down-regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie down-regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie downregulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie downregulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie downregulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie downregulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie downregulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis activator activity involved in anatomical structure development GOC:TermGenie inhibition of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie inhibition of commitment to apoptosis involved in anatomical structure development GOC:TermGenie inhibition of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie inhibition of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie inhibition of induction of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie negative regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie negative regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T14:12:34Z positive regulation of apoptotic cell death involved in anatomical structure development positive regulation of apoptotic cell death involved in development of an anatomical structure positive regulation of apoptotic process involved in anatomical structure development positive regulation of apoptotic process involved in development of an anatomical structure positive regulation of apoptotic programmed cell death involved in anatomical structure development positive regulation of apoptotic programmed cell death involved in development of an anatomical structure positive regulation of programmed cell death by apoptosis involved in anatomical structure development positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure up regulation of apoptotic cell death involved in anatomical structure development up regulation of apoptotic cell death involved in development of an anatomical structure up regulation of apoptotic process involved in anatomical structure development up regulation of apoptotic process involved in development up regulation of apoptotic process involved in development of an anatomical structure up regulation of apoptotic programmed cell death involved in anatomical structure development up regulation of apoptotic programmed cell death involved in development of an anatomical structure up regulation of programmed cell death by apoptosis involved in anatomical structure development up regulation of programmed cell death by apoptosis involved in development of an anatomical structure up-regulation of apoptotic cell death involved in anatomical structure development up-regulation of apoptotic cell death involved in development of an anatomical structure up-regulation of apoptotic process involved in anatomical structure development up-regulation of apoptotic process involved in development up-regulation of apoptotic process involved in development of an anatomical structure up-regulation of apoptotic programmed cell death involved in anatomical structure development up-regulation of apoptotic programmed cell death involved in development of an anatomical structure up-regulation of programmed cell death by apoptosis involved in anatomical structure development up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure upregulation of apoptotic cell death involved in anatomical structure development upregulation of apoptotic cell death involved in development of an anatomical structure upregulation of apoptotic process involved in anatomical structure development upregulation of apoptotic process involved in development upregulation of apoptotic process involved in development of an anatomical structure upregulation of apoptotic programmed cell death involved in anatomical structure development upregulation of apoptotic programmed cell death involved in development of an anatomical structure upregulation of programmed cell death by apoptosis involved in anatomical structure development upregulation of programmed cell death by apoptosis involved in development of an anatomical structure activation of activation of apoptosis involved in anatomical structure development activation of activation of apoptosis involved in development of an anatomical structure activation of apoptosis involved in anatomical structure development activation of apoptosis involved in development of an anatomical structure activation of apoptosis signaling involved in anatomical structure development activation of apoptosis signaling involved in development of an anatomical structure activation of apoptotic cell death involved in anatomical structure development activation of apoptotic cell death involved in development of an anatomical structure activation of apoptotic process involved in anatomical structure development activation of apoptotic process involved in development activation of apoptotic process involved in development of an anatomical structure activation of apoptotic program involved in anatomical structure development activation of apoptotic program involved in development of an anatomical structure activation of apoptotic programmed cell death involved in anatomical structure development activation of apoptotic programmed cell death involved in development of an anatomical structure activation of programmed cell death by apoptosis involved in anatomical structure development activation of programmed cell death by apoptosis involved in development of an anatomical structure activation of type I programmed cell death involved in anatomical structure development activation of type I programmed cell death involved in development of an anatomical structure positive regulation of activation of apoptosis involved in anatomical structure development positive regulation of activation of apoptosis involved in development of an anatomical structure positive regulation of apoptosis involved in anatomical structure development positive regulation of apoptosis involved in development of an anatomical structure positive regulation of apoptosis signaling involved in anatomical structure development positive regulation of apoptosis signaling involved in development of an anatomical structure positive regulation of apoptotic program involved in anatomical structure development positive regulation of apoptotic program involved in development of an anatomical structure positive regulation of type I programmed cell death involved in anatomical structure development positive regulation of type I programmed cell death involved in development of an anatomical structure up regulation of activation of apoptosis involved in anatomical structure development up regulation of activation of apoptosis involved in development of an anatomical structure up regulation of apoptosis involved in anatomical structure development up regulation of apoptosis involved in development of an anatomical structure up regulation of apoptosis signaling involved in anatomical structure development up regulation of apoptosis signaling involved in development of an anatomical structure up regulation of apoptotic program involved in anatomical structure development up regulation of apoptotic program involved in development of an anatomical structure up regulation of type I programmed cell death involved in anatomical structure development up regulation of type I programmed cell death involved in development of an anatomical structure up-regulation of activation of apoptosis involved in anatomical structure development up-regulation of activation of apoptosis involved in development of an anatomical structure up-regulation of apoptosis involved in anatomical structure development up-regulation of apoptosis involved in development of an anatomical structure up-regulation of apoptosis signaling involved in anatomical structure development up-regulation of apoptosis signaling involved in development of an anatomical structure up-regulation of apoptotic program involved in anatomical structure development up-regulation of apoptotic program involved in development of an anatomical structure up-regulation of type I programmed cell death involved in anatomical structure development up-regulation of type I programmed cell death involved in development of an anatomical structure upregulation of activation of apoptosis involved in anatomical structure development upregulation of activation of apoptosis involved in development of an anatomical structure upregulation of apoptosis involved in anatomical structure development upregulation of apoptosis involved in development of an anatomical structure upregulation of apoptosis signaling involved in anatomical structure development upregulation of apoptosis signaling involved in development of an anatomical structure upregulation of apoptotic program involved in anatomical structure development upregulation of apoptotic program involved in development of an anatomical structure upregulation of type I programmed cell death involved in anatomical structure development upregulation of type I programmed cell death involved in development of an anatomical structure biological_process activation of apoptosis activator activity involved in anatomical structure development activation of apoptosis activator activity involved in development of an anatomical structure activation of commitment to apoptosis involved in anatomical structure development activation of commitment to apoptosis involved in development of an anatomical structure activation of induction of apoptosis by p53 involved in anatomical structure development activation of induction of apoptosis by p53 involved in development of an anatomical structure activation of induction of apoptosis involved in anatomical structure development activation of induction of apoptosis involved in development of an anatomical structure activation of signaling (initiator) caspase activity involved in anatomical structure development activation of signaling (initiator) caspase activity involved in development of an anatomical structure positive regulation of apoptosis activator activity involved in anatomical structure development positive regulation of apoptosis activator activity involved in development of an anatomical structure positive regulation of commitment to apoptosis involved in anatomical structure development positive regulation of commitment to apoptosis involved in development of an anatomical structure positive regulation of induction of apoptosis by p53 involved in anatomical structure development positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure positive regulation of induction of apoptosis involved in anatomical structure development positive regulation of induction of apoptosis involved in development of an anatomical structure positive regulation of signaling (initiator) caspase activity involved in anatomical structure development positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure up regulation of apoptosis activator activity involved in anatomical structure development up regulation of apoptosis activator activity involved in development of an anatomical structure up regulation of commitment to apoptosis involved in anatomical structure development up regulation of commitment to apoptosis involved in development of an anatomical structure up regulation of induction of apoptosis by p53 involved in anatomical structure development up regulation of induction of apoptosis by p53 involved in development of an anatomical structure up regulation of induction of apoptosis involved in anatomical structure development up regulation of induction of apoptosis involved in development of an anatomical structure up regulation of signaling (initiator) caspase activity involved in anatomical structure development up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure up-regulation of apoptosis activator activity involved in anatomical structure development up-regulation of apoptosis activator activity involved in development of an anatomical structure up-regulation of commitment to apoptosis involved in anatomical structure development up-regulation of commitment to apoptosis involved in development of an anatomical structure up-regulation of induction of apoptosis by p53 involved in anatomical structure development up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure up-regulation of induction of apoptosis involved in anatomical structure development up-regulation of induction of apoptosis involved in development of an anatomical structure up-regulation of signaling (initiator) caspase activity involved in anatomical structure development up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure upregulation of apoptosis activator activity involved in anatomical structure development upregulation of apoptosis activator activity involved in development of an anatomical structure upregulation of commitment to apoptosis involved in anatomical structure development upregulation of commitment to apoptosis involved in development of an anatomical structure upregulation of induction of apoptosis by p53 involved in anatomical structure development upregulation of induction of apoptosis by p53 involved in development of an anatomical structure upregulation of induction of apoptosis involved in anatomical structure development upregulation of induction of apoptosis involved in development of an anatomical structure upregulation of signaling (initiator) caspase activity involved in anatomical structure development upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904747 U4PR86 in PMID:22801495 inferred from mutant phenotype positive regulation of apoptotic process involved in development Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 positive regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic process involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie up regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic process involved in anatomical structure development GOC:TermGenie up regulation of apoptotic process involved in development GOC:TermGenie up regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie up regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie up regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie up regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic process involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic process involved in development GOC:TermGenie up-regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie upregulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic process involved in anatomical structure development GOC:TermGenie upregulation of apoptotic process involved in development GOC:TermGenie upregulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie upregulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie upregulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie upregulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis signaling involved in anatomical structure development GOC:TermGenie activation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie activation of apoptotic cell death involved in anatomical structure development GOC:TermGenie activation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie activation of apoptotic process involved in anatomical structure development GOC:TermGenie activation of apoptotic process involved in development GOC:TermGenie activation of apoptotic process involved in development of an anatomical structure GOC:TermGenie activation of apoptotic program involved in anatomical structure development GOC:TermGenie activation of apoptotic program involved in development of an anatomical structure GOC:TermGenie activation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie activation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie activation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie activation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of type I programmed cell death involved in anatomical structure development GOC:TermGenie activation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic program involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie positive regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie positive regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie up regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie up regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic program involved in anatomical structure development GOC:TermGenie up regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie up regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie up regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic program involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie up-regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie up-regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie upregulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie upregulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic program involved in anatomical structure development GOC:TermGenie upregulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie upregulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie upregulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie activation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie activation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie activation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie activation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie activation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie activation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie activation of induction of apoptosis involved in anatomical structure development GOC:TermGenie activation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie activation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie positive regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie positive regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie up regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie up regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie up regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie up regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie up regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie up-regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie up-regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie upregulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie upregulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie upregulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie upregulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie upregulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that modulates the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T15:02:28Z regulation of apoptotic cell death involved in anatomical structure development regulation of apoptotic cell death involved in development of an anatomical structure regulation of apoptotic process involved in anatomical structure development regulation of apoptotic process involved in development of an anatomical structure regulation of apoptotic programmed cell death involved in anatomical structure development regulation of apoptotic programmed cell death involved in development of an anatomical structure regulation of programmed cell death by apoptosis involved in anatomical structure development regulation of programmed cell death by apoptosis involved in development of an anatomical structure regulation of activation of apoptosis involved in anatomical structure development regulation of activation of apoptosis involved in development of an anatomical structure regulation of apoptosis involved in anatomical structure development regulation of apoptosis involved in development of an anatomical structure regulation of apoptosis signaling involved in anatomical structure development regulation of apoptosis signaling involved in development of an anatomical structure regulation of apoptotic program involved in anatomical structure development regulation of apoptotic program involved in development of an anatomical structure regulation of type I programmed cell death involved in anatomical structure development regulation of type I programmed cell death involved in development of an anatomical structure biological_process regulation of apoptosis activator activity involved in anatomical structure development regulation of apoptosis activator activity involved in development of an anatomical structure regulation of commitment to apoptosis involved in anatomical structure development regulation of commitment to apoptosis involved in development of an anatomical structure regulation of induction of apoptosis by p53 involved in anatomical structure development regulation of induction of apoptosis by p53 involved in development of an anatomical structure regulation of induction of apoptosis involved in anatomical structure development regulation of induction of apoptosis involved in development of an anatomical structure regulation of signaling (initiator) caspase activity involved in anatomical structure development regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904748 Q10943 in PMID:22801495, inferred from mutant phenotype regulation of apoptotic process involved in development Any process that modulates the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic process involved in anatomical structure development GOC:TermGenie regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis involved in anatomical structure development GOC:TermGenie regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic program involved in anatomical structure development GOC:TermGenie regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to nucleolus. nc 2015-10-19T15:16:17Z regulation of protein localisation in nucleolus regulation of protein localisation to nucleolus regulation of protein localization in nucleolus biological_process GO:1904749 regulation of protein localization to nucleolus Any process that modulates the frequency, rate or extent of protein localization to nucleolus. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:24415760 regulation of protein localisation in nucleolus GOC:TermGenie regulation of protein localisation to nucleolus GOC:TermGenie regulation of protein localization in nucleolus GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleolus. nc 2015-10-19T15:16:24Z down regulation of protein localisation in nucleolus down regulation of protein localisation to nucleolus down regulation of protein localization in nucleolus down regulation of protein localization to nucleolus down-regulation of protein localisation in nucleolus down-regulation of protein localisation to nucleolus down-regulation of protein localization in nucleolus down-regulation of protein localization to nucleolus downregulation of protein localisation in nucleolus downregulation of protein localisation to nucleolus downregulation of protein localization in nucleolus downregulation of protein localization to nucleolus negative regulation of protein localisation in nucleolus negative regulation of protein localisation to nucleolus negative regulation of protein localization in nucleolus inhibition of protein localisation in nucleolus inhibition of protein localisation to nucleolus inhibition of protein localization in nucleolus inhibition of protein localization to nucleolus biological_process GO:1904750 negative regulation of protein localization to nucleolus Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleolus. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:24415760 down regulation of protein localisation in nucleolus GOC:TermGenie down regulation of protein localisation to nucleolus GOC:TermGenie down regulation of protein localization in nucleolus GOC:TermGenie down regulation of protein localization to nucleolus GOC:TermGenie down-regulation of protein localisation in nucleolus GOC:TermGenie down-regulation of protein localisation to nucleolus GOC:TermGenie down-regulation of protein localization in nucleolus GOC:TermGenie down-regulation of protein localization to nucleolus GOC:TermGenie downregulation of protein localisation in nucleolus GOC:TermGenie downregulation of protein localisation to nucleolus GOC:TermGenie downregulation of protein localization in nucleolus GOC:TermGenie downregulation of protein localization to nucleolus GOC:TermGenie negative regulation of protein localisation in nucleolus GOC:TermGenie negative regulation of protein localisation to nucleolus GOC:TermGenie negative regulation of protein localization in nucleolus GOC:TermGenie inhibition of protein localisation in nucleolus GOC:TermGenie inhibition of protein localisation to nucleolus GOC:TermGenie inhibition of protein localization in nucleolus GOC:TermGenie inhibition of protein localization to nucleolus GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to nucleolus. nc 2015-10-19T15:16:30Z positive regulation of protein localisation in nucleolus positive regulation of protein localisation to nucleolus positive regulation of protein localization in nucleolus up regulation of protein localisation in nucleolus up regulation of protein localisation to nucleolus up regulation of protein localization in nucleolus up regulation of protein localization to nucleolus up-regulation of protein localisation in nucleolus up-regulation of protein localisation to nucleolus up-regulation of protein localization in nucleolus up-regulation of protein localization to nucleolus upregulation of protein localisation in nucleolus upregulation of protein localisation to nucleolus upregulation of protein localization in nucleolus upregulation of protein localization to nucleolus activation of protein localisation in nucleolus activation of protein localisation to nucleolus activation of protein localization in nucleolus activation of protein localization to nucleolus biological_process GO:1904751 positive regulation of protein localization to nucleolus Any process that activates or increases the frequency, rate or extent of protein localization to nucleolus. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:24415760 positive regulation of protein localisation in nucleolus GOC:TermGenie positive regulation of protein localisation to nucleolus GOC:TermGenie positive regulation of protein localization in nucleolus GOC:TermGenie up regulation of protein localisation in nucleolus GOC:TermGenie up regulation of protein localisation to nucleolus GOC:TermGenie up regulation of protein localization in nucleolus GOC:TermGenie up regulation of protein localization to nucleolus GOC:TermGenie up-regulation of protein localisation in nucleolus GOC:TermGenie up-regulation of protein localisation to nucleolus GOC:TermGenie up-regulation of protein localization in nucleolus GOC:TermGenie up-regulation of protein localization to nucleolus GOC:TermGenie upregulation of protein localisation in nucleolus GOC:TermGenie upregulation of protein localisation to nucleolus GOC:TermGenie upregulation of protein localization in nucleolus GOC:TermGenie upregulation of protein localization to nucleolus GOC:TermGenie activation of protein localisation in nucleolus GOC:TermGenie activation of protein localisation to nucleolus GOC:TermGenie activation of protein localization in nucleolus GOC:TermGenie activation of protein localization to nucleolus GOC:TermGenie The developmental process by which an intramembranous bone is generated and organized. dos 2015-10-28T11:46:04Z biological_process intramembranous bones morphogenesis membrane bone morphogenesis GO:1904770 intramembranous bone morphogenesis The developmental process by which an intramembranous bone is generated and organized. GOC:TermGenie GO_REF:0000083 PMID:26399686 intramembranous bones morphogenesis GOC:TermGenie membrane bone morphogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to cell cortex. es 2015-10-29T16:55:01Z regulation of protein localisation to cell cortex biological_process GO:1904776 An example is cye-1 in C. elegans, UniProt ID O01501 in PMID:17115027. regulation of protein localization to cell cortex Any process that modulates the frequency, rate or extent of protein localization to cell cortex. GOC:TermGenie GO_REF:0000058 PMID:17115027 regulation of protein localisation to cell cortex GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell cortex. es 2015-10-29T16:55:08Z down regulation of protein localisation to cell cortex down regulation of protein localization to cell cortex down-regulation of protein localisation to cell cortex down-regulation of protein localization to cell cortex downregulation of protein localisation to cell cortex downregulation of protein localization to cell cortex negative regulation of protein localisation to cell cortex inhibition of protein localisation to cell cortex inhibition of protein localization to cell cortex biological_process GO:1904777 An example is cye-1 in C. elegans, UniProt ID O01501 in PMID:17115027. negative regulation of protein localization to cell cortex Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell cortex. GOC:TermGenie GO_REF:0000058 PMID:17115027 down regulation of protein localisation to cell cortex GOC:TermGenie down regulation of protein localization to cell cortex GOC:TermGenie down-regulation of protein localisation to cell cortex GOC:TermGenie down-regulation of protein localization to cell cortex GOC:TermGenie downregulation of protein localisation to cell cortex GOC:TermGenie downregulation of protein localization to cell cortex GOC:TermGenie negative regulation of protein localisation to cell cortex GOC:TermGenie inhibition of protein localisation to cell cortex GOC:TermGenie inhibition of protein localization to cell cortex GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to cell cortex. es 2015-10-29T16:55:15Z positive regulation of protein localisation to cell cortex up regulation of protein localisation to cell cortex up regulation of protein localization to cell cortex up-regulation of protein localisation to cell cortex up-regulation of protein localization to cell cortex upregulation of protein localisation to cell cortex upregulation of protein localization to cell cortex activation of protein localisation to cell cortex activation of protein localization to cell cortex biological_process GO:1904778 An example is cye-1 in C. elegans, UniProt ID O01501 in PMID:17115027. positive regulation of protein localization to cell cortex Any process that activates or increases the frequency, rate or extent of protein localization to cell cortex. GOC:TermGenie GO_REF:0000058 PMID:17115027 positive regulation of protein localisation to cell cortex GOC:TermGenie up regulation of protein localisation to cell cortex GOC:TermGenie up regulation of protein localization to cell cortex GOC:TermGenie up-regulation of protein localisation to cell cortex GOC:TermGenie up-regulation of protein localization to cell cortex GOC:TermGenie upregulation of protein localisation to cell cortex GOC:TermGenie upregulation of protein localization to cell cortex GOC:TermGenie activation of protein localisation to cell cortex GOC:TermGenie activation of protein localization to cell cortex GOC:TermGenie The process whose specific outcome is the progression of a serous membrane over time, from its formation to the mature structure. dph 2015-11-17T19:00:01Z tunica serosa development wall of serous sac development biological_process serosa development GO:1904817 serous membrane development The process whose specific outcome is the progression of a serous membrane over time, from its formation to the mature structure. GOC:TermGenie GOC:dph GO_REF:0000094 PMID:15840053 tunica serosa development GOC:TermGenie wall of serous sac development GOC:TermGenie serosa development GOC:TermGenie The process whose specific outcome is the progression of a visceral peritoneum over time, from its formation to the mature structure. dph 2015-11-17T19:00:17Z biological_process GO:1904818 visceral peritoneum development The process whose specific outcome is the progression of a visceral peritoneum over time, from its formation to the mature structure. GOC:TermGenie GOC:dph GO_REF:0000094 PMID:15840053 The process whose specific outcome is the progression of a parietal peritoneum over time, from its formation to the mature structure. dph 2015-11-17T19:00:24Z peritoneal cavity lining development biological_process GO:1904819 parietal peritoneum development The process whose specific outcome is the progression of a parietal peritoneum over time, from its formation to the mature structure. GOC:TermGenie GOC:dph GO_REF:0000094 PMID:15840053 peritoneal cavity lining development GOC:TermGenie The process whose specific outcome is the progression of a peritoneum over time, from its formation to the mature structure. dph 2015-11-18T17:23:51Z biological_process peritonaeum development GO:1904820 peritoneum development The process whose specific outcome is the progression of a peritoneum over time, from its formation to the mature structure. GOC:TermGenie GOC:dph GO_REF:0000094 PMID:15840053 peritonaeum development GOC:TermGenie Any process that modulates the frequency, rate or extent of aortic smooth muscle cell differentiation. rph 2015-11-24T10:20:40Z biological_process GO:1904829 regulation of aortic smooth muscle cell differentiation Any process that modulates the frequency, rate or extent of aortic smooth muscle cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:22034194 Any process that stops, prevents or reduces the frequency, rate or extent of aortic smooth muscle cell differentiation. rph 2015-11-24T10:20:47Z down regulation of aortic smooth muscle cell differentiation down-regulation of aortic smooth muscle cell differentiation downregulation of aortic smooth muscle cell differentiation inhibition of aortic smooth muscle cell differentiation biological_process GO:1904830 negative regulation of aortic smooth muscle cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of aortic smooth muscle cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:22034194 down regulation of aortic smooth muscle cell differentiation GOC:TermGenie down-regulation of aortic smooth muscle cell differentiation GOC:TermGenie downregulation of aortic smooth muscle cell differentiation GOC:TermGenie inhibition of aortic smooth muscle cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of aortic smooth muscle cell differentiation. rph 2015-11-24T10:20:54Z up regulation of aortic smooth muscle cell differentiation up-regulation of aortic smooth muscle cell differentiation upregulation of aortic smooth muscle cell differentiation activation of aortic smooth muscle cell differentiation biological_process GO:1904831 positive regulation of aortic smooth muscle cell differentiation Any process that activates or increases the frequency, rate or extent of aortic smooth muscle cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:22034194 up regulation of aortic smooth muscle cell differentiation GOC:TermGenie up-regulation of aortic smooth muscle cell differentiation GOC:TermGenie upregulation of aortic smooth muscle cell differentiation GOC:TermGenie activation of aortic smooth muscle cell differentiation GOC:TermGenie The process whose specific outcome is the progression of a cranial skeletal system over time, from its formation to the mature structure. The cranial skeletal system is the skeletal subdivision of the head, and includes the skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. bf 2016-01-07T13:45:06Z cranial skeleton development craniofacial development osteocranium development biological_process cranium development GO:1904888 cranial skeletal system development The process whose specific outcome is the progression of a cranial skeletal system over time, from its formation to the mature structure. The cranial skeletal system is the skeletal subdivision of the head, and includes the skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000094 PMID:11262227 cranial skeleton development GOC:TermGenie craniofacial development PMID:11262227 osteocranium development GOC:TermGenie cranium development GOC:TermGenie Any process that modulates the frequency, rate or extent of cell proliferation in midbrain. bf 2016-02-01T13:16:11Z regulation of cell proliferation in mesencephalon biological_process regulation of mesencepahalic cell proliferation GO:1904933 regulation of cell proliferation in midbrain Any process that modulates the frequency, rate or extent of cell proliferation in midbrain. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:18953410 PMID:24431302 regulation of cell proliferation in mesencephalon GOC:TermGenie regulation of mesencepahalic cell proliferation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation in midbrain. bf 2016-02-01T13:16:19Z down regulation of cell proliferation in mesencephalon down regulation of cell proliferation in midbrain down-regulation of cell proliferation in mesencephalon down-regulation of cell proliferation in midbrain downregulation of cell proliferation in mesencephalon downregulation of cell proliferation in midbrain negative regulation of cell proliferation in mesencephalon inhibition of cell proliferation in mesencephalon inhibition of cell proliferation in midbrain biological_process down regulation of mesencepahalic cell proliferation down-regulation of mesencepahalic cell proliferation downregulation of mesencepahalic cell proliferation inhibition of mesencepahalic cell proliferation negative regulation of mesencepahalic cell proliferation GO:1904934 negative regulation of cell proliferation in midbrain Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation in midbrain. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:18953410 PMID:24431302 down regulation of cell proliferation in mesencephalon GOC:TermGenie down regulation of cell proliferation in midbrain GOC:TermGenie down-regulation of cell proliferation in mesencephalon GOC:TermGenie down-regulation of cell proliferation in midbrain GOC:TermGenie downregulation of cell proliferation in mesencephalon GOC:TermGenie downregulation of cell proliferation in midbrain GOC:TermGenie negative regulation of cell proliferation in mesencephalon GOC:TermGenie inhibition of cell proliferation in mesencephalon GOC:TermGenie inhibition of cell proliferation in midbrain GOC:TermGenie down regulation of mesencepahalic cell proliferation GOC:TermGenie down-regulation of mesencepahalic cell proliferation GOC:TermGenie downregulation of mesencepahalic cell proliferation GOC:TermGenie inhibition of mesencepahalic cell proliferation GOC:TermGenie negative regulation of mesencepahalic cell proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cell proliferation in midbrain. bf 2016-02-01T13:16:27Z positive regulation of cell proliferation in mesencephalon up regulation of cell proliferation in mesencephalon up regulation of cell proliferation in midbrain up-regulation of cell proliferation in mesencephalon up-regulation of cell proliferation in midbrain upregulation of cell proliferation in mesencephalon upregulation of cell proliferation in midbrain activation of cell proliferation in mesencephalon activation of cell proliferation in midbrain biological_process activation of mesencepahalic cell proliferation positive regulation of mesencepahalic cell proliferation up regulation of mesencepahalic cell proliferation up-regulation of mesencepahalic cell proliferation upregulation of mesencepahalic cell proliferation GO:1904935 positive regulation of cell proliferation in midbrain Any process that activates or increases the frequency, rate or extent of cell proliferation in midbrain. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:24431302 positive regulation of cell proliferation in mesencephalon GOC:TermGenie up regulation of cell proliferation in mesencephalon GOC:TermGenie up regulation of cell proliferation in midbrain GOC:TermGenie up-regulation of cell proliferation in mesencephalon GOC:TermGenie up-regulation of cell proliferation in midbrain GOC:TermGenie upregulation of cell proliferation in mesencephalon GOC:TermGenie upregulation of cell proliferation in midbrain GOC:TermGenie activation of cell proliferation in mesencephalon GOC:TermGenie activation of cell proliferation in midbrain GOC:TermGenie activation of mesencepahalic cell proliferation GOC:TermGenie positive regulation of mesencepahalic cell proliferation GOC:TermGenie up regulation of mesencepahalic cell proliferation GOC:TermGenie up-regulation of mesencepahalic cell proliferation GOC:TermGenie upregulation of mesencepahalic cell proliferation GOC:TermGenie Any process that modulates the frequency, rate or extent of cardiac ventricle formation. bc 2016-02-02T16:37:16Z biological_process GO:1904942 regulation of cardiac ventricle formation Any process that modulates the frequency, rate or extent of cardiac ventricle formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:23575307 Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle formation. bc 2016-02-02T16:37:24Z down regulation of cardiac ventricle formation down-regulation of cardiac ventricle formation downregulation of cardiac ventricle formation inhibition of cardiac ventricle formation biological_process GO:1904943 negative regulation of cardiac ventricle formation Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:23575307 down regulation of cardiac ventricle formation GOC:TermGenie down-regulation of cardiac ventricle formation GOC:TermGenie downregulation of cardiac ventricle formation GOC:TermGenie inhibition of cardiac ventricle formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cardiac ventricle formation. bc 2016-02-02T16:37:31Z up regulation of cardiac ventricle formation up-regulation of cardiac ventricle formation upregulation of cardiac ventricle formation activation of cardiac ventricle formation biological_process GO:1904944 positive regulation of cardiac ventricle formation Any process that activates or increases the frequency, rate or extent of cardiac ventricle formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:23575307 up regulation of cardiac ventricle formation GOC:TermGenie up-regulation of cardiac ventricle formation GOC:TermGenie upregulation of cardiac ventricle formation GOC:TermGenie activation of cardiac ventricle formation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:24Z down regulation of establishment of protein localisation down regulation of establishment of protein localization down regulation of protein positioning down regulation of protein recruitment down-regulation of establishment of protein localisation down-regulation of establishment of protein localization down-regulation of protein positioning down-regulation of protein recruitment downregulation of establishment of protein localisation downregulation of establishment of protein localization downregulation of protein positioning downregulation of protein recruitment negative regulation of establishment of protein localisation negative regulation of protein positioning negative regulation of protein recruitment inhibition of establishment of protein localisation inhibition of establishment of protein localization inhibition of protein positioning inhibition of protein recruitment biological_process GO:1904950 negative regulation of establishment of protein localization Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 down regulation of establishment of protein localisation GOC:TermGenie down regulation of establishment of protein localization GOC:TermGenie down regulation of protein positioning GOC:TermGenie down regulation of protein recruitment GOC:TermGenie down-regulation of establishment of protein localisation GOC:TermGenie down-regulation of establishment of protein localization GOC:TermGenie down-regulation of protein positioning GOC:TermGenie down-regulation of protein recruitment GOC:TermGenie downregulation of establishment of protein localisation GOC:TermGenie downregulation of establishment of protein localization GOC:TermGenie downregulation of protein positioning GOC:TermGenie downregulation of protein recruitment GOC:TermGenie negative regulation of establishment of protein localisation GOC:TermGenie negative regulation of protein positioning GOC:TermGenie negative regulation of protein recruitment GOC:TermGenie inhibition of establishment of protein localisation GOC:TermGenie inhibition of establishment of protein localization GOC:TermGenie inhibition of protein positioning GOC:TermGenie inhibition of protein recruitment GOC:TermGenie Any process that activates or increases the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:32Z positive regulation of establishment of protein localisation positive regulation of protein positioning positive regulation of protein recruitment up regulation of establishment of protein localisation up regulation of establishment of protein localization up regulation of protein positioning up regulation of protein recruitment up-regulation of establishment of protein localisation up-regulation of establishment of protein localization up-regulation of protein positioning up-regulation of protein recruitment upregulation of establishment of protein localisation upregulation of establishment of protein localization upregulation of protein positioning upregulation of protein recruitment activation of establishment of protein localisation activation of establishment of protein localization activation of protein positioning activation of protein recruitment biological_process GO:1904951 positive regulation of establishment of protein localization Any process that activates or increases the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 positive regulation of establishment of protein localisation GOC:TermGenie positive regulation of protein positioning GOC:TermGenie positive regulation of protein recruitment GOC:TermGenie up regulation of establishment of protein localisation GOC:TermGenie up regulation of establishment of protein localization GOC:TermGenie up regulation of protein positioning GOC:TermGenie up regulation of protein recruitment GOC:TermGenie up-regulation of establishment of protein localisation GOC:TermGenie up-regulation of establishment of protein localization GOC:TermGenie up-regulation of protein positioning GOC:TermGenie up-regulation of protein recruitment GOC:TermGenie upregulation of establishment of protein localisation GOC:TermGenie upregulation of establishment of protein localization GOC:TermGenie upregulation of protein positioning GOC:TermGenie upregulation of protein recruitment GOC:TermGenie activation of establishment of protein localisation GOC:TermGenie activation of establishment of protein localization GOC:TermGenie activation of protein positioning GOC:TermGenie activation of protein recruitment GOC:TermGenie The process in which carboxylic acid is transported across a membrane. vw 2016-03-09T15:33:53Z biological_process GO:1905039 carboxylic acid transmembrane transport The process in which carboxylic acid is transported across a membrane. GOC:TermGenie GO_REF:0000069 PMID:10869563 Any process that modulates the frequency, rate or extent of vascular smooth muscle cell differentiation. rph 2016-03-21T11:14:53Z regulation of VSMC differentiation regulation of vascular smooth muscle cell differentiation biological_process GO:1905063 regulation of vascular associated smooth muscle cell differentiation Any process that modulates the frequency, rate or extent of vascular smooth muscle cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19088079 regulation of VSMC differentiation GOC:TermGenie regulation of vascular smooth muscle cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell differentiation. rph 2016-03-21T11:15:03Z down regulation of VSMC differentiation down regulation of vascular associated smooth muscle cell differentiation down regulation of vascular smooth muscle cell differentiation down-regulation of VSMC differentiation down-regulation of vascular associated smooth muscle cell differentiation down-regulation of vascular smooth muscle cell differentiation downregulation of VSMC differentiation downregulation of vascular associated smooth muscle cell differentiation downregulation of vascular smooth muscle cell differentiation negative regulation of VSMC differentiation negative regulation of vascular smooth muscle cell differentiation inhibition of VSMC differentiation inhibition of vascular associated smooth muscle cell differentiation inhibition of vascular smooth muscle cell differentiation biological_process GO:1905064 negative regulation of vascular associated smooth muscle cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19088079 down regulation of VSMC differentiation GOC:TermGenie down regulation of vascular associated smooth muscle cell differentiation GOC:TermGenie down regulation of vascular smooth muscle cell differentiation GOC:TermGenie down-regulation of VSMC differentiation GOC:TermGenie down-regulation of vascular associated smooth muscle cell differentiation GOC:TermGenie down-regulation of vascular smooth muscle cell differentiation GOC:TermGenie downregulation of VSMC differentiation GOC:TermGenie downregulation of vascular associated smooth muscle cell differentiation GOC:TermGenie downregulation of vascular smooth muscle cell differentiation GOC:TermGenie negative regulation of VSMC differentiation GOC:TermGenie negative regulation of vascular smooth muscle cell differentiation GOC:TermGenie inhibition of VSMC differentiation GOC:TermGenie inhibition of vascular associated smooth muscle cell differentiation GOC:TermGenie inhibition of vascular smooth muscle cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell differentiation. rph 2016-03-21T11:15:13Z positive regulation of VSMC differentiation positive regulation of vascular smooth muscle cell differentiation up regulation of VSMC differentiation up regulation of vascular associated smooth muscle cell differentiation up regulation of vascular smooth muscle cell differentiation up-regulation of VSMC differentiation up-regulation of vascular associated smooth muscle cell differentiation up-regulation of vascular smooth muscle cell differentiation upregulation of VSMC differentiation upregulation of vascular associated smooth muscle cell differentiation upregulation of vascular smooth muscle cell differentiation activation of VSMC differentiation activation of vascular associated smooth muscle cell differentiation activation of vascular smooth muscle cell differentiation biological_process GO:1905065 positive regulation of vascular associated smooth muscle cell differentiation Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19088079 positive regulation of VSMC differentiation GOC:TermGenie positive regulation of vascular smooth muscle cell differentiation GOC:TermGenie up regulation of VSMC differentiation GOC:TermGenie up regulation of vascular associated smooth muscle cell differentiation GOC:TermGenie up regulation of vascular smooth muscle cell differentiation GOC:TermGenie up-regulation of VSMC differentiation GOC:TermGenie up-regulation of vascular associated smooth muscle cell differentiation GOC:TermGenie up-regulation of vascular smooth muscle cell differentiation GOC:TermGenie upregulation of VSMC differentiation GOC:TermGenie upregulation of vascular associated smooth muscle cell differentiation GOC:TermGenie upregulation of vascular smooth muscle cell differentiation GOC:TermGenie activation of VSMC differentiation GOC:TermGenie activation of vascular associated smooth muscle cell differentiation GOC:TermGenie activation of vascular smooth muscle cell differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of axo-dendritic protein transport. sl 2016-04-11T20:38:31Z regulation of axonal protein transport biological_process GO:1905126 regulation of axo-dendritic protein transport Any process that modulates the frequency, rate or extent of axo-dendritic protein transport. GOC:TermGenie GO_REF:0000058 PMID:20694152 regulation of axonal protein transport GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of axo-dendritic protein transport. sl 2016-04-11T20:38:40Z down regulation of axo-dendritic protein transport down-regulation of axo-dendritic protein transport downregulation of axo-dendritic protein transport down regulation of axonal protein transport down-regulation of axonal protein transport downregulation of axonal protein transport inhibition of axo-dendritic protein transport inhibition of axonal protein transport negative regulation of axonal protein transport biological_process GO:1905127 negative regulation of axo-dendritic protein transport Any process that stops, prevents or reduces the frequency, rate or extent of axo-dendritic protein transport. GOC:TermGenie GO_REF:0000058 PMID:20694152 down regulation of axo-dendritic protein transport GOC:TermGenie down-regulation of axo-dendritic protein transport GOC:TermGenie downregulation of axo-dendritic protein transport GOC:TermGenie down regulation of axonal protein transport GOC:TermGenie down-regulation of axonal protein transport GOC:TermGenie downregulation of axonal protein transport GOC:TermGenie inhibition of axo-dendritic protein transport GOC:TermGenie inhibition of axonal protein transport GOC:TermGenie negative regulation of axonal protein transport GOC:TermGenie Any process that activates or increases the frequency, rate or extent of axo-dendritic protein transport. sl 2016-04-11T20:38:48Z up regulation of axo-dendritic protein transport up-regulation of axo-dendritic protein transport upregulation of axo-dendritic protein transport activation of axo-dendritic protein transport activation of axonal protein transport positive regulation of axonal protein transport up regulation of axonal protein transport up-regulation of axonal protein transport upregulation of axonal protein transport biological_process GO:1905128 positive regulation of axo-dendritic protein transport Any process that activates or increases the frequency, rate or extent of axo-dendritic protein transport. GOC:TermGenie GO_REF:0000058 PMID:20694152 up regulation of axo-dendritic protein transport GOC:TermGenie up-regulation of axo-dendritic protein transport GOC:TermGenie upregulation of axo-dendritic protein transport GOC:TermGenie activation of axo-dendritic protein transport GOC:TermGenie activation of axonal protein transport GOC:TermGenie positive regulation of axonal protein transport GOC:TermGenie up regulation of axonal protein transport GOC:TermGenie up-regulation of axonal protein transport GOC:TermGenie upregulation of axonal protein transport GOC:TermGenie The process that gives rise to the apical ectodermal ridge. This process pertains to the initial formation of a structure from unspecified parts. dph 2016-04-13T11:46:40Z apical epidermal ridge formation biological_process AER formation crista ectodermalis apicalis formation GO:1905139 apical ectodermal ridge formation The process that gives rise to the apical ectodermal ridge. This process pertains to the initial formation of a structure from unspecified parts. GOC:TermGenie GO_REF:0000081 PMID:18359901 PMID:9323126 PMID:9596583 apical epidermal ridge formation GOC:TermGenie AER formation GOC:TermGenie crista ectodermalis apicalis formation GOC:TermGenie Any process that modulates the frequency, rate or extent of apical ectodermal ridge formation. dph 2016-04-13T12:16:40Z regulation of apical epidermal ridge formation biological_process regulation of AER formation regulation of crista ectodermalis apicalis formation GO:1905140 regulation of apical ectodermal ridge formation Any process that modulates the frequency, rate or extent of apical ectodermal ridge formation. GOC:TermGenie GO_REF:0000058 PMID:18359901 regulation of apical epidermal ridge formation GOC:TermGenie regulation of AER formation GOC:TermGenie regulation of crista ectodermalis apicalis formation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apical ectodermal ridge formation. dph 2016-04-13T12:16:48Z down regulation of apical ectodermal ridge formation down regulation of apical epidermal ridge formation down-regulation of apical ectodermal ridge formation down-regulation of apical epidermal ridge formation downregulation of apical ectodermal ridge formation downregulation of apical epidermal ridge formation negative regulation of apical epidermal ridge formation inhibition of apical ectodermal ridge formation inhibition of apical epidermal ridge formation biological_process down regulation of AER formation down regulation of crista ectodermalis apicalis formation down-regulation of AER formation down-regulation of crista ectodermalis apicalis formation downregulation of AER formation downregulation of crista ectodermalis apicalis formation inhibition of AER formation inhibition of crista ectodermalis apicalis formation negative regulation of AER formation negative regulation of crista ectodermalis apicalis formation GO:1905141 negative regulation of apical ectodermal ridge formation Any process that stops, prevents or reduces the frequency, rate or extent of apical ectodermal ridge formation. GOC:TermGenie GO_REF:0000058 PMID:18359901 down regulation of apical ectodermal ridge formation GOC:TermGenie down regulation of apical epidermal ridge formation GOC:TermGenie down-regulation of apical ectodermal ridge formation GOC:TermGenie down-regulation of apical epidermal ridge formation GOC:TermGenie downregulation of apical ectodermal ridge formation GOC:TermGenie downregulation of apical epidermal ridge formation GOC:TermGenie negative regulation of apical epidermal ridge formation GOC:TermGenie inhibition of apical ectodermal ridge formation GOC:TermGenie inhibition of apical epidermal ridge formation GOC:TermGenie down regulation of AER formation GOC:TermGenie down regulation of crista ectodermalis apicalis formation GOC:TermGenie down-regulation of AER formation GOC:TermGenie down-regulation of crista ectodermalis apicalis formation GOC:TermGenie downregulation of AER formation GOC:TermGenie downregulation of crista ectodermalis apicalis formation GOC:TermGenie inhibition of AER formation GOC:TermGenie inhibition of crista ectodermalis apicalis formation GOC:TermGenie negative regulation of AER formation GOC:TermGenie negative regulation of crista ectodermalis apicalis formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apical ectodermal ridge formation. dph 2016-04-13T12:16:57Z positive regulation of apical epidermal ridge formation up regulation of apical ectodermal ridge formation up regulation of apical epidermal ridge formation up-regulation of apical ectodermal ridge formation up-regulation of apical epidermal ridge formation upregulation of apical ectodermal ridge formation upregulation of apical epidermal ridge formation biological_process activation of AER formation positive regulation of AER formation positive regulation of crista ectodermalis apicalis formation up regulation of AER formation up regulation of crista ectodermalis apicalis formation up-regulation of AER formation up-regulation of crista ectodermalis apicalis formation upregulation of AER formation upregulation of crista ectodermalis apicalis formation GO:1905142 positive regulation of apical ectodermal ridge formation Any process that activates or increases the frequency, rate or extent of apical ectodermal ridge formation. GOC:TermGenie GO_REF:0000058 PMID:18359901 positive regulation of apical epidermal ridge formation GOC:TermGenie up regulation of apical ectodermal ridge formation GOC:TermGenie up regulation of apical epidermal ridge formation GOC:TermGenie up-regulation of apical ectodermal ridge formation GOC:TermGenie up-regulation of apical epidermal ridge formation GOC:TermGenie upregulation of apical ectodermal ridge formation GOC:TermGenie upregulation of apical epidermal ridge formation GOC:TermGenie activation of AER formation GOC:TermGenie positive regulation of AER formation GOC:TermGenie positive regulation of crista ectodermalis apicalis formation GOC:TermGenie up regulation of AER formation GOC:TermGenie up regulation of crista ectodermalis apicalis formation GOC:TermGenie up-regulation of AER formation GOC:TermGenie up-regulation of crista ectodermalis apicalis formation GOC:TermGenie upregulation of AER formation GOC:TermGenie upregulation of crista ectodermalis apicalis formation GOC:TermGenie Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus. dos 2016-04-14T08:54:49Z biological_process GO:1905144 response to acetylcholine Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus. GOC:TermGenie GO_REF:0000071 PMID:21238497 Any process that modulates the frequency, rate or extent of smooth muscle hypertrophy. bc 2016-04-15T12:47:07Z biological_process GO:1905147 regulation of smooth muscle hypertrophy Any process that modulates the frequency, rate or extent of smooth muscle hypertrophy. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:22161164 Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle hypertrophy. bc 2016-04-15T12:47:16Z down regulation of smooth muscle hypertrophy down-regulation of smooth muscle hypertrophy downregulation of smooth muscle hypertrophy inhibition of smooth muscle hypertrophy biological_process GO:1905148 negative regulation of smooth muscle hypertrophy Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle hypertrophy. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:22161164 down regulation of smooth muscle hypertrophy GOC:TermGenie down-regulation of smooth muscle hypertrophy GOC:TermGenie downregulation of smooth muscle hypertrophy GOC:TermGenie inhibition of smooth muscle hypertrophy GOC:TermGenie Any process that activates or increases the frequency, rate or extent of smooth muscle hypertrophy. bc 2016-04-15T12:47:24Z up regulation of smooth muscle hypertrophy up-regulation of smooth muscle hypertrophy upregulation of smooth muscle hypertrophy activation of smooth muscle hypertrophy biological_process GO:1905149 positive regulation of smooth muscle hypertrophy Any process that activates or increases the frequency, rate or extent of smooth muscle hypertrophy. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:22161164 up regulation of smooth muscle hypertrophy GOC:TermGenie up-regulation of smooth muscle hypertrophy GOC:TermGenie upregulation of smooth muscle hypertrophy GOC:TermGenie activation of smooth muscle hypertrophy GOC:TermGenie Any process that modulates the frequency, rate or extent of cardiocyte differentiation. bc 2016-06-02T07:20:01Z regulation of cardiac cell differentiation regulation of heart cell differentiation biological_process GO:1905207 regulation of cardiocyte differentiation Any process that modulates the frequency, rate or extent of cardiocyte differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:23069713 regulation of cardiac cell differentiation GOC:TermGenie regulation of heart cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cardiocyte differentiation. bc 2016-06-02T07:20:09Z down regulation of cardiac cell differentiation down regulation of cardiocyte differentiation down regulation of heart cell differentiation down-regulation of cardiac cell differentiation down-regulation of cardiocyte differentiation down-regulation of heart cell differentiation downregulation of cardiac cell differentiation downregulation of cardiocyte differentiation downregulation of heart cell differentiation negative regulation of cardiac cell differentiation negative regulation of heart cell differentiation inhibition of cardiac cell differentiation inhibition of cardiocyte differentiation inhibition of heart cell differentiation biological_process GO:1905208 negative regulation of cardiocyte differentiation Any process that stops, prevents or reduces the frequency, rate or extent of cardiocyte differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:23069713 down regulation of cardiac cell differentiation GOC:TermGenie down regulation of cardiocyte differentiation GOC:TermGenie down regulation of heart cell differentiation GOC:TermGenie down-regulation of cardiac cell differentiation GOC:TermGenie down-regulation of cardiocyte differentiation GOC:TermGenie down-regulation of heart cell differentiation GOC:TermGenie downregulation of cardiac cell differentiation GOC:TermGenie downregulation of cardiocyte differentiation GOC:TermGenie downregulation of heart cell differentiation GOC:TermGenie negative regulation of cardiac cell differentiation GOC:TermGenie negative regulation of heart cell differentiation GOC:TermGenie inhibition of cardiac cell differentiation GOC:TermGenie inhibition of cardiocyte differentiation GOC:TermGenie inhibition of heart cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cardiocyte differentiation. bc 2016-06-02T07:20:16Z positive regulation of cardiac cell differentiation positive regulation of heart cell differentiation up regulation of cardiac cell differentiation up regulation of cardiocyte differentiation up regulation of heart cell differentiation up-regulation of cardiac cell differentiation up-regulation of cardiocyte differentiation up-regulation of heart cell differentiation upregulation of cardiac cell differentiation upregulation of cardiocyte differentiation upregulation of heart cell differentiation activation of cardiac cell differentiation activation of cardiocyte differentiation activation of heart cell differentiation biological_process GO:1905209 positive regulation of cardiocyte differentiation Any process that activates or increases the frequency, rate or extent of cardiocyte differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:bc GO_REF:0000058 PMID:23069713 positive regulation of cardiac cell differentiation GOC:TermGenie positive regulation of heart cell differentiation GOC:TermGenie up regulation of cardiac cell differentiation GOC:TermGenie up regulation of cardiocyte differentiation GOC:TermGenie up regulation of heart cell differentiation GOC:TermGenie up-regulation of cardiac cell differentiation GOC:TermGenie up-regulation of cardiocyte differentiation GOC:TermGenie up-regulation of heart cell differentiation GOC:TermGenie upregulation of cardiac cell differentiation GOC:TermGenie upregulation of cardiocyte differentiation GOC:TermGenie upregulation of heart cell differentiation GOC:TermGenie activation of cardiac cell differentiation GOC:TermGenie activation of cardiocyte differentiation GOC:TermGenie activation of heart cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation. vw 2016-06-03T08:41:08Z biological_process GO:1905213 negative regulation of mitotic chromosome condensation Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:23219725 The developmental process by which an epicardium is generated and organized. rl 2016-06-07T10:02:32Z heart epicardium morphogenesis visceral serous pericardium of heart morphogenesis visceral serous pericardium proper morphogenesis biological_process pericardium visceral mesothelium morphogenesis GO:1905223 epicardium morphogenesis The developmental process by which an epicardium is generated and organized. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000083 PMID:18718461 heart epicardium morphogenesis GOC:TermGenie visceral serous pericardium of heart morphogenesis GOC:TermGenie visceral serous pericardium proper morphogenesis GOC:TermGenie pericardium visceral mesothelium morphogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization. https://github.com/geneontology/go-ontology/issues/22766 pr 2016-06-15T20:14:47Z GO:0045798 GO:1903309 down regulation of chromatin organisation down regulation of chromatin organization down regulation of establishment or maintenance of chromatin architecture down-regulation of chromatin organisation down-regulation of chromatin organization down-regulation of establishment or maintenance of chromatin architecture downregulation of chromatin organisation downregulation of chromatin organization downregulation of establishment or maintenance of chromatin architecture negative regulation of chromatin assembly/disassembly negative regulation of chromatin organisation negative regulation of establishment or maintenance of chromatin architecture inhibition of chromatin assembly or disassembly inhibition of chromatin organisation inhibition of chromatin organization inhibition of establishment or maintenance of chromatin architecture biological_process down regulation of chromatin assembly or disassembly down-regulation of chromatin assembly or disassembly downregulation of chromatin assembly or disassembly negative regulation of chromatin assembly or disassembly negative regulation of chromatin modification GO:1905268 negative regulation of chromatin organization Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization. GOC:TermGenie GOC:pr GOC:vw GO_REF:0000058 PMID:654321 down regulation of chromatin organisation GOC:TermGenie down regulation of chromatin organization GOC:TermGenie down regulation of establishment or maintenance of chromatin architecture GOC:TermGenie down-regulation of chromatin organisation GOC:TermGenie down-regulation of chromatin organization GOC:TermGenie down-regulation of establishment or maintenance of chromatin architecture GOC:TermGenie downregulation of chromatin organisation GOC:TermGenie downregulation of chromatin organization GOC:TermGenie downregulation of establishment or maintenance of chromatin architecture GOC:TermGenie negative regulation of chromatin organisation GOC:TermGenie negative regulation of establishment or maintenance of chromatin architecture GOC:TermGenie inhibition of chromatin organisation GOC:TermGenie inhibition of chromatin organization GOC:TermGenie inhibition of establishment or maintenance of chromatin architecture GOC:TermGenie Any process that activates or increases the frequency, rate or extent of chromatin organization. https://github.com/geneontology/go-ontology/issues/22766 pr 2016-06-15T20:14:56Z GO:0045799 GO:1903310 positive regulation of chromatin organisation positive regulation of establishment or maintenance of chromatin architecture up regulation of chromatin organisation up regulation of chromatin organization up regulation of establishment or maintenance of chromatin architecture up-regulation of chromatin organisation up-regulation of chromatin organization up-regulation of establishment or maintenance of chromatin architecture upregulation of chromatin assembly or disassembly upregulation of chromatin organisation upregulation of chromatin organization upregulation of establishment or maintenance of chromatin architecture activation of chromatin assembly or disassembly activation of chromatin organisation activation of chromatin organization activation of establishment or maintenance of chromatin architecture stimulation of chromatin assembly or disassembly biological_process positive regulation of chromatin assembly or disassembly positive regulation of chromatin assembly/disassembly positive regulation of chromatin modification up regulation of chromatin assembly or disassembly up-regulation of chromatin assembly or disassembly GO:1905269 positive regulation of chromatin organization Any process that activates or increases the frequency, rate or extent of chromatin organization. GOC:TermGenie GOC:pr GOC:vw GO_REF:0000058 PMID:654321 positive regulation of chromatin organisation GOC:TermGenie positive regulation of establishment or maintenance of chromatin architecture GOC:TermGenie up regulation of chromatin organisation GOC:TermGenie up regulation of chromatin organization GOC:TermGenie up regulation of establishment or maintenance of chromatin architecture GOC:TermGenie up-regulation of chromatin organisation GOC:TermGenie up-regulation of chromatin organization GOC:TermGenie up-regulation of establishment or maintenance of chromatin architecture GOC:TermGenie upregulation of chromatin organisation GOC:TermGenie upregulation of chromatin organization GOC:TermGenie upregulation of establishment or maintenance of chromatin architecture GOC:TermGenie activation of chromatin organisation GOC:TermGenie activation of chromatin organization GOC:TermGenie activation of establishment or maintenance of chromatin architecture GOC:TermGenie Any process that modulates the frequency, rate or extent of epithelial tube formation. bhm 2016-06-20T09:35:41Z biological_process GO:1905276 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). regulation of epithelial tube formation Any process that modulates the frequency, rate or extent of epithelial tube formation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 Any process that stops, prevents or reduces the frequency, rate or extent of epithelial tube formation. bhm 2016-06-20T09:35:49Z down regulation of epithelial tube formation down-regulation of epithelial tube formation downregulation of epithelial tube formation inhibition of epithelial tube formation biological_process GO:1905277 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). negative regulation of epithelial tube formation Any process that stops, prevents or reduces the frequency, rate or extent of epithelial tube formation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 down regulation of epithelial tube formation GOC:TermGenie down-regulation of epithelial tube formation GOC:TermGenie downregulation of epithelial tube formation GOC:TermGenie inhibition of epithelial tube formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of epithelial tube formation. bhm 2016-06-20T09:35:57Z up regulation of epithelial tube formation up-regulation of epithelial tube formation upregulation of epithelial tube formation activation of epithelial tube formation biological_process GO:1905278 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). positive regulation of epithelial tube formation Any process that activates or increases the frequency, rate or extent of epithelial tube formation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 up regulation of epithelial tube formation GOC:TermGenie up-regulation of epithelial tube formation GOC:TermGenie upregulation of epithelial tube formation GOC:TermGenie activation of epithelial tube formation GOC:TermGenie Any apoptotic process in a vascular associated smooth muscle cell. rph 2016-06-23T13:24:20Z VSMC apoptotic process vascular smooth muscle cell apoptotic process VSMC apoptosis vascular associated smooth muscle cell apoptosis vascular smooth muscle cell apoptosis biological_process GO:1905288 vascular associated smooth muscle cell apoptotic process Any apoptotic process in a vascular associated smooth muscle cell. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000085 PMID:26493107 VSMC apoptotic process GOC:TermGenie vascular smooth muscle cell apoptotic process GOC:TermGenie VSMC apoptosis GOC:TermGenie vascular associated smooth muscle cell apoptosis GOC:TermGenie vascular smooth muscle cell apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of neural crest cell differentiation. rl 2016-06-28T15:02:01Z biological_process GO:1905292 regulation of neural crest cell differentiation Any process that modulates the frequency, rate or extent of neural crest cell differentiation. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:15073157 Any process that stops, prevents or reduces the frequency, rate or extent of neural crest cell differentiation. rl 2016-06-28T15:02:09Z down regulation of neural crest cell differentiation down-regulation of neural crest cell differentiation downregulation of neural crest cell differentiation inhibition of neural crest cell differentiation biological_process GO:1905293 negative regulation of neural crest cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of neural crest cell differentiation. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:15073157 down regulation of neural crest cell differentiation GOC:TermGenie down-regulation of neural crest cell differentiation GOC:TermGenie downregulation of neural crest cell differentiation GOC:TermGenie inhibition of neural crest cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of neural crest cell differentiation. rl 2016-06-28T15:02:16Z up regulation of neural crest cell differentiation up-regulation of neural crest cell differentiation upregulation of neural crest cell differentiation activation of neural crest cell differentiation biological_process GO:1905294 positive regulation of neural crest cell differentiation Any process that activates or increases the frequency, rate or extent of neural crest cell differentiation. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:15073157 up regulation of neural crest cell differentiation GOC:TermGenie up-regulation of neural crest cell differentiation GOC:TermGenie upregulation of neural crest cell differentiation GOC:TermGenie activation of neural crest cell differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of intestinal epithelial cell development. rph 2016-06-30T11:40:47Z biological_process GO:1905298 regulation of intestinal epithelial cell development Any process that modulates the frequency, rate or extent of intestinal epithelial cell development. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23904268 Any process that stops, prevents or reduces the frequency, rate or extent of intestinal epithelial cell development. rph 2016-06-30T11:40:55Z down regulation of intestinal epithelial cell development down-regulation of intestinal epithelial cell development downregulation of intestinal epithelial cell development inhibition of intestinal epithelial cell development biological_process GO:1905299 negative regulation of intestinal epithelial cell development Any process that stops, prevents or reduces the frequency, rate or extent of intestinal epithelial cell development. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23904268 down regulation of intestinal epithelial cell development GOC:TermGenie down-regulation of intestinal epithelial cell development GOC:TermGenie downregulation of intestinal epithelial cell development GOC:TermGenie inhibition of intestinal epithelial cell development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of intestinal epithelial cell development. rph 2016-06-30T11:41:02Z up regulation of intestinal epithelial cell development up-regulation of intestinal epithelial cell development upregulation of intestinal epithelial cell development activation of intestinal epithelial cell development biological_process GO:1905300 positive regulation of intestinal epithelial cell development Any process that activates or increases the frequency, rate or extent of intestinal epithelial cell development. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23904268 up regulation of intestinal epithelial cell development GOC:TermGenie up-regulation of intestinal epithelial cell development GOC:TermGenie upregulation of intestinal epithelial cell development GOC:TermGenie activation of intestinal epithelial cell development GOC:TermGenie Any process that modulates the frequency, rate or extent of cardiac myofibril assembly. rl 2016-07-06T10:01:49Z regulation of cardiac myofibril development regulation of cardiac myofibril morphogenesis biological_process regulation of heart myofibril assembly GO:1905304 regulation of cardiac myofibril assembly Any process that modulates the frequency, rate or extent of cardiac myofibril assembly. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:16151019 regulation of cardiac myofibril development GOC:TermGenie regulation of cardiac myofibril morphogenesis GOC:TermGenie regulation of heart myofibril assembly GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cardiac myofibril assembly. rl 2016-07-06T10:01:58Z down regulation of cardiac myofibril assembly down regulation of cardiac myofibril development down regulation of cardiac myofibril morphogenesis down-regulation of cardiac myofibril assembly down-regulation of cardiac myofibril development down-regulation of cardiac myofibril morphogenesis downregulation of cardiac myofibril assembly downregulation of cardiac myofibril development downregulation of cardiac myofibril morphogenesis negative regulation of cardiac myofibril development negative regulation of cardiac myofibril morphogenesis inhibition of cardiac myofibril assembly inhibition of cardiac myofibril development inhibition of cardiac myofibril morphogenesis biological_process down regulation of heart myofibril assembly down-regulation of heart myofibril assembly downregulation of heart myofibril assembly inhibition of heart myofibril assembly negative regulation of heart myofibril assembly GO:1905305 negative regulation of cardiac myofibril assembly Any process that stops, prevents or reduces the frequency, rate or extent of cardiac myofibril assembly. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:16151019 down regulation of cardiac myofibril assembly GOC:TermGenie down regulation of cardiac myofibril development GOC:TermGenie down regulation of cardiac myofibril morphogenesis GOC:TermGenie down-regulation of cardiac myofibril assembly GOC:TermGenie down-regulation of cardiac myofibril development GOC:TermGenie down-regulation of cardiac myofibril morphogenesis GOC:TermGenie downregulation of cardiac myofibril assembly GOC:TermGenie downregulation of cardiac myofibril development GOC:TermGenie downregulation of cardiac myofibril morphogenesis GOC:TermGenie negative regulation of cardiac myofibril development GOC:TermGenie negative regulation of cardiac myofibril morphogenesis GOC:TermGenie inhibition of cardiac myofibril assembly GOC:TermGenie inhibition of cardiac myofibril development GOC:TermGenie inhibition of cardiac myofibril morphogenesis GOC:TermGenie down regulation of heart myofibril assembly GOC:TermGenie down-regulation of heart myofibril assembly GOC:TermGenie downregulation of heart myofibril assembly GOC:TermGenie inhibition of heart myofibril assembly GOC:TermGenie negative regulation of heart myofibril assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cardiac myofibril assembly. rl 2016-07-06T10:02:07Z positive regulation of cardiac myofibril development positive regulation of cardiac myofibril morphogenesis up regulation of cardiac myofibril assembly up regulation of cardiac myofibril development up regulation of cardiac myofibril morphogenesis up-regulation of cardiac myofibril assembly up-regulation of cardiac myofibril development up-regulation of cardiac myofibril morphogenesis upregulation of cardiac myofibril assembly upregulation of cardiac myofibril development upregulation of cardiac myofibril morphogenesis activation of cardiac myofibril assembly activation of cardiac myofibril development activation of cardiac myofibril morphogenesis biological_process activation of heart myofibril assembly positive regulation of heart myofibril assembly up regulation of heart myofibril assembly up-regulation of heart myofibril assembly upregulation of heart myofibril assembly GO:1905306 positive regulation of cardiac myofibril assembly Any process that activates or increases the frequency, rate or extent of cardiac myofibril assembly. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:16151019 positive regulation of cardiac myofibril development GOC:TermGenie positive regulation of cardiac myofibril morphogenesis GOC:TermGenie up regulation of cardiac myofibril assembly GOC:TermGenie up regulation of cardiac myofibril development GOC:TermGenie up regulation of cardiac myofibril morphogenesis GOC:TermGenie up-regulation of cardiac myofibril assembly GOC:TermGenie up-regulation of cardiac myofibril development GOC:TermGenie up-regulation of cardiac myofibril morphogenesis GOC:TermGenie upregulation of cardiac myofibril assembly GOC:TermGenie upregulation of cardiac myofibril development GOC:TermGenie upregulation of cardiac myofibril morphogenesis GOC:TermGenie activation of cardiac myofibril assembly GOC:TermGenie activation of cardiac myofibril development GOC:TermGenie activation of cardiac myofibril morphogenesis GOC:TermGenie activation of heart myofibril assembly GOC:TermGenie positive regulation of heart myofibril assembly GOC:TermGenie up regulation of heart myofibril assembly GOC:TermGenie up-regulation of heart myofibril assembly GOC:TermGenie upregulation of heart myofibril assembly GOC:TermGenie Any cell proliferation that is involved in endocardial cushion morphogenesis. rl 2016-07-12T13:56:36Z biological_process GO:1905315 cell proliferation involved in endocardial cushion morphogenesis Any cell proliferation that is involved in endocardial cushion morphogenesis. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000060 PMID:20652948 Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium. bhm 2016-07-22T07:13:49Z regulation of epithelium morphogenesis biological_process GO:1905330 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). regulation of morphogenesis of an epithelium Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 regulation of epithelium morphogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium. bhm 2016-07-22T07:13:57Z down regulation of epithelium morphogenesis down regulation of morphogenesis of an epithelium down-regulation of epithelium morphogenesis down-regulation of morphogenesis of an epithelium downregulation of epithelium morphogenesis downregulation of morphogenesis of an epithelium negative regulation of epithelium morphogenesis inhibition of epithelium morphogenesis inhibition of morphogenesis of an epithelium biological_process GO:1905331 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). negative regulation of morphogenesis of an epithelium Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 down regulation of epithelium morphogenesis GOC:TermGenie down regulation of morphogenesis of an epithelium GOC:TermGenie down-regulation of epithelium morphogenesis GOC:TermGenie down-regulation of morphogenesis of an epithelium GOC:TermGenie downregulation of epithelium morphogenesis GOC:TermGenie downregulation of morphogenesis of an epithelium GOC:TermGenie negative regulation of epithelium morphogenesis GOC:TermGenie inhibition of epithelium morphogenesis GOC:TermGenie inhibition of morphogenesis of an epithelium GOC:TermGenie Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium. bhm 2016-07-22T07:14:05Z positive regulation of epithelium morphogenesis up regulation of epithelium morphogenesis up regulation of morphogenesis of an epithelium up-regulation of epithelium morphogenesis up-regulation of morphogenesis of an epithelium upregulation of epithelium morphogenesis upregulation of morphogenesis of an epithelium activation of epithelium morphogenesis activation of morphogenesis of an epithelium biological_process GO:1905332 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). positive regulation of morphogenesis of an epithelium Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 positive regulation of epithelium morphogenesis GOC:TermGenie up regulation of epithelium morphogenesis GOC:TermGenie up regulation of morphogenesis of an epithelium GOC:TermGenie up-regulation of epithelium morphogenesis GOC:TermGenie up-regulation of morphogenesis of an epithelium GOC:TermGenie upregulation of epithelium morphogenesis GOC:TermGenie upregulation of morphogenesis of an epithelium GOC:TermGenie activation of epithelium morphogenesis GOC:TermGenie activation of morphogenesis of an epithelium GOC:TermGenie The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. pr 2016-08-04T14:49:43Z cilial transition zone assembly cilial transition zone formation ciliary transition zone formation cilium transition zone assembly cilium transition zone formation biological_process GO:1905349 ciliary transition zone assembly The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. GOC:TermGenie GOC:cilia GO_REF:0000079 PMID:21725307 PMID:23644468 PMID:24448408 PMID:26595381 PMID:26982032 cilial transition zone assembly GOC:TermGenie cilial transition zone formation GOC:TermGenie ciliary transition zone formation GOC:TermGenie cilium transition zone assembly GOC:TermGenie cilium transition zone formation GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a presynapse. dos 2016-08-18T14:42:59Z protein localisation in presynapse protein localisation to presynapse protein localization in presynapse recruitment of presynaptic proteins biological_process GO:1905383 protein localization to presynapse A process in which a protein is transported to, or maintained in, a location within a presynapse. GOC:TermGenie GO_REF:0000087 PMID:24449494 protein localisation in presynapse GOC:TermGenie protein localisation to presynapse GOC:TermGenie protein localization in presynapse GOC:TermGenie recruitment of presynaptic proteins PMID:24449494 Any process that modulates the frequency, rate or extent of protein localization to presynapse. dos 2016-08-18T14:56:00Z regulation of protein localisation in presynapse regulation of protein localisation to presynapse regulation of protein localization in presynapse regulation of recruitment of presynaptic proteins biological_process GO:1905384 regulation of protein localization to presynapse Any process that modulates the frequency, rate or extent of protein localization to presynapse. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:24449494 regulation of protein localisation in presynapse GOC:TermGenie regulation of protein localisation to presynapse GOC:TermGenie regulation of protein localization in presynapse GOC:TermGenie regulation of recruitment of presynaptic proteins GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to presynapse. dos 2016-08-18T14:56:08Z down regulation of protein localisation in presynapse down regulation of protein localisation to presynapse down regulation of protein localization in presynapse down regulation of protein localization to presynapse down regulation of recruitment of presynaptic proteins down-regulation of protein localisation in presynapse down-regulation of protein localisation to presynapse down-regulation of protein localization in presynapse down-regulation of protein localization to presynapse down-regulation of recruitment of presynaptic proteins downregulation of protein localisation in presynapse downregulation of protein localisation to presynapse downregulation of protein localization in presynapse downregulation of protein localization to presynapse downregulation of recruitment of presynaptic proteins negative regulation of protein localisation in presynapse negative regulation of protein localisation to presynapse negative regulation of protein localization in presynapse negative regulation of recruitment of presynaptic proteins inhibition of protein localisation in presynapse inhibition of protein localisation to presynapse inhibition of protein localization in presynapse inhibition of protein localization to presynapse inhibition of recruitment of presynaptic proteins biological_process GO:1905385 negative regulation of protein localization to presynapse Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to presynapse. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:24449494 down regulation of protein localisation in presynapse GOC:TermGenie down regulation of protein localisation to presynapse GOC:TermGenie down regulation of protein localization in presynapse GOC:TermGenie down regulation of protein localization to presynapse GOC:TermGenie down regulation of recruitment of presynaptic proteins GOC:TermGenie down-regulation of protein localisation in presynapse GOC:TermGenie down-regulation of protein localisation to presynapse GOC:TermGenie down-regulation of protein localization in presynapse GOC:TermGenie down-regulation of protein localization to presynapse GOC:TermGenie down-regulation of recruitment of presynaptic proteins GOC:TermGenie downregulation of protein localisation in presynapse GOC:TermGenie downregulation of protein localisation to presynapse GOC:TermGenie downregulation of protein localization in presynapse GOC:TermGenie downregulation of protein localization to presynapse GOC:TermGenie downregulation of recruitment of presynaptic proteins GOC:TermGenie negative regulation of protein localisation in presynapse GOC:TermGenie negative regulation of protein localisation to presynapse GOC:TermGenie negative regulation of protein localization in presynapse GOC:TermGenie negative regulation of recruitment of presynaptic proteins GOC:TermGenie inhibition of protein localisation in presynapse GOC:TermGenie inhibition of protein localisation to presynapse GOC:TermGenie inhibition of protein localization in presynapse GOC:TermGenie inhibition of protein localization to presynapse GOC:TermGenie inhibition of recruitment of presynaptic proteins GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to presynapse. dos 2016-08-18T14:56:21Z positive regulation of protein localisation in presynapse positive regulation of protein localisation to presynapse positive regulation of protein localization in presynapse positive regulation of recruitment of presynaptic proteins up regulation of protein localisation in presynapse up regulation of protein localisation to presynapse up regulation of protein localization in presynapse up regulation of protein localization to presynapse up regulation of recruitment of presynaptic proteins up-regulation of protein localisation in presynapse up-regulation of protein localisation to presynapse up-regulation of protein localization in presynapse up-regulation of protein localization to presynapse up-regulation of recruitment of presynaptic proteins upregulation of protein localisation in presynapse upregulation of protein localisation to presynapse upregulation of protein localization in presynapse upregulation of protein localization to presynapse upregulation of recruitment of presynaptic proteins activation of protein localisation in presynapse activation of protein localisation to presynapse activation of protein localization in presynapse activation of protein localization to presynapse activation of recruitment of presynaptic proteins biological_process GO:1905386 positive regulation of protein localization to presynapse Any process that activates or increases the frequency, rate or extent of protein localization to presynapse. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:24449494 positive regulation of protein localisation in presynapse GOC:TermGenie positive regulation of protein localisation to presynapse GOC:TermGenie positive regulation of protein localization in presynapse GOC:TermGenie positive regulation of recruitment of presynaptic proteins GOC:TermGenie up regulation of protein localisation in presynapse GOC:TermGenie up regulation of protein localisation to presynapse GOC:TermGenie up regulation of protein localization in presynapse GOC:TermGenie up regulation of protein localization to presynapse GOC:TermGenie up regulation of recruitment of presynaptic proteins GOC:TermGenie up-regulation of protein localisation in presynapse GOC:TermGenie up-regulation of protein localisation to presynapse GOC:TermGenie up-regulation of protein localization in presynapse GOC:TermGenie up-regulation of protein localization to presynapse GOC:TermGenie up-regulation of recruitment of presynaptic proteins GOC:TermGenie upregulation of protein localisation in presynapse GOC:TermGenie upregulation of protein localisation to presynapse GOC:TermGenie upregulation of protein localization in presynapse GOC:TermGenie upregulation of protein localization to presynapse GOC:TermGenie upregulation of recruitment of presynaptic proteins GOC:TermGenie activation of protein localisation in presynapse GOC:TermGenie activation of protein localisation to presynapse GOC:TermGenie activation of protein localization in presynapse GOC:TermGenie activation of protein localization to presynapse GOC:TermGenie activation of recruitment of presynaptic proteins GOC:TermGenie Any intracellular signal transduction that is involved in positive regulation of cell growth. dph 2016-09-07T18:15:01Z intracellular signal transduction involved in up regulation of cell growth intracellular signal transduction involved in up-regulation of cell growth intracellular signal transduction involved in upregulation of cell growth intracellular signaling chain involved in positive regulation of cell growth intracellular signaling chain involved in up regulation of cell growth intracellular signaling chain involved in up-regulation of cell growth intracellular signaling chain involved in upregulation of cell growth intracellular protein kinase cascade involved in activation of cell growth intracellular protein kinase cascade involved in positive regulation of cell growth intracellular protein kinase cascade involved in stimulation of cell growth intracellular protein kinase cascade involved in up regulation of cell growth intracellular protein kinase cascade involved in up-regulation of cell growth intracellular protein kinase cascade involved in upregulation of cell growth intracellular signal transduction involved in activation of cell growth intracellular signal transduction involved in stimulation of cell growth intracellular signal transduction pathway involved in activation of cell growth intracellular signal transduction pathway involved in positive regulation of cell growth intracellular signal transduction pathway involved in stimulation of cell growth intracellular signal transduction pathway involved in up regulation of cell growth intracellular signal transduction pathway involved in up-regulation of cell growth intracellular signal transduction pathway involved in upregulation of cell growth intracellular signaling chain involved in activation of cell growth intracellular signaling chain involved in stimulation of cell growth protein kinase cascade involved in activation of cell growth protein kinase cascade involved in positive regulation of cell growth protein kinase cascade involved in stimulation of cell growth protein kinase cascade involved in up regulation of cell growth protein kinase cascade involved in up-regulation of cell growth protein kinase cascade involved in upregulation of cell growth signal transmission via intracellular cascade involved in activation of cell growth signal transmission via intracellular cascade involved in positive regulation of cell growth signal transmission via intracellular cascade involved in stimulation of cell growth signal transmission via intracellular cascade involved in up regulation of cell growth signal transmission via intracellular cascade involved in up-regulation of cell growth signal transmission via intracellular cascade involved in upregulation of cell growth biological_process intracellular signaling cascade involved in activation of cell growth intracellular signaling cascade involved in positive regulation of cell growth intracellular signaling cascade involved in stimulation of cell growth intracellular signaling cascade involved in up regulation of cell growth intracellular signaling cascade involved in up-regulation of cell growth intracellular signaling cascade involved in upregulation of cell growth intracellular signaling pathway involved in activation of cell growth intracellular signaling pathway involved in positive regulation of cell growth intracellular signaling pathway involved in stimulation of cell growth intracellular signaling pathway involved in up regulation of cell growth intracellular signaling pathway involved in up-regulation of cell growth intracellular signaling pathway involved in upregulation of cell growth signal transduction via intracellular signaling cascade involved in activation of cell growth signal transduction via intracellular signaling cascade involved in positive regulation of cell growth signal transduction via intracellular signaling cascade involved in stimulation of cell growth signal transduction via intracellular signaling cascade involved in up regulation of cell growth signal transduction via intracellular signaling cascade involved in up-regulation of cell growth signal transduction via intracellular signaling cascade involved in upregulation of cell growth GO:1905427 intracellular signal transduction involved in positive regulation of cell growth Any intracellular signal transduction that is involved in positive regulation of cell growth. GOC:TermGenie GOC:al GOC:vw GO_REF:0000060 PMID:15917811 intracellular signal transduction involved in up regulation of cell growth GOC:TermGenie intracellular signal transduction involved in up-regulation of cell growth GOC:TermGenie intracellular signal transduction involved in upregulation of cell growth GOC:TermGenie intracellular signaling chain involved in positive regulation of cell growth GOC:TermGenie intracellular signaling chain involved in up regulation of cell growth GOC:TermGenie intracellular signaling chain involved in up-regulation of cell growth GOC:TermGenie intracellular signaling chain involved in upregulation of cell growth GOC:TermGenie intracellular protein kinase cascade involved in activation of cell growth GOC:TermGenie intracellular protein kinase cascade involved in positive regulation of cell growth GOC:TermGenie intracellular protein kinase cascade involved in stimulation of cell growth GOC:TermGenie intracellular protein kinase cascade involved in up regulation of cell growth GOC:TermGenie intracellular protein kinase cascade involved in up-regulation of cell growth GOC:TermGenie intracellular protein kinase cascade involved in upregulation of cell growth GOC:TermGenie intracellular signal transduction involved in activation of cell growth GOC:TermGenie intracellular signal transduction involved in stimulation of cell growth GOC:TermGenie intracellular signal transduction pathway involved in activation of cell growth GOC:TermGenie intracellular signal transduction pathway involved in positive regulation of cell growth GOC:TermGenie intracellular signal transduction pathway involved in stimulation of cell growth GOC:TermGenie intracellular signal transduction pathway involved in up regulation of cell growth GOC:TermGenie intracellular signal transduction pathway involved in up-regulation of cell growth GOC:TermGenie intracellular signal transduction pathway involved in upregulation of cell growth GOC:TermGenie intracellular signaling chain involved in activation of cell growth GOC:TermGenie intracellular signaling chain involved in stimulation of cell growth GOC:TermGenie protein kinase cascade involved in activation of cell growth GOC:TermGenie protein kinase cascade involved in positive regulation of cell growth GOC:TermGenie protein kinase cascade involved in stimulation of cell growth GOC:TermGenie protein kinase cascade involved in up regulation of cell growth GOC:TermGenie protein kinase cascade involved in up-regulation of cell growth GOC:TermGenie protein kinase cascade involved in upregulation of cell growth GOC:TermGenie signal transmission via intracellular cascade involved in activation of cell growth GOC:TermGenie signal transmission via intracellular cascade involved in positive regulation of cell growth GOC:TermGenie signal transmission via intracellular cascade involved in stimulation of cell growth GOC:TermGenie signal transmission via intracellular cascade involved in up regulation of cell growth GOC:TermGenie signal transmission via intracellular cascade involved in up-regulation of cell growth GOC:TermGenie signal transmission via intracellular cascade involved in upregulation of cell growth GOC:TermGenie intracellular signaling cascade involved in activation of cell growth GOC:TermGenie intracellular signaling cascade involved in positive regulation of cell growth GOC:TermGenie intracellular signaling cascade involved in stimulation of cell growth GOC:TermGenie intracellular signaling cascade involved in up regulation of cell growth GOC:TermGenie intracellular signaling cascade involved in up-regulation of cell growth GOC:TermGenie intracellular signaling cascade involved in upregulation of cell growth GOC:TermGenie intracellular signaling pathway involved in activation of cell growth GOC:TermGenie intracellular signaling pathway involved in positive regulation of cell growth GOC:TermGenie intracellular signaling pathway involved in stimulation of cell growth GOC:TermGenie intracellular signaling pathway involved in up regulation of cell growth GOC:TermGenie intracellular signaling pathway involved in up-regulation of cell growth GOC:TermGenie intracellular signaling pathway involved in upregulation of cell growth GOC:TermGenie signal transduction via intracellular signaling cascade involved in activation of cell growth GOC:TermGenie signal transduction via intracellular signaling cascade involved in positive regulation of cell growth GOC:TermGenie signal transduction via intracellular signaling cascade involved in stimulation of cell growth GOC:TermGenie signal transduction via intracellular signaling cascade involved in up regulation of cell growth GOC:TermGenie signal transduction via intracellular signaling cascade involved in up-regulation of cell growth GOC:TermGenie signal transduction via intracellular signaling cascade involved in upregulation of cell growth GOC:TermGenie Any process that modulates the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide. bf 2016-09-14T10:56:47Z biological_process regulation of neuropeptide-mediated retrograde trans-synaptic signaling GO:1905432 regulation of retrograde trans-synaptic signaling by neuropeptide Any process that modulates the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:19448629 regulation of neuropeptide-mediated retrograde trans-synaptic signaling GOC:bf Any process that stops, prevents or reduces the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide. bf 2016-09-14T10:56:55Z down regulation of retrograde trans-synaptic signaling by neuropeptide down-regulation of retrograde trans-synaptic signaling by neuropeptide downregulation of retrograde trans-synaptic signaling by neuropeptide inhibition of retrograde trans-synaptic signaling by neuropeptide biological_process inhibition of neuropeptide-mediated retrograde trans-synaptic signaling negative regulation of neuropeptide-mediated retrograde trans-synaptic signaling GO:1905433 negative regulation of retrograde trans-synaptic signaling by neuropeptide Any process that stops, prevents or reduces the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:19448629 down regulation of retrograde trans-synaptic signaling by neuropeptide GOC:TermGenie down-regulation of retrograde trans-synaptic signaling by neuropeptide GOC:TermGenie downregulation of retrograde trans-synaptic signaling by neuropeptide GOC:TermGenie inhibition of retrograde trans-synaptic signaling by neuropeptide GOC:TermGenie inhibition of neuropeptide-mediated retrograde trans-synaptic signaling GOC:bf negative regulation of neuropeptide-mediated retrograde trans-synaptic signaling GOC:bf Any process that activates or increases the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide. bf 2016-09-14T10:57:02Z up regulation of retrograde trans-synaptic signaling by neuropeptide up-regulation of retrograde trans-synaptic signaling by neuropeptide upregulation of retrograde trans-synaptic signaling by neuropeptide activation of retrograde trans-synaptic signaling by neuropeptide biological_process positive regulation of neuropeptide-mediated retrograde trans-synaptic signaling GO:1905434 positive regulation of retrograde trans-synaptic signaling by neuropeptide Any process that activates or increases the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:19448629 up regulation of retrograde trans-synaptic signaling by neuropeptide GOC:TermGenie up-regulation of retrograde trans-synaptic signaling by neuropeptide GOC:TermGenie upregulation of retrograde trans-synaptic signaling by neuropeptide GOC:TermGenie activation of retrograde trans-synaptic signaling by neuropeptide GOC:TermGenie positive regulation of neuropeptide-mediated retrograde trans-synaptic signaling GOC:bf Any process that modulates the frequency, rate or extent of myeloid progenitor cell differentiation. rz 2016-09-16T12:32:18Z biological_process GO:1905453 regulation of myeloid progenitor cell differentiation Any process that modulates the frequency, rate or extent of myeloid progenitor cell differentiation. GOC:TermGenie GO_REF:0000058 PMID:27010503 Any process that stops, prevents or reduces the frequency, rate or extent of myeloid progenitor cell differentiation. rz 2016-09-16T12:32:26Z down regulation of myeloid progenitor cell differentiation down-regulation of myeloid progenitor cell differentiation downregulation of myeloid progenitor cell differentiation inhibition of myeloid progenitor cell differentiation biological_process GO:1905454 negative regulation of myeloid progenitor cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of myeloid progenitor cell differentiation. GOC:TermGenie GO_REF:0000058 PMID:27010503 down regulation of myeloid progenitor cell differentiation GOC:TermGenie down-regulation of myeloid progenitor cell differentiation GOC:TermGenie downregulation of myeloid progenitor cell differentiation GOC:TermGenie inhibition of myeloid progenitor cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of myeloid progenitor cell differentiation. rz 2016-09-16T12:32:33Z up regulation of myeloid progenitor cell differentiation up-regulation of myeloid progenitor cell differentiation upregulation of myeloid progenitor cell differentiation activation of myeloid progenitor cell differentiation biological_process GO:1905455 positive regulation of myeloid progenitor cell differentiation Any process that activates or increases the frequency, rate or extent of myeloid progenitor cell differentiation. GOC:TermGenie GO_REF:0000058 PMID:27010503 up regulation of myeloid progenitor cell differentiation GOC:TermGenie up-regulation of myeloid progenitor cell differentiation GOC:TermGenie upregulation of myeloid progenitor cell differentiation GOC:TermGenie activation of myeloid progenitor cell differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process. rph 2016-09-19T11:33:54Z regulation of VSMC apoptotic process regulation of vascular smooth muscle cell apoptotic process regulation of VSMC apoptosis regulation of vascular associated smooth muscle cell apoptosis regulation of vascular smooth muscle cell apoptosis biological_process GO:1905459 regulation of vascular associated smooth muscle cell apoptotic process Any process that modulates the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:26493107 regulation of VSMC apoptotic process GOC:TermGenie regulation of vascular smooth muscle cell apoptotic process GOC:TermGenie regulation of VSMC apoptosis GOC:TermGenie regulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie regulation of vascular smooth muscle cell apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process. rph 2016-09-19T11:34:03Z down regulation of VSMC apoptotic process down regulation of vascular associated smooth muscle cell apoptotic process down regulation of vascular smooth muscle cell apoptotic process down-regulation of VSMC apoptotic process down-regulation of vascular associated smooth muscle cell apoptotic process down-regulation of vascular smooth muscle cell apoptotic process downregulation of VSMC apoptotic process downregulation of vascular associated smooth muscle cell apoptotic process downregulation of vascular smooth muscle cell apoptotic process negative regulation of VSMC apoptotic process negative regulation of vascular smooth muscle cell apoptotic process down regulation of VSMC apoptosis down regulation of vascular associated smooth muscle cell apoptosis down regulation of vascular smooth muscle cell apoptosis down-regulation of VSMC apoptosis down-regulation of vascular associated smooth muscle cell apoptosis down-regulation of vascular smooth muscle cell apoptosis downregulation of VSMC apoptosis downregulation of vascular associated smooth muscle cell apoptosis downregulation of vascular smooth muscle cell apoptosis inhibition of VSMC apoptosis inhibition of VSMC apoptotic process inhibition of vascular associated smooth muscle cell apoptosis inhibition of vascular associated smooth muscle cell apoptotic process inhibition of vascular smooth muscle cell apoptosis inhibition of vascular smooth muscle cell apoptotic process negative regulation of VSMC apoptosis negative regulation of vascular associated smooth muscle cell apoptosis negative regulation of vascular smooth muscle cell apoptosis biological_process GO:1905460 negative regulation of vascular associated smooth muscle cell apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:26493107 down regulation of VSMC apoptotic process GOC:TermGenie down regulation of vascular associated smooth muscle cell apoptotic process GOC:TermGenie down regulation of vascular smooth muscle cell apoptotic process GOC:TermGenie down-regulation of VSMC apoptotic process GOC:TermGenie down-regulation of vascular associated smooth muscle cell apoptotic process GOC:TermGenie down-regulation of vascular smooth muscle cell apoptotic process GOC:TermGenie downregulation of VSMC apoptotic process GOC:TermGenie downregulation of vascular associated smooth muscle cell apoptotic process GOC:TermGenie downregulation of vascular smooth muscle cell apoptotic process GOC:TermGenie negative regulation of VSMC apoptotic process GOC:TermGenie negative regulation of vascular smooth muscle cell apoptotic process GOC:TermGenie down regulation of VSMC apoptosis GOC:TermGenie down regulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie down regulation of vascular smooth muscle cell apoptosis GOC:TermGenie down-regulation of VSMC apoptosis GOC:TermGenie down-regulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie down-regulation of vascular smooth muscle cell apoptosis GOC:TermGenie downregulation of VSMC apoptosis GOC:TermGenie downregulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie downregulation of vascular smooth muscle cell apoptosis GOC:TermGenie inhibition of VSMC apoptosis GOC:TermGenie inhibition of VSMC apoptotic process GOC:TermGenie inhibition of vascular associated smooth muscle cell apoptosis GOC:TermGenie inhibition of vascular associated smooth muscle cell apoptotic process GOC:TermGenie inhibition of vascular smooth muscle cell apoptosis GOC:TermGenie inhibition of vascular smooth muscle cell apoptotic process GOC:TermGenie negative regulation of VSMC apoptosis GOC:TermGenie negative regulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie negative regulation of vascular smooth muscle cell apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process. rph 2016-09-19T11:34:10Z positive regulation of VSMC apoptotic process positive regulation of vascular smooth muscle cell apoptotic process up regulation of VSMC apoptotic process up regulation of vascular associated smooth muscle cell apoptotic process up regulation of vascular smooth muscle cell apoptotic process up-regulation of VSMC apoptotic process up-regulation of vascular associated smooth muscle cell apoptotic process up-regulation of vascular smooth muscle cell apoptotic process upregulation of VSMC apoptotic process upregulation of vascular associated smooth muscle cell apoptotic process upregulation of vascular smooth muscle cell apoptotic process activation of VSMC apoptosis activation of VSMC apoptotic process activation of vascular associated smooth muscle cell apoptosis activation of vascular associated smooth muscle cell apoptotic process activation of vascular smooth muscle cell apoptosis activation of vascular smooth muscle cell apoptotic process positive regulation of VSMC apoptosis positive regulation of vascular associated smooth muscle cell apoptosis positive regulation of vascular smooth muscle cell apoptosis up regulation of VSMC apoptosis up regulation of vascular associated smooth muscle cell apoptosis up regulation of vascular smooth muscle cell apoptosis up-regulation of VSMC apoptosis up-regulation of vascular associated smooth muscle cell apoptosis up-regulation of vascular smooth muscle cell apoptosis upregulation of VSMC apoptosis upregulation of vascular associated smooth muscle cell apoptosis upregulation of vascular smooth muscle cell apoptosis biological_process GO:1905461 positive regulation of vascular associated smooth muscle cell apoptotic process Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:26493107 positive regulation of VSMC apoptotic process GOC:TermGenie positive regulation of vascular smooth muscle cell apoptotic process GOC:TermGenie up regulation of VSMC apoptotic process GOC:TermGenie up regulation of vascular associated smooth muscle cell apoptotic process GOC:TermGenie up regulation of vascular smooth muscle cell apoptotic process GOC:TermGenie up-regulation of VSMC apoptotic process GOC:TermGenie up-regulation of vascular associated smooth muscle cell apoptotic process GOC:TermGenie up-regulation of vascular smooth muscle cell apoptotic process GOC:TermGenie upregulation of VSMC apoptotic process GOC:TermGenie upregulation of vascular associated smooth muscle cell apoptotic process GOC:TermGenie upregulation of vascular smooth muscle cell apoptotic process GOC:TermGenie activation of VSMC apoptosis GOC:TermGenie activation of VSMC apoptotic process GOC:TermGenie activation of vascular associated smooth muscle cell apoptosis GOC:TermGenie activation of vascular associated smooth muscle cell apoptotic process GOC:TermGenie activation of vascular smooth muscle cell apoptosis GOC:TermGenie activation of vascular smooth muscle cell apoptotic process GOC:TermGenie positive regulation of VSMC apoptosis GOC:TermGenie positive regulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie positive regulation of vascular smooth muscle cell apoptosis GOC:TermGenie up regulation of VSMC apoptosis GOC:TermGenie up regulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie up regulation of vascular smooth muscle cell apoptosis GOC:TermGenie up-regulation of VSMC apoptosis GOC:TermGenie up-regulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie up-regulation of vascular smooth muscle cell apoptosis GOC:TermGenie upregulation of VSMC apoptosis GOC:TermGenie upregulation of vascular associated smooth muscle cell apoptosis GOC:TermGenie upregulation of vascular smooth muscle cell apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to membrane. bc 2016-09-21T16:20:03Z regulation of protein localisation in membrane regulation of protein localization in membrane biological_process GO:1905475 regulation of protein localization to membrane Any process that modulates the frequency, rate or extent of protein localization to membrane. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:26911690 regulation of protein localisation in membrane GOC:TermGenie regulation of protein localization in membrane GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to membrane. bc 2016-09-21T16:20:10Z down regulation of protein localisation in membrane down regulation of protein localization in membrane down regulation of protein localization to membrane down-regulation of protein localisation in membrane down-regulation of protein localization in membrane down-regulation of protein localization to membrane downregulation of protein localisation in membrane downregulation of protein localization in membrane downregulation of protein localization to membrane negative regulation of protein localisation in membrane negative regulation of protein localization in membrane inhibition of protein localisation in membrane inhibition of protein localization in membrane inhibition of protein localization to membrane biological_process GO:1905476 negative regulation of protein localization to membrane Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to membrane. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:26911690 down regulation of protein localisation in membrane GOC:TermGenie down regulation of protein localization in membrane GOC:TermGenie down regulation of protein localization to membrane GOC:TermGenie down-regulation of protein localisation in membrane GOC:TermGenie down-regulation of protein localization in membrane GOC:TermGenie down-regulation of protein localization to membrane GOC:TermGenie downregulation of protein localisation in membrane GOC:TermGenie downregulation of protein localization in membrane GOC:TermGenie downregulation of protein localization to membrane GOC:TermGenie negative regulation of protein localisation in membrane GOC:TermGenie negative regulation of protein localization in membrane GOC:TermGenie inhibition of protein localisation in membrane GOC:TermGenie inhibition of protein localization in membrane GOC:TermGenie inhibition of protein localization to membrane GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to membrane. bc 2016-09-21T16:20:18Z positive regulation of protein localisation in membrane positive regulation of protein localization in membrane up regulation of protein localisation in membrane up regulation of protein localization in membrane up regulation of protein localization to membrane up-regulation of protein localisation in membrane up-regulation of protein localization in membrane up-regulation of protein localization to membrane upregulation of protein localisation in membrane upregulation of protein localization in membrane upregulation of protein localization to membrane activation of protein localisation in membrane activation of protein localization in membrane activation of protein localization to membrane biological_process GO:1905477 positive regulation of protein localization to membrane Any process that activates or increases the frequency, rate or extent of protein localization to membrane. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:26911690 positive regulation of protein localisation in membrane GOC:TermGenie positive regulation of protein localization in membrane GOC:TermGenie up regulation of protein localisation in membrane GOC:TermGenie up regulation of protein localization in membrane GOC:TermGenie up regulation of protein localization to membrane GOC:TermGenie up-regulation of protein localisation in membrane GOC:TermGenie up-regulation of protein localization in membrane GOC:TermGenie up-regulation of protein localization to membrane GOC:TermGenie upregulation of protein localisation in membrane GOC:TermGenie upregulation of protein localization in membrane GOC:TermGenie upregulation of protein localization to membrane GOC:TermGenie activation of protein localisation in membrane GOC:TermGenie activation of protein localization in membrane GOC:TermGenie activation of protein localization to membrane GOC:TermGenie Any process that activates or increases the frequency, rate or extent of branching morphogenesis of a nerve. hbye 2016-09-23T14:11:52Z up regulation of branching morphogenesis of a nerve up-regulation of branching morphogenesis of a nerve upregulation of branching morphogenesis of a nerve activation of branching morphogenesis of a nerve biological_process GO:1905492 positive regulation of branching morphogenesis of a nerve Any process that activates or increases the frequency, rate or extent of branching morphogenesis of a nerve. GOC:TermGenie GO_REF:0000058 PMID:16516839 up regulation of branching morphogenesis of a nerve GOC:TermGenie up-regulation of branching morphogenesis of a nerve GOC:TermGenie upregulation of branching morphogenesis of a nerve GOC:TermGenie activation of branching morphogenesis of a nerve GOC:TermGenie Any process that activates or increases the frequency, rate or extent of fertilization. pr 2016-09-30T14:32:32Z positive regulation of syngamy up regulation of fertilization up regulation of syngamy up-regulation of fertilization up-regulation of syngamy upregulation of fertilization upregulation of syngamy activation of fertilization activation of syngamy biological_process GO:1905516 positive regulation of fertilization Any process that activates or increases the frequency, rate or extent of fertilization. GOC:TermGenie GOC:hbye GO_REF:0000058 PMID:27564576 positive regulation of syngamy GOC:TermGenie up regulation of fertilization GOC:TermGenie up regulation of syngamy GOC:TermGenie up-regulation of fertilization GOC:TermGenie up-regulation of syngamy GOC:TermGenie upregulation of fertilization GOC:TermGenie upregulation of syngamy GOC:TermGenie activation of fertilization GOC:TermGenie activation of syngamy GOC:TermGenie Any process that modulates the frequency, rate or extent of blood vessel branching. nc 2016-10-12T14:19:33Z regulation of branching involved in blood vessel morphogenesis biological_process GO:1905553 regulation of blood vessel branching Any process that modulates the frequency, rate or extent of blood vessel branching. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:23201774 regulation of branching involved in blood vessel morphogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of blood vessel branching. nc 2016-10-12T14:19:41Z down regulation of branching involved in blood vessel morphogenesis down regulation of patterning of blood vessels down-regulation of branching involved in blood vessel morphogenesis down-regulation of patterning of blood vessels downregulation of branching involved in blood vessel morphogenesis downregulation of patterning of blood vessels negative regulation of branching involved in blood vessel morphogenesis inhibition of branching involved in blood vessel morphogenesis inhibition of patterning of blood vessels biological_process GO:1905554 negative regulation of vessel branching Any process that stops, prevents or reduces the frequency, rate or extent of blood vessel branching. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:23201774 down regulation of branching involved in blood vessel morphogenesis GOC:TermGenie down regulation of patterning of blood vessels GOC:TermGenie down-regulation of branching involved in blood vessel morphogenesis GOC:TermGenie down-regulation of patterning of blood vessels GOC:TermGenie downregulation of branching involved in blood vessel morphogenesis GOC:TermGenie downregulation of patterning of blood vessels GOC:TermGenie negative regulation of branching involved in blood vessel morphogenesis GOC:TermGenie inhibition of branching involved in blood vessel morphogenesis GOC:TermGenie inhibition of patterning of blood vessels GOC:TermGenie Any process that activates or increases the frequency, rate or extent of blood vessel branching. nc 2016-10-12T14:19:49Z positive regulation of branching involved in blood vessel morphogenesis up regulation of branching involved in blood vessel morphogenesis up regulation of patterning of blood vessels up-regulation of branching involved in blood vessel morphogenesis up-regulation of patterning of blood vessels upregulation of branching involved in blood vessel morphogenesis upregulation of patterning of blood vessels activation of branching involved in blood vessel morphogenesis activation of patterning of blood vessels biological_process GO:1905555 positive regulation of blood vessel branching Any process that activates or increases the frequency, rate or extent of blood vessel branching. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:23201774 positive regulation of branching involved in blood vessel morphogenesis GOC:TermGenie up regulation of branching involved in blood vessel morphogenesis GOC:TermGenie up regulation of patterning of blood vessels GOC:TermGenie up-regulation of branching involved in blood vessel morphogenesis GOC:TermGenie up-regulation of patterning of blood vessels GOC:TermGenie upregulation of branching involved in blood vessel morphogenesis GOC:TermGenie upregulation of patterning of blood vessels GOC:TermGenie activation of branching involved in blood vessel morphogenesis GOC:TermGenie activation of patterning of blood vessels GOC:TermGenie Any process that modulates the frequency, rate or extent of mitotic nuclear envelope disassembly. hbye 2016-10-14T13:14:57Z regulation of mitotic nuclear envelope breakdown regulation of mitotic nuclear envelope catabolism regulation of mitotic nuclear envelope degradation biological_process GO:1905557 regulation of mitotic nuclear envelope disassembly Any process that modulates the frequency, rate or extent of mitotic nuclear envelope disassembly. GOC:TermGenie GO_REF:0000058 PMID:18765790 regulation of mitotic nuclear envelope breakdown GOC:TermGenie regulation of mitotic nuclear envelope catabolism GOC:TermGenie regulation of mitotic nuclear envelope degradation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of mitotic nuclear envelope disassembly. hbye 2016-10-14T13:15:08Z down regulation of mitotic nuclear envelope breakdown down regulation of mitotic nuclear envelope catabolism down regulation of mitotic nuclear envelope degradation down regulation of mitotic nuclear envelope disassembly down-regulation of mitotic nuclear envelope breakdown down-regulation of mitotic nuclear envelope catabolism down-regulation of mitotic nuclear envelope degradation down-regulation of mitotic nuclear envelope disassembly downregulation of mitotic nuclear envelope breakdown downregulation of mitotic nuclear envelope catabolism downregulation of mitotic nuclear envelope degradation downregulation of mitotic nuclear envelope disassembly negative regulation of mitotic nuclear envelope breakdown negative regulation of mitotic nuclear envelope catabolism negative regulation of mitotic nuclear envelope degradation inhibition of mitotic nuclear envelope breakdown inhibition of mitotic nuclear envelope catabolism inhibition of mitotic nuclear envelope degradation inhibition of mitotic nuclear envelope disassembly biological_process GO:1905558 negative regulation of mitotic nuclear envelope disassembly Any process that stops, prevents or reduces the frequency, rate or extent of mitotic nuclear envelope disassembly. GOC:TermGenie GO_REF:0000058 PMID:18765790 down regulation of mitotic nuclear envelope breakdown GOC:TermGenie down regulation of mitotic nuclear envelope catabolism GOC:TermGenie down regulation of mitotic nuclear envelope degradation GOC:TermGenie down regulation of mitotic nuclear envelope disassembly GOC:TermGenie down-regulation of mitotic nuclear envelope breakdown GOC:TermGenie down-regulation of mitotic nuclear envelope catabolism GOC:TermGenie down-regulation of mitotic nuclear envelope degradation GOC:TermGenie down-regulation of mitotic nuclear envelope disassembly GOC:TermGenie downregulation of mitotic nuclear envelope breakdown GOC:TermGenie downregulation of mitotic nuclear envelope catabolism GOC:TermGenie downregulation of mitotic nuclear envelope degradation GOC:TermGenie downregulation of mitotic nuclear envelope disassembly GOC:TermGenie negative regulation of mitotic nuclear envelope breakdown GOC:TermGenie negative regulation of mitotic nuclear envelope catabolism GOC:TermGenie negative regulation of mitotic nuclear envelope degradation GOC:TermGenie inhibition of mitotic nuclear envelope breakdown GOC:TermGenie inhibition of mitotic nuclear envelope catabolism GOC:TermGenie inhibition of mitotic nuclear envelope degradation GOC:TermGenie inhibition of mitotic nuclear envelope disassembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of mitotic nuclear envelope disassembly. hbye 2016-10-14T13:15:17Z positive regulation of mitotic nuclear envelope breakdown positive regulation of mitotic nuclear envelope catabolism positive regulation of mitotic nuclear envelope degradation up regulation of mitotic nuclear envelope breakdown up regulation of mitotic nuclear envelope catabolism up regulation of mitotic nuclear envelope degradation up regulation of mitotic nuclear envelope disassembly up-regulation of mitotic nuclear envelope breakdown up-regulation of mitotic nuclear envelope catabolism up-regulation of mitotic nuclear envelope degradation up-regulation of mitotic nuclear envelope disassembly upregulation of mitotic nuclear envelope breakdown upregulation of mitotic nuclear envelope catabolism upregulation of mitotic nuclear envelope degradation upregulation of mitotic nuclear envelope disassembly activation of mitotic nuclear envelope breakdown activation of mitotic nuclear envelope catabolism activation of mitotic nuclear envelope degradation activation of mitotic nuclear envelope disassembly biological_process GO:1905559 positive regulation of mitotic nuclear envelope disassembly Any process that activates or increases the frequency, rate or extent of mitotic nuclear envelope disassembly. GOC:TermGenie GO_REF:0000058 PMID:18765790 positive regulation of mitotic nuclear envelope breakdown GOC:TermGenie positive regulation of mitotic nuclear envelope catabolism GOC:TermGenie positive regulation of mitotic nuclear envelope degradation GOC:TermGenie up regulation of mitotic nuclear envelope breakdown GOC:TermGenie up regulation of mitotic nuclear envelope catabolism GOC:TermGenie up regulation of mitotic nuclear envelope degradation GOC:TermGenie up regulation of mitotic nuclear envelope disassembly GOC:TermGenie up-regulation of mitotic nuclear envelope breakdown GOC:TermGenie up-regulation of mitotic nuclear envelope catabolism GOC:TermGenie up-regulation of mitotic nuclear envelope degradation GOC:TermGenie up-regulation of mitotic nuclear envelope disassembly GOC:TermGenie upregulation of mitotic nuclear envelope breakdown GOC:TermGenie upregulation of mitotic nuclear envelope catabolism GOC:TermGenie upregulation of mitotic nuclear envelope degradation GOC:TermGenie upregulation of mitotic nuclear envelope disassembly GOC:TermGenie activation of mitotic nuclear envelope breakdown GOC:TermGenie activation of mitotic nuclear envelope catabolism GOC:TermGenie activation of mitotic nuclear envelope degradation GOC:TermGenie activation of mitotic nuclear envelope disassembly GOC:TermGenie Any process that modulates the frequency, rate or extent of vascular endothelial cell proliferation. nc 2016-10-17T09:24:17Z biological_process GO:1905562 regulation of vascular endothelial cell proliferation Any process that modulates the frequency, rate or extent of vascular endothelial cell proliferation. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:23201774 Any process that stops, prevents or reduces the frequency, rate or extent of vascular endothelial cell proliferation. nc 2016-10-17T09:24:26Z down regulation of vascular endothelial cell proliferation down-regulation of vascular endothelial cell proliferation downregulation of vascular endothelial cell proliferation inhibition of vascular endothelial cell proliferation biological_process GO:1905563 negative regulation of vascular endothelial cell proliferation Any process that stops, prevents or reduces the frequency, rate or extent of vascular endothelial cell proliferation. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:23201774 down regulation of vascular endothelial cell proliferation GOC:TermGenie down-regulation of vascular endothelial cell proliferation GOC:TermGenie downregulation of vascular endothelial cell proliferation GOC:TermGenie inhibition of vascular endothelial cell proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of vascular endothelial cell proliferation. nc 2016-10-17T09:24:35Z up regulation of vascular endothelial cell proliferation up-regulation of vascular endothelial cell proliferation upregulation of vascular endothelial cell proliferation activation of vascular endothelial cell proliferation biological_process GO:1905564 positive regulation of vascular endothelial cell proliferation Any process that activates or increases the frequency, rate or extent of vascular endothelial cell proliferation. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000058 PMID:23201774 up regulation of vascular endothelial cell proliferation GOC:TermGenie up-regulation of vascular endothelial cell proliferation GOC:TermGenie upregulation of vascular endothelial cell proliferation GOC:TermGenie activation of vascular endothelial cell proliferation GOC:TermGenie Any process that modulates the frequency, rate or extent of presynapse assembly. bc 2016-10-27T16:08:13Z regulation of presynapse biogenesis regulation of presynaptic terminal assembly biological_process GO:1905606 regulation of presynapse assembly Any process that modulates the frequency, rate or extent of presynapse assembly. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:25533483 regulation of presynapse biogenesis GOC:TermGenie regulation of presynaptic terminal assembly GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of presynapse assembly. bc 2016-10-27T16:08:20Z down regulation of presynapse assembly down regulation of presynapse biogenesis down regulation of presynaptic terminal assembly down-regulation of presynapse assembly down-regulation of presynapse biogenesis down-regulation of presynaptic terminal assembly downregulation of presynapse assembly downregulation of presynapse biogenesis downregulation of presynaptic terminal assembly negative regulation of presynapse biogenesis negative regulation of presynaptic terminal assembly inhibition of presynapse assembly inhibition of presynapse biogenesis inhibition of presynaptic terminal assembly biological_process GO:1905607 negative regulation of presynapse assembly Any process that stops, prevents or reduces the frequency, rate or extent of presynapse assembly. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:25533483 down regulation of presynapse assembly GOC:TermGenie down regulation of presynapse biogenesis GOC:TermGenie down regulation of presynaptic terminal assembly GOC:TermGenie down-regulation of presynapse assembly GOC:TermGenie down-regulation of presynapse biogenesis GOC:TermGenie down-regulation of presynaptic terminal assembly GOC:TermGenie downregulation of presynapse assembly GOC:TermGenie downregulation of presynapse biogenesis GOC:TermGenie downregulation of presynaptic terminal assembly GOC:TermGenie negative regulation of presynapse biogenesis GOC:TermGenie negative regulation of presynaptic terminal assembly GOC:TermGenie inhibition of presynapse assembly GOC:TermGenie inhibition of presynapse biogenesis GOC:TermGenie inhibition of presynaptic terminal assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of presynapse assembly. bc 2016-10-27T16:08:28Z positive regulation of presynapse biogenesis positive regulation of presynaptic terminal assembly up regulation of presynapse assembly up regulation of presynapse biogenesis up regulation of presynaptic terminal assembly up-regulation of presynapse assembly up-regulation of presynapse biogenesis up-regulation of presynaptic terminal assembly upregulation of presynapse assembly upregulation of presynapse biogenesis upregulation of presynaptic terminal assembly activation of presynapse assembly activation of presynapse biogenesis activation of presynaptic terminal assembly biological_process GO:1905608 positive regulation of presynapse assembly Any process that activates or increases the frequency, rate or extent of presynapse assembly. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:25533483 positive regulation of presynapse biogenesis GOC:TermGenie positive regulation of presynaptic terminal assembly GOC:TermGenie up regulation of presynapse assembly GOC:TermGenie up regulation of presynapse biogenesis GOC:TermGenie up regulation of presynaptic terminal assembly GOC:TermGenie up-regulation of presynapse assembly GOC:TermGenie up-regulation of presynapse biogenesis GOC:TermGenie up-regulation of presynaptic terminal assembly GOC:TermGenie upregulation of presynapse assembly GOC:TermGenie upregulation of presynapse biogenesis GOC:TermGenie upregulation of presynaptic terminal assembly GOC:TermGenie activation of presynapse assembly GOC:TermGenie activation of presynapse biogenesis GOC:TermGenie activation of presynaptic terminal assembly GOC:TermGenie Any process that modulates the frequency, rate or extent of serotonin biosynthetic process. pad 2016-10-31T14:26:20Z regulation of serotonin anabolism regulation of serotonin biosynthesis regulation of serotonin formation regulation of serotonin synthesis biological_process GO:1905627 regulation of serotonin biosynthetic process Any process that modulates the frequency, rate or extent of serotonin biosynthetic process. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:25642596 regulation of serotonin anabolism GOC:TermGenie regulation of serotonin biosynthesis GOC:TermGenie regulation of serotonin formation GOC:TermGenie regulation of serotonin synthesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of serotonin biosynthetic process. pad 2016-10-31T14:26:28Z down regulation of serotonin anabolism down regulation of serotonin biosynthesis down regulation of serotonin biosynthetic process down regulation of serotonin formation down regulation of serotonin synthesis down-regulation of serotonin anabolism down-regulation of serotonin biosynthesis down-regulation of serotonin biosynthetic process down-regulation of serotonin formation down-regulation of serotonin synthesis downregulation of serotonin anabolism downregulation of serotonin biosynthesis downregulation of serotonin biosynthetic process downregulation of serotonin formation downregulation of serotonin synthesis negative regulation of serotonin anabolism negative regulation of serotonin biosynthesis negative regulation of serotonin formation negative regulation of serotonin synthesis inhibition of serotonin anabolism inhibition of serotonin biosynthesis inhibition of serotonin biosynthetic process inhibition of serotonin formation inhibition of serotonin synthesis biological_process GO:1905628 negative regulation of serotonin biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of serotonin biosynthetic process. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:25642596 down regulation of serotonin anabolism GOC:TermGenie down regulation of serotonin biosynthesis GOC:TermGenie down regulation of serotonin biosynthetic process GOC:TermGenie down regulation of serotonin formation GOC:TermGenie down regulation of serotonin synthesis GOC:TermGenie down-regulation of serotonin anabolism GOC:TermGenie down-regulation of serotonin biosynthesis GOC:TermGenie down-regulation of serotonin biosynthetic process GOC:TermGenie down-regulation of serotonin formation GOC:TermGenie down-regulation of serotonin synthesis GOC:TermGenie downregulation of serotonin anabolism GOC:TermGenie downregulation of serotonin biosynthesis GOC:TermGenie downregulation of serotonin biosynthetic process GOC:TermGenie downregulation of serotonin formation GOC:TermGenie downregulation of serotonin synthesis GOC:TermGenie negative regulation of serotonin anabolism GOC:TermGenie negative regulation of serotonin biosynthesis GOC:TermGenie negative regulation of serotonin formation GOC:TermGenie negative regulation of serotonin synthesis GOC:TermGenie inhibition of serotonin anabolism GOC:TermGenie inhibition of serotonin biosynthesis GOC:TermGenie inhibition of serotonin biosynthetic process GOC:TermGenie inhibition of serotonin formation GOC:TermGenie inhibition of serotonin synthesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of serotonin biosynthetic process. pad 2016-10-31T14:26:36Z positive regulation of serotonin anabolism positive regulation of serotonin biosynthesis positive regulation of serotonin formation positive regulation of serotonin synthesis up regulation of serotonin anabolism up regulation of serotonin biosynthesis up regulation of serotonin biosynthetic process up regulation of serotonin formation up regulation of serotonin synthesis up-regulation of serotonin anabolism up-regulation of serotonin biosynthesis up-regulation of serotonin biosynthetic process up-regulation of serotonin formation up-regulation of serotonin synthesis upregulation of serotonin anabolism upregulation of serotonin biosynthesis upregulation of serotonin biosynthetic process upregulation of serotonin formation upregulation of serotonin synthesis activation of serotonin anabolism activation of serotonin biosynthesis activation of serotonin biosynthetic process activation of serotonin formation activation of serotonin synthesis biological_process GO:1905629 positive regulation of serotonin biosynthetic process Any process that activates or increases the frequency, rate or extent of serotonin biosynthetic process. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:25642596 positive regulation of serotonin anabolism GOC:TermGenie positive regulation of serotonin biosynthesis GOC:TermGenie positive regulation of serotonin formation GOC:TermGenie positive regulation of serotonin synthesis GOC:TermGenie up regulation of serotonin anabolism GOC:TermGenie up regulation of serotonin biosynthesis GOC:TermGenie up regulation of serotonin biosynthetic process GOC:TermGenie up regulation of serotonin formation GOC:TermGenie up regulation of serotonin synthesis GOC:TermGenie up-regulation of serotonin anabolism GOC:TermGenie up-regulation of serotonin biosynthesis GOC:TermGenie up-regulation of serotonin biosynthetic process GOC:TermGenie up-regulation of serotonin formation GOC:TermGenie up-regulation of serotonin synthesis GOC:TermGenie upregulation of serotonin anabolism GOC:TermGenie upregulation of serotonin biosynthesis GOC:TermGenie upregulation of serotonin biosynthetic process GOC:TermGenie upregulation of serotonin formation GOC:TermGenie upregulation of serotonin synthesis GOC:TermGenie activation of serotonin anabolism GOC:TermGenie activation of serotonin biosynthesis GOC:TermGenie activation of serotonin biosynthetic process GOC:TermGenie activation of serotonin formation GOC:TermGenie activation of serotonin synthesis GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to chromatin. pga 2016-11-01T16:33:52Z regulation of protein localisation to chromatin biological_process GO:1905634 regulation of protein localization to chromatin Any process that modulates the frequency, rate or extent of protein localization to chromatin. GOC:TermGenie GO_REF:0000058 PMID:20889714 regulation of protein localisation to chromatin GOC:TermGenie Any process that modulates the frequency, rate or extent of artery morphogenesis. rph 2016-11-09T12:19:37Z regulation of arterial morphogenesis regulation of arteriogenesis biological_process GO:1905651 regulation of artery morphogenesis Any process that modulates the frequency, rate or extent of artery morphogenesis. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:27389411 regulation of arterial morphogenesis GOC:TermGenie regulation of arteriogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of artery morphogenesis. rph 2016-11-09T12:19:53Z down regulation of arterial morphogenesis down regulation of arteriogenesis down regulation of artery morphogenesis down-regulation of arterial morphogenesis down-regulation of arteriogenesis down-regulation of artery morphogenesis downregulation of arterial morphogenesis downregulation of arteriogenesis downregulation of artery morphogenesis negative regulation of arterial morphogenesis negative regulation of arteriogenesis inhibition of arterial morphogenesis inhibition of arteriogenesis inhibition of artery morphogenesis biological_process GO:1905652 negative regulation of artery morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of artery morphogenesis. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:27389411 down regulation of arterial morphogenesis GOC:TermGenie down regulation of arteriogenesis GOC:TermGenie down regulation of artery morphogenesis GOC:TermGenie down-regulation of arterial morphogenesis GOC:TermGenie down-regulation of arteriogenesis GOC:TermGenie down-regulation of artery morphogenesis GOC:TermGenie downregulation of arterial morphogenesis GOC:TermGenie downregulation of arteriogenesis GOC:TermGenie downregulation of artery morphogenesis GOC:TermGenie negative regulation of arterial morphogenesis GOC:TermGenie negative regulation of arteriogenesis GOC:TermGenie inhibition of arterial morphogenesis GOC:TermGenie inhibition of arteriogenesis GOC:TermGenie inhibition of artery morphogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of artery morphogenesis. rph 2016-11-09T12:20:01Z positive regulation of arterial morphogenesis positive regulation of arteriogenesis up regulation of arterial morphogenesis up regulation of arteriogenesis up regulation of artery morphogenesis up-regulation of arterial morphogenesis up-regulation of arteriogenesis up-regulation of artery morphogenesis upregulation of arterial morphogenesis upregulation of arteriogenesis upregulation of artery morphogenesis activation of arterial morphogenesis activation of arteriogenesis activation of artery morphogenesis biological_process GO:1905653 positive regulation of artery morphogenesis Any process that activates or increases the frequency, rate or extent of artery morphogenesis. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:27389411 positive regulation of arterial morphogenesis GOC:TermGenie positive regulation of arteriogenesis GOC:TermGenie up regulation of arterial morphogenesis GOC:TermGenie up regulation of arteriogenesis GOC:TermGenie up regulation of artery morphogenesis GOC:TermGenie up-regulation of arterial morphogenesis GOC:TermGenie up-regulation of arteriogenesis GOC:TermGenie up-regulation of artery morphogenesis GOC:TermGenie upregulation of arterial morphogenesis GOC:TermGenie upregulation of arteriogenesis GOC:TermGenie upregulation of artery morphogenesis GOC:TermGenie activation of arterial morphogenesis GOC:TermGenie activation of arteriogenesis GOC:TermGenie activation of artery morphogenesis GOC:TermGenie The disaggregation of a nucleus into its constituent components. pr 2016-11-14T13:38:57Z cell nucleus disassembly biological_process GO:1905690 nucleus disassembly The disaggregation of a nucleus into its constituent components. GOC:TermGenie GOC:autophagy GOC:pr GO_REF:0000079 cell nucleus disassembly GOC:TermGenie Any microtubule bundle that is part of a cytoplasm. mah 2016-11-24T16:52:02Z microtubule bundle of cytoplasm microtubule fascicle of cytoplasm cellular_component GO:1905720 cytoplasmic microtubule bundle Any microtubule bundle that is part of a cytoplasm. GOC:TermGenie GO_REF:0000064 PMID:11007487 PMID:26124291 microtubule bundle of cytoplasm GOC:TermGenie microtubule fascicle of cytoplasm GOC:TermGenie A process in which a protein is transported to, or maintained in, a location within a cytoplasmic microtubule. mah 2016-12-12T15:31:07Z protein localisation to cytoplasmic microtubule biological_process GO:1905755 protein localization to cytoplasmic microtubule A process in which a protein is transported to, or maintained in, a location within a cytoplasmic microtubule. GOC:TermGenie GO_REF:0000087 PMID:15177031 protein localisation to cytoplasmic microtubule GOC:TermGenie Any process that modulates the frequency, rate or extent of mesodermal cell differentiation. rph 2016-12-21T12:44:13Z regulation of mesoderm cell differentiation biological_process GO:1905770 regulation of mesodermal cell differentiation Any process that modulates the frequency, rate or extent of mesodermal cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23765923 regulation of mesoderm cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of mesodermal cell differentiation. rph 2016-12-21T12:44:23Z down regulation of mesoderm cell differentiation down regulation of mesodermal cell differentiation down-regulation of mesoderm cell differentiation down-regulation of mesodermal cell differentiation downregulation of mesoderm cell differentiation downregulation of mesodermal cell differentiation negative regulation of mesoderm cell differentiation inhibition of mesoderm cell differentiation inhibition of mesodermal cell differentiation biological_process GO:1905771 negative regulation of mesodermal cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of mesodermal cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23765923 down regulation of mesoderm cell differentiation GOC:TermGenie down regulation of mesodermal cell differentiation GOC:TermGenie down-regulation of mesoderm cell differentiation GOC:TermGenie down-regulation of mesodermal cell differentiation GOC:TermGenie downregulation of mesoderm cell differentiation GOC:TermGenie downregulation of mesodermal cell differentiation GOC:TermGenie negative regulation of mesoderm cell differentiation GOC:TermGenie inhibition of mesoderm cell differentiation GOC:TermGenie inhibition of mesodermal cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of mesodermal cell differentiation. rph 2016-12-21T12:44:32Z positive regulation of mesoderm cell differentiation up regulation of mesoderm cell differentiation up regulation of mesodermal cell differentiation up-regulation of mesoderm cell differentiation up-regulation of mesodermal cell differentiation upregulation of mesoderm cell differentiation upregulation of mesodermal cell differentiation activation of mesoderm cell differentiation activation of mesodermal cell differentiation biological_process GO:1905772 positive regulation of mesodermal cell differentiation Any process that activates or increases the frequency, rate or extent of mesodermal cell differentiation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23765923 positive regulation of mesoderm cell differentiation GOC:TermGenie up regulation of mesoderm cell differentiation GOC:TermGenie up regulation of mesodermal cell differentiation GOC:TermGenie up-regulation of mesoderm cell differentiation GOC:TermGenie up-regulation of mesodermal cell differentiation GOC:TermGenie upregulation of mesoderm cell differentiation GOC:TermGenie upregulation of mesodermal cell differentiation GOC:TermGenie activation of mesoderm cell differentiation GOC:TermGenie activation of mesodermal cell differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of synapse pruning. tb 2017-01-11T22:03:15Z regulation of synapse clearance regulation of synapse disassembly regulation of synapse elimination regulation of synapse removal biological_process GO:1905806 regulation of synapse pruning Any process that modulates the frequency, rate or extent of synapse pruning. GOC:TermGenie GO_REF:0000058 PMID:27779093 regulation of synapse disassembly Any process that stops, prevents or reduces the frequency, rate or extent of synapse pruning. tb 2017-01-11T22:03:24Z regulation of synapse clearance regulation of synapse disassembly regulation of synapse elimination regulation of synapse removal down regulation of synapse disassembly down-regulation of synapse disassembly downregulation of synapse disassembly inhibition of synapse disassembly biological_process GO:1905807 negative regulation of synapse pruning Any process that stops, prevents or reduces the frequency, rate or extent of synapse pruning. GOC:TermGenie GO_REF:0000058 PMID:27779093 down regulation of synapse disassembly GOC:TermGenie down-regulation of synapse disassembly GOC:TermGenie downregulation of synapse disassembly GOC:TermGenie inhibition of synapse disassembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of synapse pruning. tb 2017-01-11T22:03:33Z regulation of synapse clearance regulation of synapse disassembly regulation of synapse elimination regulation of synapse removal up regulation of synapse disassembly up-regulation of synapse disassembly upregulation of synapse disassembly activation of synapse disassembly biological_process GO:1905808 positive regulation of synapse pruning Any process that activates or increases the frequency, rate or extent of synapse pruning. GOC:TermGenie GO_REF:0000058 PMID:27779093 up regulation of synapse disassembly GOC:TermGenie up-regulation of synapse disassembly GOC:TermGenie upregulation of synapse disassembly GOC:TermGenie activation of synapse disassembly GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of synapse organization. tb 2017-01-11T22:03:41Z down regulation of synapse development down regulation of synapse organisation down regulation of synapse organization down-regulation of synapse development down-regulation of synapse organisation down-regulation of synapse organization downregulation of synapse development downregulation of synapse organisation downregulation of synapse organization negative regulation of synapse development negative regulation of synapse organisation inhibition of synapse development inhibition of synapse organisation inhibition of synapse organization biological_process down regulation of synapse morphogenesis down regulation of synapse organization and biogenesis down-regulation of synapse morphogenesis down-regulation of synapse organization and biogenesis downregulation of synapse morphogenesis downregulation of synapse organization and biogenesis inhibition of synapse morphogenesis inhibition of synapse organization and biogenesis negative regulation of synapse morphogenesis negative regulation of synapse organization and biogenesis GO:1905809 negative regulation of synapse organization Any process that stops, prevents or reduces the frequency, rate or extent of synapse organization. GOC:TermGenie GO_REF:0000058 PMID:27779093 down regulation of synapse development GOC:TermGenie down regulation of synapse organisation GOC:TermGenie down regulation of synapse organization GOC:TermGenie down-regulation of synapse development GOC:TermGenie down-regulation of synapse organisation GOC:TermGenie down-regulation of synapse organization GOC:TermGenie downregulation of synapse development GOC:TermGenie downregulation of synapse organisation GOC:TermGenie downregulation of synapse organization GOC:TermGenie negative regulation of synapse development GOC:TermGenie negative regulation of synapse organisation GOC:TermGenie inhibition of synapse development GOC:TermGenie inhibition of synapse organisation GOC:TermGenie inhibition of synapse organization GOC:TermGenie down regulation of synapse morphogenesis GOC:TermGenie down regulation of synapse organization and biogenesis GOC:TermGenie down-regulation of synapse morphogenesis GOC:TermGenie down-regulation of synapse organization and biogenesis GOC:TermGenie downregulation of synapse morphogenesis GOC:TermGenie downregulation of synapse organization and biogenesis GOC:TermGenie inhibition of synapse morphogenesis GOC:TermGenie inhibition of synapse organization and biogenesis GOC:TermGenie negative regulation of synapse morphogenesis GOC:TermGenie negative regulation of synapse organization and biogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of chromosome condensation. bhm 2017-01-13T14:13:44Z positive regulation of eukaryotic chromosome condensation positive regulation of nuclear chromosome condensation up regulation of chromosome condensation up regulation of eukaryotic chromosome condensation up regulation of nuclear chromosome condensation up-regulation of chromosome condensation up-regulation of eukaryotic chromosome condensation up-regulation of nuclear chromosome condensation upregulation of chromosome condensation upregulation of eukaryotic chromosome condensation upregulation of nuclear chromosome condensation activation of chromosome condensation activation of eukaryotic chromosome condensation activation of nuclear chromosome condensation biological_process GO:1905821 positive regulation of chromosome condensation Any process that activates or increases the frequency, rate or extent of chromosome condensation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:17268547 positive regulation of eukaryotic chromosome condensation GOC:TermGenie positive regulation of nuclear chromosome condensation GOC:TermGenie up regulation of chromosome condensation GOC:TermGenie up regulation of eukaryotic chromosome condensation GOC:TermGenie up regulation of nuclear chromosome condensation GOC:TermGenie up-regulation of chromosome condensation GOC:TermGenie up-regulation of eukaryotic chromosome condensation GOC:TermGenie up-regulation of nuclear chromosome condensation GOC:TermGenie upregulation of chromosome condensation GOC:TermGenie upregulation of eukaryotic chromosome condensation GOC:TermGenie upregulation of nuclear chromosome condensation GOC:TermGenie activation of chromosome condensation GOC:TermGenie activation of eukaryotic chromosome condensation GOC:TermGenie activation of nuclear chromosome condensation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of microtubule nucleation. hbye 2017-01-17T12:00:56Z down regulation of microtubule nucleation down-regulation of microtubule nucleation downregulation of microtubule nucleation inhibition of microtubule nucleation biological_process GO:1905833 negative regulation of microtubule nucleation Any process that stops, prevents or reduces the frequency, rate or extent of microtubule nucleation. GOC:TermGenie GO_REF:0000058 PMID:27689799 down regulation of microtubule nucleation GOC:TermGenie down-regulation of microtubule nucleation GOC:TermGenie downregulation of microtubule nucleation GOC:TermGenie inhibition of microtubule nucleation GOC:TermGenie Any process that modulates the frequency, rate or extent of cellular response to gamma radiation. rz 2017-01-19T10:24:39Z biological_process regulation of cellular response to gamma ray regulation of cellular response to gamma-ray photon GO:1905843 regulation of cellular response to gamma radiation Any process that modulates the frequency, rate or extent of cellular response to gamma radiation. GOC:TermGenie GO_REF:0000058 PMID:23505386 regulation of cellular response to gamma ray GOC:TermGenie regulation of cellular response to gamma-ray photon GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to gamma radiation. rz 2017-01-19T10:24:48Z down regulation of cellular response to gamma radiation down-regulation of cellular response to gamma radiation downregulation of cellular response to gamma radiation inhibition of cellular response to gamma radiation biological_process down regulation of cellular response to gamma ray down regulation of cellular response to gamma-ray photon down-regulation of cellular response to gamma ray down-regulation of cellular response to gamma-ray photon downregulation of cellular response to gamma ray downregulation of cellular response to gamma-ray photon inhibition of cellular response to gamma ray inhibition of cellular response to gamma-ray photon negative regulation of cellular response to gamma ray negative regulation of cellular response to gamma-ray photon GO:1905844 negative regulation of cellular response to gamma radiation Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to gamma radiation. GOC:TermGenie GO_REF:0000058 PMID:23505386 down regulation of cellular response to gamma radiation GOC:TermGenie down-regulation of cellular response to gamma radiation GOC:TermGenie downregulation of cellular response to gamma radiation GOC:TermGenie inhibition of cellular response to gamma radiation GOC:TermGenie down regulation of cellular response to gamma ray GOC:TermGenie down regulation of cellular response to gamma-ray photon GOC:TermGenie down-regulation of cellular response to gamma ray GOC:TermGenie down-regulation of cellular response to gamma-ray photon GOC:TermGenie downregulation of cellular response to gamma ray GOC:TermGenie downregulation of cellular response to gamma-ray photon GOC:TermGenie inhibition of cellular response to gamma ray GOC:TermGenie inhibition of cellular response to gamma-ray photon GOC:TermGenie negative regulation of cellular response to gamma ray GOC:TermGenie negative regulation of cellular response to gamma-ray photon GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cellular response to gamma radiation. rz 2017-01-19T10:24:57Z up regulation of cellular response to gamma radiation up-regulation of cellular response to gamma radiation upregulation of cellular response to gamma radiation activation of cellular response to gamma radiation biological_process activation of cellular response to gamma ray activation of cellular response to gamma-ray photon positive regulation of cellular response to gamma ray positive regulation of cellular response to gamma-ray photon up regulation of cellular response to gamma ray up regulation of cellular response to gamma-ray photon up-regulation of cellular response to gamma ray up-regulation of cellular response to gamma-ray photon upregulation of cellular response to gamma ray upregulation of cellular response to gamma-ray photon GO:1905845 positive regulation of cellular response to gamma radiation Any process that activates or increases the frequency, rate or extent of cellular response to gamma radiation. GOC:TermGenie GO_REF:0000058 PMID:23505386 up regulation of cellular response to gamma radiation GOC:TermGenie up-regulation of cellular response to gamma radiation GOC:TermGenie upregulation of cellular response to gamma radiation GOC:TermGenie activation of cellular response to gamma radiation GOC:TermGenie activation of cellular response to gamma ray GOC:TermGenie activation of cellular response to gamma-ray photon GOC:TermGenie positive regulation of cellular response to gamma ray GOC:TermGenie positive regulation of cellular response to gamma-ray photon GOC:TermGenie up regulation of cellular response to gamma ray GOC:TermGenie up regulation of cellular response to gamma-ray photon GOC:TermGenie up-regulation of cellular response to gamma ray GOC:TermGenie up-regulation of cellular response to gamma-ray photon GOC:TermGenie upregulation of cellular response to gamma ray GOC:TermGenie upregulation of cellular response to gamma-ray photon GOC:TermGenie Any process that modulates the frequency, rate or extent of protein localization to cell leading edge. sl 2017-01-27T19:34:55Z regulation of protein localisation in cell leading edge regulation of protein localisation to cell leading edge regulation of protein localization in cell leading edge biological_process GO:1905871 regulation of protein localization to cell leading edge Any process that modulates the frequency, rate or extent of protein localization to cell leading edge. GOC:TermGenie GO_REF:0000058 PMID:26324884 regulation of protein localisation in cell leading edge GOC:TermGenie regulation of protein localisation to cell leading edge GOC:TermGenie regulation of protein localization in cell leading edge GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell leading edge. sl 2017-01-27T19:35:04Z down regulation of protein localisation in cell leading edge down regulation of protein localisation to cell leading edge down regulation of protein localization in cell leading edge down regulation of protein localization to cell leading edge down-regulation of protein localisation in cell leading edge down-regulation of protein localisation to cell leading edge down-regulation of protein localization in cell leading edge down-regulation of protein localization to cell leading edge downregulation of protein localisation in cell leading edge downregulation of protein localisation to cell leading edge downregulation of protein localization in cell leading edge downregulation of protein localization to cell leading edge negative regulation of protein localisation in cell leading edge negative regulation of protein localisation to cell leading edge negative regulation of protein localization in cell leading edge inhibition of protein localisation in cell leading edge inhibition of protein localisation to cell leading edge inhibition of protein localization in cell leading edge inhibition of protein localization to cell leading edge biological_process GO:1905872 negative regulation of protein localization to cell leading edge Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell leading edge. GOC:TermGenie GO_REF:0000058 PMID:26324884 down regulation of protein localisation in cell leading edge GOC:TermGenie down regulation of protein localisation to cell leading edge GOC:TermGenie down regulation of protein localization in cell leading edge GOC:TermGenie down regulation of protein localization to cell leading edge GOC:TermGenie down-regulation of protein localisation in cell leading edge GOC:TermGenie down-regulation of protein localisation to cell leading edge GOC:TermGenie down-regulation of protein localization in cell leading edge GOC:TermGenie down-regulation of protein localization to cell leading edge GOC:TermGenie downregulation of protein localisation in cell leading edge GOC:TermGenie downregulation of protein localisation to cell leading edge GOC:TermGenie downregulation of protein localization in cell leading edge GOC:TermGenie downregulation of protein localization to cell leading edge GOC:TermGenie negative regulation of protein localisation in cell leading edge GOC:TermGenie negative regulation of protein localisation to cell leading edge GOC:TermGenie negative regulation of protein localization in cell leading edge GOC:TermGenie inhibition of protein localisation in cell leading edge GOC:TermGenie inhibition of protein localisation to cell leading edge GOC:TermGenie inhibition of protein localization in cell leading edge GOC:TermGenie inhibition of protein localization to cell leading edge GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to cell leading edge. sl 2017-01-27T19:35:13Z positive regulation of protein localisation in cell leading edge positive regulation of protein localisation to cell leading edge positive regulation of protein localization in cell leading edge up regulation of protein localisation in cell leading edge up regulation of protein localisation to cell leading edge up regulation of protein localization in cell leading edge up regulation of protein localization to cell leading edge up-regulation of protein localisation in cell leading edge up-regulation of protein localisation to cell leading edge up-regulation of protein localization in cell leading edge up-regulation of protein localization to cell leading edge upregulation of protein localisation in cell leading edge upregulation of protein localisation to cell leading edge upregulation of protein localization in cell leading edge upregulation of protein localization to cell leading edge activation of protein localisation in cell leading edge activation of protein localisation to cell leading edge activation of protein localization in cell leading edge activation of protein localization to cell leading edge biological_process GO:1905873 positive regulation of protein localization to cell leading edge Any process that activates or increases the frequency, rate or extent of protein localization to cell leading edge. GOC:TermGenie GO_REF:0000058 PMID:26324884 positive regulation of protein localisation in cell leading edge GOC:TermGenie positive regulation of protein localisation to cell leading edge GOC:TermGenie positive regulation of protein localization in cell leading edge GOC:TermGenie up regulation of protein localisation in cell leading edge GOC:TermGenie up regulation of protein localisation to cell leading edge GOC:TermGenie up regulation of protein localization in cell leading edge GOC:TermGenie up regulation of protein localization to cell leading edge GOC:TermGenie up-regulation of protein localisation in cell leading edge GOC:TermGenie up-regulation of protein localisation to cell leading edge GOC:TermGenie up-regulation of protein localization in cell leading edge GOC:TermGenie up-regulation of protein localization to cell leading edge GOC:TermGenie upregulation of protein localisation in cell leading edge GOC:TermGenie upregulation of protein localisation to cell leading edge GOC:TermGenie upregulation of protein localization in cell leading edge GOC:TermGenie upregulation of protein localization to cell leading edge GOC:TermGenie activation of protein localisation in cell leading edge GOC:TermGenie activation of protein localisation to cell leading edge GOC:TermGenie activation of protein localization in cell leading edge GOC:TermGenie activation of protein localization to cell leading edge GOC:TermGenie Any process that modulates the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:05Z regulation of ovum development biological_process GO:1905879 regulation of oogenesis Any process that modulates the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 regulation of ovum development GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:15Z down regulation of oogenesis down regulation of ovum development down-regulation of oogenesis down-regulation of ovum development downregulation of oogenesis downregulation of ovum development negative regulation of ovum development inhibition of oogenesis inhibition of ovum development biological_process GO:1905880 negative regulation of oogenesis Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 down regulation of oogenesis GOC:TermGenie down regulation of ovum development GOC:TermGenie down-regulation of oogenesis GOC:TermGenie down-regulation of ovum development GOC:TermGenie downregulation of oogenesis GOC:TermGenie downregulation of ovum development GOC:TermGenie negative regulation of ovum development GOC:TermGenie inhibition of oogenesis GOC:TermGenie inhibition of ovum development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:23Z positive regulation of ovum development up regulation of oogenesis up regulation of ovum development up-regulation of oogenesis up-regulation of ovum development upregulation of oogenesis upregulation of ovum development activation of oogenesis activation of ovum development biological_process GO:1905881 positive regulation of oogenesis Any process that activates or increases the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 positive regulation of ovum development GOC:TermGenie up regulation of oogenesis GOC:TermGenie up regulation of ovum development GOC:TermGenie up-regulation of oogenesis GOC:TermGenie up-regulation of ovum development GOC:TermGenie upregulation of oogenesis GOC:TermGenie upregulation of ovum development GOC:TermGenie activation of oogenesis GOC:TermGenie activation of ovum development GOC:TermGenie Any process that modulates the frequency, rate or extent of smooth muscle tissue development. bhm 2017-02-01T14:31:16Z biological_process GO:1905899 regulation of smooth muscle tissue development Any process that modulates the frequency, rate or extent of smooth muscle tissue development. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:14709716 Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle tissue development. bhm 2017-02-01T14:31:24Z down regulation of smooth muscle tissue development down-regulation of smooth muscle tissue development downregulation of smooth muscle tissue development inhibition of smooth muscle tissue development biological_process GO:1905900 negative regulation of smooth muscle tissue development Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle tissue development. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:14709716 down regulation of smooth muscle tissue development GOC:TermGenie down-regulation of smooth muscle tissue development GOC:TermGenie downregulation of smooth muscle tissue development GOC:TermGenie inhibition of smooth muscle tissue development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of smooth muscle tissue development. bhm 2017-02-01T14:31:33Z up regulation of smooth muscle tissue development up-regulation of smooth muscle tissue development upregulation of smooth muscle tissue development activation of smooth muscle tissue development biological_process GO:1905901 positive regulation of smooth muscle tissue development Any process that activates or increases the frequency, rate or extent of smooth muscle tissue development. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:14709716 up regulation of smooth muscle tissue development GOC:TermGenie up-regulation of smooth muscle tissue development GOC:TermGenie upregulation of smooth muscle tissue development GOC:TermGenie activation of smooth muscle tissue development GOC:TermGenie Any process that modulates the frequency, rate or extent of mesoderm formation. rph 2017-02-03T12:28:20Z biological_process GO:1905902 regulation of mesoderm formation Any process that modulates the frequency, rate or extent of mesoderm formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23939491 Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm formation. rph 2017-02-03T12:28:29Z down regulation of mesoderm formation down-regulation of mesoderm formation downregulation of mesoderm formation inhibition of mesoderm formation biological_process GO:1905903 negative regulation of mesoderm formation Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23939491 down regulation of mesoderm formation GOC:TermGenie down-regulation of mesoderm formation GOC:TermGenie downregulation of mesoderm formation GOC:TermGenie inhibition of mesoderm formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of mesoderm formation. rph 2017-02-03T12:28:38Z up regulation of mesoderm formation up-regulation of mesoderm formation upregulation of mesoderm formation activation of mesoderm formation biological_process GO:1905904 positive regulation of mesoderm formation Any process that activates or increases the frequency, rate or extent of mesoderm formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23939491 up regulation of mesoderm formation GOC:TermGenie up-regulation of mesoderm formation GOC:TermGenie upregulation of mesoderm formation GOC:TermGenie activation of mesoderm formation GOC:TermGenie Any process that modulates the frequency, rate or extent of acetylcholine biosynthetic process. bc 2017-02-08T13:08:30Z regulation of acetylcholine anabolism regulation of acetylcholine biosynthesis regulation of acetylcholine formation regulation of acetylcholine synthesis biological_process GO:1905921 regulation of acetylcholine biosynthetic process Any process that modulates the frequency, rate or extent of acetylcholine biosynthetic process. GOC:TermGenie GOC:aruk GOC:bc GO_REF:0000058 PMID:20164328 regulation of acetylcholine anabolism GOC:TermGenie regulation of acetylcholine biosynthesis GOC:TermGenie regulation of acetylcholine formation GOC:TermGenie regulation of acetylcholine synthesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of acetylcholine biosynthetic process. bc 2017-02-08T13:08:39Z down regulation of acetylcholine anabolism down regulation of acetylcholine biosynthesis down regulation of acetylcholine biosynthetic process down regulation of acetylcholine formation down regulation of acetylcholine synthesis down-regulation of acetylcholine anabolism down-regulation of acetylcholine biosynthesis down-regulation of acetylcholine biosynthetic process down-regulation of acetylcholine formation down-regulation of acetylcholine synthesis downregulation of acetylcholine anabolism downregulation of acetylcholine biosynthesis downregulation of acetylcholine biosynthetic process downregulation of acetylcholine formation downregulation of acetylcholine synthesis negative regulation of acetylcholine anabolism negative regulation of acetylcholine biosynthesis negative regulation of acetylcholine formation negative regulation of acetylcholine synthesis inhibition of acetylcholine anabolism inhibition of acetylcholine biosynthesis inhibition of acetylcholine biosynthetic process inhibition of acetylcholine formation inhibition of acetylcholine synthesis biological_process GO:1905922 negative regulation of acetylcholine biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of acetylcholine biosynthetic process. GOC:TermGenie GOC:aruk GOC:bc GO_REF:0000058 PMID:20164328 down regulation of acetylcholine anabolism GOC:TermGenie down regulation of acetylcholine biosynthesis GOC:TermGenie down regulation of acetylcholine biosynthetic process GOC:TermGenie down regulation of acetylcholine formation GOC:TermGenie down regulation of acetylcholine synthesis GOC:TermGenie down-regulation of acetylcholine anabolism GOC:TermGenie down-regulation of acetylcholine biosynthesis GOC:TermGenie down-regulation of acetylcholine biosynthetic process GOC:TermGenie down-regulation of acetylcholine formation GOC:TermGenie down-regulation of acetylcholine synthesis GOC:TermGenie downregulation of acetylcholine anabolism GOC:TermGenie downregulation of acetylcholine biosynthesis GOC:TermGenie downregulation of acetylcholine biosynthetic process GOC:TermGenie downregulation of acetylcholine formation GOC:TermGenie downregulation of acetylcholine synthesis GOC:TermGenie negative regulation of acetylcholine anabolism GOC:TermGenie negative regulation of acetylcholine biosynthesis GOC:TermGenie negative regulation of acetylcholine formation GOC:TermGenie negative regulation of acetylcholine synthesis GOC:TermGenie inhibition of acetylcholine anabolism GOC:TermGenie inhibition of acetylcholine biosynthesis GOC:TermGenie inhibition of acetylcholine biosynthetic process GOC:TermGenie inhibition of acetylcholine formation GOC:TermGenie inhibition of acetylcholine synthesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of acetylcholine biosynthetic process. bc 2017-02-08T13:08:48Z positive regulation of acetylcholine anabolism positive regulation of acetylcholine biosynthesis positive regulation of acetylcholine formation positive regulation of acetylcholine synthesis up regulation of acetylcholine anabolism up regulation of acetylcholine biosynthesis up regulation of acetylcholine biosynthetic process up regulation of acetylcholine formation up regulation of acetylcholine synthesis up-regulation of acetylcholine anabolism up-regulation of acetylcholine biosynthesis up-regulation of acetylcholine biosynthetic process up-regulation of acetylcholine formation up-regulation of acetylcholine synthesis upregulation of acetylcholine anabolism upregulation of acetylcholine biosynthesis upregulation of acetylcholine biosynthetic process upregulation of acetylcholine formation upregulation of acetylcholine synthesis activation of acetylcholine anabolism activation of acetylcholine biosynthesis activation of acetylcholine biosynthetic process activation of acetylcholine formation activation of acetylcholine synthesis biological_process GO:1905923 positive regulation of acetylcholine biosynthetic process Any process that activates or increases the frequency, rate or extent of acetylcholine biosynthetic process. GOC:TermGenie GOC:aruk GOC:bc GO_REF:0000058 PMID:20164328 positive regulation of acetylcholine anabolism GOC:TermGenie positive regulation of acetylcholine biosynthesis GOC:TermGenie positive regulation of acetylcholine formation GOC:TermGenie positive regulation of acetylcholine synthesis GOC:TermGenie up regulation of acetylcholine anabolism GOC:TermGenie up regulation of acetylcholine biosynthesis GOC:TermGenie up regulation of acetylcholine biosynthetic process GOC:TermGenie up regulation of acetylcholine formation GOC:TermGenie up regulation of acetylcholine synthesis GOC:TermGenie up-regulation of acetylcholine anabolism GOC:TermGenie up-regulation of acetylcholine biosynthesis GOC:TermGenie up-regulation of acetylcholine biosynthetic process GOC:TermGenie up-regulation of acetylcholine formation GOC:TermGenie up-regulation of acetylcholine synthesis GOC:TermGenie upregulation of acetylcholine anabolism GOC:TermGenie upregulation of acetylcholine biosynthesis GOC:TermGenie upregulation of acetylcholine biosynthetic process GOC:TermGenie upregulation of acetylcholine formation GOC:TermGenie upregulation of acetylcholine synthesis GOC:TermGenie activation of acetylcholine anabolism GOC:TermGenie activation of acetylcholine biosynthesis GOC:TermGenie activation of acetylcholine biosynthetic process GOC:TermGenie activation of acetylcholine formation GOC:TermGenie activation of acetylcholine synthesis GOC:TermGenie Any process that modulates the frequency, rate or extent of germ cell proliferation. hbye 2017-02-09T14:51:31Z biological_process GO:1905936 regulation of germ cell proliferation Any process that modulates the frequency, rate or extent of germ cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:15342467 Any process that stops, prevents or reduces the frequency, rate or extent of germ cell proliferation. hbye 2017-02-09T14:51:41Z down regulation of germ cell proliferation down-regulation of germ cell proliferation downregulation of germ cell proliferation inhibition of germ cell proliferation biological_process GO:1905937 negative regulation of germ cell proliferation Any process that stops, prevents or reduces the frequency, rate or extent of germ cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:15342467 down regulation of germ cell proliferation GOC:TermGenie down-regulation of germ cell proliferation GOC:TermGenie downregulation of germ cell proliferation GOC:TermGenie inhibition of germ cell proliferation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of germ cell proliferation. hbye 2017-02-09T14:51:51Z up regulation of germ cell proliferation up-regulation of germ cell proliferation upregulation of germ cell proliferation activation of germ cell proliferation biological_process GO:1905938 positive regulation of germ cell proliferation Any process that activates or increases the frequency, rate or extent of germ cell proliferation. GOC:TermGenie GO_REF:0000058 PMID:15342467 up regulation of germ cell proliferation GOC:TermGenie up-regulation of germ cell proliferation GOC:TermGenie upregulation of germ cell proliferation GOC:TermGenie activation of germ cell proliferation GOC:TermGenie Any process that modulates the frequency, rate or extent of gonad development. hbye 2017-02-09T17:01:50Z regulation of gonadogenesis biological_process GO:1905939 regulation of gonad development Any process that modulates the frequency, rate or extent of gonad development. GOC:TermGenie GO_REF:0000058 PMID:15342467 regulation of gonadogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of gonad development. hbye 2017-02-09T17:01:59Z down regulation of gonad development down regulation of gonadogenesis down-regulation of gonad development down-regulation of gonadogenesis downregulation of gonad development downregulation of gonadogenesis negative regulation of gonadogenesis inhibition of gonad development inhibition of gonadogenesis biological_process GO:1905940 negative regulation of gonad development Any process that stops, prevents or reduces the frequency, rate or extent of gonad development. GOC:TermGenie GO_REF:0000058 PMID:15342467 down regulation of gonad development GOC:TermGenie down regulation of gonadogenesis GOC:TermGenie down-regulation of gonad development GOC:TermGenie down-regulation of gonadogenesis GOC:TermGenie downregulation of gonad development GOC:TermGenie downregulation of gonadogenesis GOC:TermGenie negative regulation of gonadogenesis GOC:TermGenie inhibition of gonad development GOC:TermGenie inhibition of gonadogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of gonad development. hbye 2017-02-09T17:02:08Z positive regulation of gonadogenesis up regulation of gonad development up regulation of gonadogenesis up-regulation of gonad development up-regulation of gonadogenesis upregulation of gonad development upregulation of gonadogenesis activation of gonad development activation of gonadogenesis biological_process GO:1905941 positive regulation of gonad development Any process that activates or increases the frequency, rate or extent of gonad development. GOC:TermGenie GO_REF:0000058 PMID:15342467 positive regulation of gonadogenesis GOC:TermGenie up regulation of gonad development GOC:TermGenie up regulation of gonadogenesis GOC:TermGenie up-regulation of gonad development GOC:TermGenie up-regulation of gonadogenesis GOC:TermGenie upregulation of gonad development GOC:TermGenie upregulation of gonadogenesis GOC:TermGenie activation of gonad development GOC:TermGenie activation of gonadogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:22Z regulation of lipid localisation biological_process GO:1905952 regulation of lipid localization Any process that modulates the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 regulation of lipid localisation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:41Z down regulation of lipid localisation down regulation of lipid localization down-regulation of lipid localisation down-regulation of lipid localization downregulation of lipid localisation downregulation of lipid localization negative regulation of lipid localisation inhibition of lipid localisation inhibition of lipid localization biological_process GO:1905953 negative regulation of lipid localization Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 down regulation of lipid localisation GOC:TermGenie down regulation of lipid localization GOC:TermGenie down-regulation of lipid localisation GOC:TermGenie down-regulation of lipid localization GOC:TermGenie downregulation of lipid localisation GOC:TermGenie downregulation of lipid localization GOC:TermGenie negative regulation of lipid localisation GOC:TermGenie inhibition of lipid localisation GOC:TermGenie inhibition of lipid localization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:49Z positive regulation of lipid localisation up regulation of lipid localisation up regulation of lipid localization up-regulation of lipid localisation up-regulation of lipid localization upregulation of lipid localisation upregulation of lipid localization activation of lipid localisation activation of lipid localization biological_process GO:1905954 positive regulation of lipid localization Any process that activates or increases the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 positive regulation of lipid localisation GOC:TermGenie up regulation of lipid localisation GOC:TermGenie up regulation of lipid localization GOC:TermGenie up-regulation of lipid localisation GOC:TermGenie up-regulation of lipid localization GOC:TermGenie upregulation of lipid localisation GOC:TermGenie upregulation of lipid localization GOC:TermGenie activation of lipid localisation GOC:TermGenie activation of lipid localization GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of endothelial tube morphogenesis. rph 2017-02-21T15:17:31Z down regulation of endothelial tube morphogenesis down-regulation of endothelial tube morphogenesis downregulation of endothelial tube morphogenesis inhibition of endothelial tube morphogenesis biological_process GO:1905955 negative regulation of endothelial tube morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of endothelial tube morphogenesis. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:25961718 down regulation of endothelial tube morphogenesis GOC:TermGenie down-regulation of endothelial tube morphogenesis GOC:TermGenie downregulation of endothelial tube morphogenesis GOC:TermGenie inhibition of endothelial tube morphogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of endothelial tube morphogenesis. rph 2017-02-21T15:17:39Z up regulation of endothelial tube morphogenesis up-regulation of endothelial tube morphogenesis upregulation of endothelial tube morphogenesis activation of endothelial tube morphogenesis biological_process GO:1905956 positive regulation of endothelial tube morphogenesis Any process that activates or increases the frequency, rate or extent of endothelial tube morphogenesis. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:25961718 up regulation of endothelial tube morphogenesis GOC:TermGenie up-regulation of endothelial tube morphogenesis GOC:TermGenie upregulation of endothelial tube morphogenesis GOC:TermGenie activation of endothelial tube morphogenesis GOC:TermGenie Any apoptotic process in a retinal cell. pr 2012-12-12T10:15:08Z GO:0046674 biological_process induction of retinal programmed cell death GO:1990009 retinal cell apoptotic process Any apoptotic process in a retinal cell. GOC:mtg_apoptosis PMID:15558487 PMID:24664675 Any apoptotic process in a compound eye retinal cell. pr 2012-12-12T10:21:07Z biological_process GO:1990010 compound eye retinal cell apoptotic process Any apoptotic process in a compound eye retinal cell. GOC:mtg_apoptosis PMID:12021768 The process whereby a membrane-bounded vesicle is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. hjd 2013-09-04T21:08:14Z exosomal secretory pathway extracellular vesicular exosome secretion multi-vesicular body fusion with plasma membrane secretion of exosome exosomal protein secretion biological_process GO:1990182 exosomal secretion The process whereby a membrane-bounded vesicle is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. GOC:hjd PMID:10572093 PMID:12154376 PMID:16773132 PMID:18617898 exosomal secretory pathway PMID:18617898 extracellular vesicular exosome secretion GOC:hjd secretion of exosome PMID:18617898 exosomal protein secretion PMID:18617898 A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). bhm 2013-11-12T13:20:12Z cellular_component GO:1990234 transferase complex A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). GOC:bhm PMID:16540464 A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin. mah 2014-01-30T15:55:34Z RNA localisation to chromatin biological_process GO:1990280 RNA localization to chromatin A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin. GOC:dos GOC:mah PMID:22582262 A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells. bhm 2014-03-26T14:23:27Z cellular_component GO:1990351 An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay). transporter complex A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells. GOC:bhm PMID:15449578 Steps required to transform a dense core granule generated at the trans-Golgi network into a fully formed and transmissible dense core granule. Dense core granule maturation proceeds through clathrin-mediated membrane remodeling events and is essential for efficient processing of cargo within dense core granules as well as for removing factors that might otherwise interfere with dense core granule trafficking and exocytosis. kmv 2014-09-30T20:35:11Z dense core vesicle maturation biological_process GO:1990502 dense core granule maturation Steps required to transform a dense core granule generated at the trans-Golgi network into a fully formed and transmissible dense core granule. Dense core granule maturation proceeds through clathrin-mediated membrane remodeling events and is essential for efficient processing of cargo within dense core granules as well as for removing factors that might otherwise interfere with dense core granule trafficking and exocytosis. GOC:kmv PMID:22654674 The multiplication or reproduction of cholangiocytes, resulting in the expansion of the cholangiocyte population. A cholangiocyte is an epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. 2015-03-16T23:23:50Z hepatoblast proliferation biological_process GO:1990705 cholangiocyte proliferation The multiplication or reproduction of cholangiocytes, resulting in the expansion of the cholangiocyte population. A cholangiocyte is an epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. PMID:24434010 Any process carried out at the cellular level that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. vw 2015-05-18T16:17:46Z biological_process GO:1990748 cellular detoxification Any process carried out at the cellular level that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. GOC:vw A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry of the large intestine, exclusive of the rectum. The colon is that part of the large intestine that connects the small intestine to the rectum. sl 2015-06-10T18:29:21Z biological_process GO:1990765 colon smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry of the large intestine, exclusive of the rectum. The colon is that part of the large intestine that connects the small intestine to the rectum. PMID:24170253 The flow of blood through the gastric mucosa of an animal, enabling the transport of nutrients and the removal of waste products. sl 2015-06-10T20:11:09Z stomach mucosal blood circulation biological_process GO:1990768 gastric mucosal blood circulation The flow of blood through the gastric mucosa of an animal, enabling the transport of nutrients and the removal of waste products. PMID:10807413 A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry in the intestine between the stomach and the large intestine. sl 2015-06-11T18:02:33Z biological_process GO:1990770 small intestine smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry in the intestine between the stomach and the large intestine. PMID:11991626 A process in which a protein is transported to, or maintained in, the cell periphery. 2015-06-18T22:37:39Z biological_process GO:1990778 protein localization to cell periphery A process in which a protein is transported to, or maintained in, the cell periphery. PMID:18216290 Any process in which the vacuole is transported to, and/or maintained in, a specific location within the cell. https://github.com/geneontology/go-ontology/issues/22182 mcc 2015-09-10T08:16:02Z maintenance of vacuolar localization maintenance of vacuole localization maintenance of vacuole location maintenance of vacuolar location biological_process GO:1990849 vacuolar localization Any process in which the vacuole is transported to, and/or maintained in, a specific location within the cell. PMID:26283797 The multiplication or reproduction of acinar cells, resulting in the expansion of a cell population. An acinar cell is a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini (singular acinus). sl 2015-09-25T14:26:09Z acinic cell proliferation acinous cell proliferation biological_process GO:1990863 acinar cell proliferation The multiplication or reproduction of acinar cells, resulting in the expansion of a cell population. An acinar cell is a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini (singular acinus). PMID:9788538 The multiplication or reproduction of vascular smooth muscle cells, resulting in the expansion of a cell population. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels. sl 2015-09-29T16:34:59Z VSMC proliferation vascular smooth muscle cell proliferation biological_process GO:1990874 vascular associated smooth muscle cell proliferation The multiplication or reproduction of vascular smooth muscle cells, resulting in the expansion of a cell population. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels. PMID:23246467 A macromolecular complex that contains both RNA and protein molecules. pr 2015-11-19T12:26:37Z GO:0030529 GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP protein-RNA complex extracellular ribonucleoprotein complex intracellular ribonucleoprotein complex cellular_component GO:1990904 ribonucleoprotein complex A macromolecular complex that contains both RNA and protein molecules. GOC:krc GOC:vesicles The cytoplasm of an ovum. sl 2015-12-10T21:40:16Z cellular_component GO:1990917 ooplasm The cytoplasm of an ovum. PMID:19022436 Any process that modulates the frequency, rate or extent of multicellular organismal development. tb 2010-08-05T11:25:59Z biological_process GO:2000026 regulation of multicellular organismal development Any process that modulates the frequency, rate or extent of multicellular organismal development. GOC:obol Any process that modulates the frequency, rate or extent of animal organ morphogenesis. tb 2010-08-05T11:26:27Z biological_process regulation of histogenesis and organogenesis GO:2000027 regulation of animal organ morphogenesis Any process that modulates the frequency, rate or extent of animal organ morphogenesis. GOC:obol regulation of histogenesis and organogenesis GOC:obol Any process that modulates the frequency, rate or extent of stem cell division. tb 2010-08-05T11:34:53Z regulation of stem cell renewal biological_process GO:2000035 regulation of stem cell division Any process that modulates the frequency, rate or extent of stem cell division. GOC:obol regulation of stem cell renewal GOC:obol Any process that modulates the frequency, rate or extent of pancreatic B cell development. tb 2010-08-27T11:19:37Z regulation of pancreatic B cell development regulation of pancreatic beta cell development biological_process GO:2000074 regulation of type B pancreatic cell development Any process that modulates the frequency, rate or extent of pancreatic B cell development. GOC:obol GOC:yaf regulation of pancreatic B cell development GOC:mah regulation of pancreatic beta cell development GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic B cell development. tb 2010-08-27T11:21:17Z negative regulation of pancreatic B cell development negative regulation of pancreatic beta cell development biological_process GO:2000077 negative regulation of type B pancreatic cell development Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic B cell development. GOC:obol GOC:yaf negative regulation of pancreatic B cell development GOC:mah negative regulation of pancreatic beta cell development GOC:obol Any process that activates or increases the frequency, rate or extent of pancreatic B cell development. tb 2010-08-27T11:21:19Z positive regulation of pancreatic B cell development positive regulation of pancreatic beta cell development biological_process GO:2000078 positive regulation of type B pancreatic cell development Any process that activates or increases the frequency, rate or extent of pancreatic B cell development. GOC:obol GOC:yaf positive regulation of pancreatic B cell development GOC:mah positive regulation of pancreatic beta cell development GOC:obol Any process that modulates the frequency, rate or extent of leukocyte apoptotic process. mah 2010-09-15T01:42:05Z regulation of leukocyte apoptosis biological_process GO:2000106 regulation of leukocyte apoptotic process Any process that modulates the frequency, rate or extent of leukocyte apoptotic process. GOC:BHF GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process. mah 2010-09-15T01:42:09Z negative regulation of leukocyte apoptosis biological_process GO:2000107 negative regulation of leukocyte apoptotic process Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process. GOC:BHF GOC:mtg_apoptosis Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process. mah 2010-09-15T01:42:12Z positive regulation of leukocyte apoptosis biological_process GO:2000108 positive regulation of leukocyte apoptotic process Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process. GOC:BHF GOC:mtg_apoptosis Any process that modulates the frequency, rate or extent of establishment of cell polarity. dph 2010-09-16T01:22:36Z regulation of cell polarization biological_process regulation of bud site selection/establishment of cell polarity GO:2000114 regulation of establishment of cell polarity Any process that modulates the frequency, rate or extent of establishment of cell polarity. GOC:dph regulation of cell polarization GOC:obol regulation of bud site selection/establishment of cell polarity GOC:obol Any process that modulates the frequency, rate or extent of cell proliferation involved in heart morphogenesis. dph 2010-09-29T12:43:53Z biological_process GO:2000136 regulation of cell proliferation involved in heart morphogenesis Any process that modulates the frequency, rate or extent of cell proliferation involved in heart morphogenesis. GOC:dph Any process that stops, prevents, or reduces the frequency, rate or extent of cell proliferation involved in heart morphogenesis. dph 2010-09-29T12:43:55Z biological_process GO:2000137 negative regulation of cell proliferation involved in heart morphogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of cell proliferation involved in heart morphogenesis. GOC:dph Any process that activates or increases the frequency, rate or extent of cell proliferation involved in heart morphogenesis. dph 2010-09-29T12:43:57Z biological_process GO:2000138 positive regulation of cell proliferation involved in heart morphogenesis Any process that activates or increases the frequency, rate or extent of cell proliferation involved in heart morphogenesis. GOC:dph Any process that modulates the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:21Z regulation of cell locomotion regulation of movement of a cell biological_process regulation of cell movement GO:2000145 regulation of cell motility Any process that modulates the frequency, rate or extent of cell motility. GOC:mah regulation of cell locomotion GOC:obol regulation of movement of a cell GOC:obol regulation of cell movement GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:26Z negative regulation of cell locomotion negative regulation of movement of a cell biological_process negative regulation of cell movement GO:2000146 negative regulation of cell motility Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility. GOC:mah negative regulation of cell locomotion GOC:obol negative regulation of movement of a cell GOC:obol negative regulation of cell movement GOC:obol Any process that activates or increases the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:30Z positive regulation of cell locomotion positive regulation of movement of a cell biological_process positive regulation of cell movement GO:2000147 positive regulation of cell motility Any process that activates or increases the frequency, rate or extent of cell motility. GOC:mah positive regulation of cell locomotion GOC:obol positive regulation of movement of a cell GOC:obol positive regulation of cell movement GOC:obol Any process that modulates the frequency, rate or extent of branching morphogenesis of a nerve. rl 2010-10-07T12:07:54Z biological_process GO:2000172 regulation of branching morphogenesis of a nerve Any process that modulates the frequency, rate or extent of branching morphogenesis of a nerve. GOC:BHF Any process that stops, prevents, or reduces the frequency, rate or extent of branching morphogenesis of a nerve. rl 2010-10-07T12:07:56Z biological_process GO:2000173 negative regulation of branching morphogenesis of a nerve Any process that stops, prevents, or reduces the frequency, rate or extent of branching morphogenesis of a nerve. GOC:BHF Any process that modulates the frequency, rate or extent of neural precursor cell proliferation. dph 2010-10-13T12:40:41Z biological_process GO:2000177 regulation of neural precursor cell proliferation Any process that modulates the frequency, rate or extent of neural precursor cell proliferation. GOC:dph GOC:yaf Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation. dph 2010-10-13T12:40:43Z biological_process GO:2000178 negative regulation of neural precursor cell proliferation Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation. GOC:dph GOC:yaf Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation. dph 2010-10-13T12:40:45Z biological_process GO:2000179 positive regulation of neural precursor cell proliferation Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation. GOC:dph GOC:yaf Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis. dph 2010-10-13T12:46:31Z biological_process GO:2000181 negative regulation of blood vessel morphogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis. GOC:dph GOC:yaf Any process that modulates the frequency, rate or extent of phosphate transmembrane transport. vw 2010-10-15T11:33:04Z regulation of phosphate membrane transport biological_process GO:2000185 regulation of phosphate transmembrane transport Any process that modulates the frequency, rate or extent of phosphate transmembrane transport. GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of phosphate transmembrane transport. vw 2010-10-15T11:33:08Z negative regulation of phosphate membrane transport biological_process GO:2000186 negative regulation of phosphate transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of phosphate transmembrane transport. GOC:obol Any process that activates or increases the frequency, rate or extent of phosphate transmembrane transport. vw 2010-10-15T11:33:10Z positive regulation of phosphate membrane transport biological_process GO:2000187 positive regulation of phosphate transmembrane transport Any process that activates or increases the frequency, rate or extent of phosphate transmembrane transport. GOC:obol Any process that modulates the frequency, rate or extent of female gonad development. yaf 2010-10-19T10:45:34Z regulation of ovarian development regulation of ovary development biological_process GO:2000194 regulation of female gonad development Any process that modulates the frequency, rate or extent of female gonad development. GOC:obol regulation of ovarian development GOC:obol regulation of ovary development GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development. yaf 2010-10-19T10:45:38Z negative regulation of ovarian development negative regulation of ovary development biological_process GO:2000195 negative regulation of female gonad development Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development. GOC:obol negative regulation of ovarian development GOC:obol negative regulation of ovary development GOC:obol Any process that activates or increases the frequency, rate or extent of female gonad development. yaf 2010-10-19T10:45:41Z positive regulation of ovarian development positive regulation of ovary development biological_process GO:2000196 positive regulation of female gonad development Any process that activates or increases the frequency, rate or extent of female gonad development. GOC:obol positive regulation of ovarian development GOC:obol positive regulation of ovary development GOC:obol Any process that modulates the frequency, rate or extent of pancreatic A cell differentiation. mah 2010-11-09T03:43:37Z regulation of pancreatic alpha cell differentiation biological_process GO:2000226 regulation of pancreatic A cell differentiation Any process that modulates the frequency, rate or extent of pancreatic A cell differentiation. GOC:mah regulation of pancreatic alpha cell differentiation GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic A cell differentiation. mah 2010-11-09T03:43:40Z negative regulation of pancreatic alpha cell differentiation biological_process GO:2000227 negative regulation of pancreatic A cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic A cell differentiation. GOC:mah negative regulation of pancreatic alpha cell differentiation GOC:obol Any process that activates or increases the frequency, rate or extent of pancreatic A cell differentiation. mah 2010-11-09T03:43:42Z positive regulation of pancreatic alpha cell differentiation biological_process GO:2000228 positive regulation of pancreatic A cell differentiation Any process that activates or increases the frequency, rate or extent of pancreatic A cell differentiation. GOC:mah positive regulation of pancreatic alpha cell differentiation GOC:obol Any process that modulates the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:02Z biological_process GO:2000241 regulation of reproductive process Any process that modulates the frequency, rate or extent of reproductive process. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:05Z biological_process GO:2000242 negative regulation of reproductive process Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process. GOC:mah Any process that activates or increases the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:08Z biological_process GO:2000243 positive regulation of reproductive process Any process that activates or increases the frequency, rate or extent of reproductive process. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or maintenance of neuroblast polarity. vw 2010-11-11T11:40:34Z negative regulation of establishment and/or maintenance of neuroblast cell polarity biological_process GO:2000248 negative regulation of establishment or maintenance of neuroblast polarity Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or maintenance of neuroblast polarity. GOC:obol negative regulation of establishment and/or maintenance of neuroblast cell polarity GOC:obol Any process that modulates the frequency, rate or extent of fibroblast apoptotic process. jl 2010-11-23T01:07:23Z regulation of fibroblast apoptosis biological_process GO:2000269 regulation of fibroblast apoptotic process Any process that modulates the frequency, rate or extent of fibroblast apoptotic process. GOC:mtg_apoptosis GOC:obol GOC:yaf Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process. jl 2010-11-23T01:07:27Z negative regulation of fibroblast apoptosis biological_process GO:2000270 negative regulation of fibroblast apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process. GOC:mtg_apoptosis GOC:obol GOC:yaf Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process. jl 2010-11-23T01:07:29Z positive regulation of fibroblast apoptosis biological_process GO:2000271 positive regulation of fibroblast apoptotic process Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process. GOC:mtg_apoptosis GOC:obol GOC:yaf Any process that modulates the frequency, rate or extent of DNA biosynthetic process. yaf 2010-12-08T04:48:15Z regulation of DNA anabolism regulation of DNA biosynthesis regulation of DNA formation regulation of DNA synthesis biological_process GO:2000278 regulation of DNA biosynthetic process Any process that modulates the frequency, rate or extent of DNA biosynthetic process. GOC:obol regulation of DNA anabolism GOC:obol regulation of DNA biosynthesis GOC:obol regulation of DNA formation GOC:obol regulation of DNA synthesis GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process. yaf 2010-12-08T04:48:20Z negative regulation of DNA anabolism negative regulation of DNA biosynthesis negative regulation of DNA formation negative regulation of DNA synthesis biological_process GO:2000279 negative regulation of DNA biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process. GOC:obol negative regulation of DNA anabolism GOC:obol negative regulation of DNA biosynthesis GOC:obol negative regulation of DNA formation GOC:obol negative regulation of DNA synthesis GOC:obol Any process that modulates the frequency, rate or extent of cellular amino acid biosynthetic process. vw 2010-12-10T11:54:19Z regulation of amino acid biosynthetic process regulation of cellular amino acid anabolism regulation of cellular amino acid biosynthesis regulation of cellular amino acid formation regulation of cellular amino acid synthesis biological_process GO:2000282 regulation of cellular amino acid biosynthetic process Any process that modulates the frequency, rate or extent of cellular amino acid biosynthetic process. GOC:obol regulation of amino acid biosynthetic process GOC:obol regulation of cellular amino acid anabolism GOC:obol regulation of cellular amino acid biosynthesis GOC:obol regulation of cellular amino acid formation GOC:obol regulation of cellular amino acid synthesis GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of an amino acid biosynthetic process. vw 2010-12-10T11:54:23Z negative regulation of amino acid anabolism negative regulation of amino acid biosynthesis negative regulation of amino acid formation negative regulation of amino acid synthesis negative regulation of cellular amino acid biosynthetic process biological_process GO:2000283 negative regulation of amino acid biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of an amino acid biosynthetic process. GOC:obol negative regulation of amino acid anabolism GOC:obol negative regulation of amino acid biosynthesis GOC:obol negative regulation of amino acid formation GOC:obol negative regulation of amino acid synthesis GOC:obol negative regulation of cellular amino acid biosynthetic process GOC:obol Any process that activates or increases the frequency, rate or extent of cellular amino acid biosynthetic process. vw 2010-12-10T11:54:27Z positive regulation of amino acid anabolism positive regulation of amino acid biosynthesis positive regulation of amino acid formation positive regulation of amino acid synthesis positive regulation of cellular amino acid biosynthetic process biological_process GO:2000284 positive regulation of amino acid biosynthetic process Any process that activates or increases the frequency, rate or extent of cellular amino acid biosynthetic process. GOC:obol positive regulation of amino acid anabolism GOC:obol positive regulation of amino acid biosynthesis GOC:obol positive regulation of amino acid formation GOC:obol positive regulation of amino acid synthesis GOC:obol positive regulation of cellular amino acid biosynthetic process GOC:obol Any process that activates or increases the frequency, rate or extent of myotome development. rl 2010-12-16T05:17:15Z biological_process GO:2000287 positive regulation of myotome development Any process that activates or increases the frequency, rate or extent of myotome development. GOC:BHF Any process that activates or increases the frequency, rate or extent of myoblast proliferation. rl 2010-12-16T05:20:52Z biological_process GO:2000288 positive regulation of myoblast proliferation Any process that activates or increases the frequency, rate or extent of myoblast proliferation. GOC:BHF Any process that modulates the frequency, rate or extent of myotome development. mah 2010-12-20T10:22:05Z biological_process GO:2000290 regulation of myotome development Any process that modulates the frequency, rate or extent of myotome development. GOC:mah Any process that modulates the frequency, rate or extent of myoblast proliferation. mah 2010-12-20T10:34:26Z biological_process GO:2000291 regulation of myoblast proliferation Any process that modulates the frequency, rate or extent of myoblast proliferation. GOC:mah Any process that modulates the frequency, rate or extent of defecation. bf 2010-12-21T09:23:08Z biological_process GO:2000292 regulation of defecation Any process that modulates the frequency, rate or extent of defecation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of defecation. bf 2010-12-21T09:23:13Z biological_process GO:2000293 negative regulation of defecation Any process that stops, prevents or reduces the frequency, rate or extent of defecation. GOC:obol Any process that activates or increases the frequency, rate or extent of defecation. bf 2010-12-21T09:23:16Z biological_process GO:2000294 positive regulation of defecation Any process that activates or increases the frequency, rate or extent of defecation. GOC:obol Any process that modulates the frequency, rate or extent of endothelial cell apoptotic process. mah 2011-02-03T10:43:16Z regulation of apoptosis of endothelial cells regulation of endothelial cell programmed cell death by apoptosis regulation of killing of endothelial cells regulation of programmed cell death of endothelial cells by apoptosis regulation of programmed cell death, endothelial cells regulation of endothelial cell apoptosis biological_process GO:2000351 regulation of endothelial cell apoptotic process Any process that modulates the frequency, rate or extent of endothelial cell apoptotic process. GOC:mah GOC:mtg_apoptosis regulation of apoptosis of endothelial cells GOC:obol regulation of endothelial cell programmed cell death by apoptosis GOC:obol regulation of killing of endothelial cells GOC:obol regulation of programmed cell death of endothelial cells by apoptosis GOC:obol regulation of programmed cell death, endothelial cells GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process. mah 2011-02-03T10:43:20Z negative regulation of apoptosis of endothelial cells negative regulation of endothelial cell programmed cell death by apoptosis negative regulation of killing of endothelial cells negative regulation of programmed cell death of endothelial cells by apoptosis negative regulation of programmed cell death, endothelial cells negative regulation of endothelial cell apoptosis biological_process GO:2000352 negative regulation of endothelial cell apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process. GOC:BHF GOC:mah GOC:mtg_apoptosis negative regulation of apoptosis of endothelial cells GOC:obol negative regulation of endothelial cell programmed cell death by apoptosis GOC:obol negative regulation of killing of endothelial cells GOC:obol negative regulation of programmed cell death of endothelial cells by apoptosis GOC:obol negative regulation of programmed cell death, endothelial cells GOC:obol Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process. mah 2011-02-03T10:43:23Z positive regulation of apoptosis of endothelial cells positive regulation of endothelial cell programmed cell death by apoptosis positive regulation of killing of endothelial cells positive regulation of programmed cell death of endothelial cells by apoptosis positive regulation of programmed cell death, endothelial cells positive regulation of endothelial cell apoptosis biological_process GO:2000353 positive regulation of endothelial cell apoptotic process Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process. GOC:BHF GOC:mah GOC:mtg_apoptosis positive regulation of apoptosis of endothelial cells GOC:obol positive regulation of endothelial cell programmed cell death by apoptosis GOC:obol positive regulation of killing of endothelial cells GOC:obol positive regulation of programmed cell death of endothelial cells by apoptosis GOC:obol positive regulation of programmed cell death, endothelial cells GOC:obol Any process that modulates the frequency, rate or extent of oxygen metabolic process. mah 2011-02-11T02:03:32Z regulation of diatomic oxygen metabolic process regulation of oxygen metabolism biological_process GO:2000374 regulation of oxygen metabolic process Any process that modulates the frequency, rate or extent of oxygen metabolic process. GOC:mah regulation of diatomic oxygen metabolic process GOC:obol regulation of oxygen metabolism GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of oxygen metabolic process. mah 2011-02-11T02:03:44Z negative regulation of diatomic oxygen metabolic process negative regulation of oxygen metabolism biological_process GO:2000375 negative regulation of oxygen metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of oxygen metabolic process. GOC:mah negative regulation of diatomic oxygen metabolic process GOC:obol negative regulation of oxygen metabolism GOC:obol Any process that activates or increases the frequency, rate or extent of oxygen metabolic process. mah 2011-02-11T02:03:52Z positive regulation of diatomic oxygen metabolic process positive regulation of oxygen metabolism biological_process GO:2000376 positive regulation of oxygen metabolic process Any process that activates or increases the frequency, rate or extent of oxygen metabolic process. GOC:mah positive regulation of diatomic oxygen metabolic process GOC:obol positive regulation of oxygen metabolism GOC:obol Any process that modulates the frequency, rate or extent of mesoderm development. vk 2011-02-15T03:09:46Z biological_process GO:2000380 regulation of mesoderm development Any process that modulates the frequency, rate or extent of mesoderm development. GOC:BHF Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm development. vk 2011-02-15T03:10:02Z biological_process GO:2000381 negative regulation of mesoderm development Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm development. GOC:BHF Any process that activates or increases the frequency, rate or extent of mesoderm development. vk 2011-02-15T03:10:12Z biological_process GO:2000382 positive regulation of mesoderm development Any process that activates or increases the frequency, rate or extent of mesoderm development. GOC:BHF Any process that modulates the frequency, rate or extent of ectoderm development. vk 2011-02-15T03:17:10Z biological_process GO:2000383 regulation of ectoderm development Any process that modulates the frequency, rate or extent of ectoderm development. GOC:BHF Any process that stops, prevents or reduces the frequency, rate or extent of ectoderm development. vk 2011-02-15T03:17:27Z biological_process GO:2000384 negative regulation of ectoderm development Any process that stops, prevents or reduces the frequency, rate or extent of ectoderm development. GOC:BHF Any process that activates or increases the frequency, rate or extent of ectoderm development. vk 2011-02-15T03:17:39Z biological_process GO:2000385 positive regulation of ectoderm development Any process that activates or increases the frequency, rate or extent of ectoderm development. GOC:BHF Any process that modulates the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis. bf 2011-03-18T02:18:34Z biological_process GO:2000495 regulation of cell proliferation involved in compound eye morphogenesis Any process that modulates the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis. bf 2011-03-18T02:19:22Z biological_process GO:2000496 negative regulation of cell proliferation involved in compound eye morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis. GOC:obol Any process that activates or increases the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis. bf 2011-03-18T02:19:54Z biological_process GO:2000497 positive regulation of cell proliferation involved in compound eye morphogenesis Any process that activates or increases the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of gastrulation. yaf 2011-04-01T04:10:08Z biological_process GO:2000542 negative regulation of gastrulation Any process that stops, prevents or reduces the frequency, rate or extent of gastrulation. GOC:obol Any process that activates or increases the frequency, rate or extent of gastrulation. yaf 2011-04-01T04:10:15Z biological_process GO:2000543 positive regulation of gastrulation Any process that activates or increases the frequency, rate or extent of gastrulation. GOC:obol Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process. yaf 2011-04-04T10:01:20Z positive regulation of DNA anabolism positive regulation of DNA biosynthesis positive regulation of DNA formation positive regulation of DNA synthesis biological_process GO:2000573 positive regulation of DNA biosynthetic process Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process. GOC:obol positive regulation of DNA anabolism GOC:obol positive regulation of DNA biosynthesis GOC:obol positive regulation of DNA formation GOC:obol positive regulation of DNA synthesis GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of stem cell proliferation. dph 2011-04-27T01:04:22Z biological_process GO:2000647 negative regulation of stem cell proliferation Any process that stops, prevents or reduces the frequency, rate or extent of stem cell proliferation. GOC:dph Any process that activates or increases the frequency, rate or extent of stem cell proliferation. dph 2011-04-27T01:04:25Z biological_process GO:2000648 positive regulation of stem cell proliferation Any process that activates or increases the frequency, rate or extent of stem cell proliferation. GOC:dph Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity. yaf 2011-04-28T08:42:53Z regulation of sodium transporter activity biological_process GO:2000649 regulation of sodium ion transmembrane transporter activity Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity. GOC:obol regulation of sodium transporter activity GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transporter activity. yaf 2011-04-28T08:42:57Z negative regulation of sodium transporter activity biological_process GO:2000650 negative regulation of sodium ion transmembrane transporter activity Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transporter activity. GOC:obol negative regulation of sodium transporter activity GOC:obol Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transporter activity. yaf 2011-04-28T08:43:00Z positive regulation of sodium transporter activity biological_process GO:2000651 positive regulation of sodium ion transmembrane transporter activity Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transporter activity. GOC:obol positive regulation of sodium transporter activity GOC:obol Any process that modulates the frequency, rate or extent of motor neuron apoptotic process. pr 2011-05-09T10:56:17Z regulation of motoneuron apoptosis regulation of motor neuron apoptosis biological_process GO:2000671 regulation of motor neuron apoptotic process Any process that modulates the frequency, rate or extent of motor neuron apoptotic process. GOC:mtg_apoptosis GOC:obol regulation of motoneuron apoptosis GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron apoptotic process. pr 2011-05-09T10:56:21Z negative regulation of motoneuron apoptosis negative regulation of motor neuron apoptosis biological_process GO:2000672 negative regulation of motor neuron apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron apoptotic process. GOC:mtg_apoptosis GOC:obol negative regulation of motoneuron apoptosis GOC:obol Any process that activates or increases the frequency, rate or extent of motor neuron apoptotic process. pr 2011-05-09T10:56:24Z positive regulation of motoneuron apoptosis positive regulation of motor neuron apoptosis biological_process GO:2000673 positive regulation of motor neuron apoptotic process Any process that activates or increases the frequency, rate or extent of motor neuron apoptotic process. GOC:mtg_apoptosis GOC:obol positive regulation of motoneuron apoptosis GOC:obol Any process that modulates the frequency, rate or extent of type B pancreatic cell apoptotic process. pr 2011-05-09T11:51:09Z regulation of pancreatic B cell apoptosis regulation of pancreatic beta cell apoptosis regulation of type B pancreatic cell apoptosis biological_process GO:2000674 regulation of type B pancreatic cell apoptotic process Any process that modulates the frequency, rate or extent of type B pancreatic cell apoptotic process. GOC:mtg_apoptosis GOC:obol regulation of pancreatic B cell apoptosis GOC:obol regulation of pancreatic beta cell apoptosis GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell apoptotic process. pr 2011-05-09T11:51:12Z negative regulation of pancreatic B cell apoptosis negative regulation of pancreatic beta cell apoptosis negative regulation of type B pancreatic cell apoptosis biological_process GO:2000675 negative regulation of type B pancreatic cell apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell apoptotic process. GOC:mtg_apoptosis GOC:obol negative regulation of pancreatic B cell apoptosis GOC:obol negative regulation of pancreatic beta cell apoptosis GOC:obol Any process that activates or increases the frequency, rate or extent of type B pancreatic cell apoptotic process. pr 2011-05-09T11:51:15Z positive regulation of pancreatic B cell apoptosis positive regulation of pancreatic beta cell apoptosis positive regulation of type B pancreatic cell apoptosis biological_process GO:2000676 positive regulation of type B pancreatic cell apoptotic process Any process that activates or increases the frequency, rate or extent of type B pancreatic cell apoptotic process. GOC:mtg_apoptosis GOC:obol positive regulation of pancreatic B cell apoptosis GOC:obol positive regulation of pancreatic beta cell apoptosis GOC:obol Any process that modulates the frequency, rate or extent of cellular response to X-ray. yaf 2011-05-10T01:40:41Z regulation of cellular response to X-ray radiation stimulus biological_process GO:2000683 regulation of cellular response to X-ray Any process that modulates the frequency, rate or extent of cellular response to X-ray. GOC:obol regulation of cellular response to X-ray radiation stimulus GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to X-ray. yaf 2011-05-10T01:40:45Z negative regulation of cellular response to X-ray radiation stimulus biological_process GO:2000684 negative regulation of cellular response to X-ray Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to X-ray. GOC:obol negative regulation of cellular response to X-ray radiation stimulus GOC:obol Any process that activates or increases the frequency, rate or extent of cellular response to X-ray. yaf 2011-05-10T01:40:49Z positive regulation of cellular response to X-ray radiation stimulus biological_process GO:2000685 positive regulation of cellular response to X-ray Any process that activates or increases the frequency, rate or extent of cellular response to X-ray. GOC:obol positive regulation of cellular response to X-ray radiation stimulus GOC:obol Any process that modulates the frequency, rate or extent of cardiac muscle cell myoblast differentiation. yaf 2011-05-25T09:08:01Z regulation of myocardial precursor cell differentiation biological_process regulation of cardiac myoblast differentiation GO:2000690 regulation of cardiac muscle cell myoblast differentiation Any process that modulates the frequency, rate or extent of cardiac muscle cell myoblast differentiation. GOC:obol regulation of myocardial precursor cell differentiation GOC:obol regulation of cardiac myoblast differentiation GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell myoblast differentiation. yaf 2011-05-25T09:08:06Z negative regulation of myocardial precursor cell differentiation biological_process negative regulation of cardiac myoblast differentiation GO:2000691 negative regulation of cardiac muscle cell myoblast differentiation Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell myoblast differentiation. GOC:obol negative regulation of myocardial precursor cell differentiation GOC:obol negative regulation of cardiac myoblast differentiation GOC:obol Any process that activates or increases the frequency, rate or extent of cardiac muscle cell myoblast differentiation. yaf 2011-05-25T09:08:09Z positive regulation of myocardial precursor cell differentiation biological_process positive regulation of cardiac myoblast differentiation GO:2000700 positive regulation of cardiac muscle cell myoblast differentiation Any process that activates or increases the frequency, rate or extent of cardiac muscle cell myoblast differentiation. GOC:obol positive regulation of myocardial precursor cell differentiation GOC:obol positive regulation of cardiac myoblast differentiation GOC:obol Any process that modulates the frequency, rate or extent of cardiac muscle cell differentiation. vk 2011-06-08T10:51:06Z regulation of cardiomyocyte differentiation biological_process regulation of heart muscle cell differentiation GO:2000725 regulation of cardiac muscle cell differentiation Any process that modulates the frequency, rate or extent of cardiac muscle cell differentiation. GOC:BHF regulation of cardiomyocyte differentiation GOC:obol regulation of heart muscle cell differentiation GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell differentiation. vk 2011-06-08T10:51:11Z negative regulation of cardiomyocyte differentiation biological_process negative regulation of heart muscle cell differentiation GO:2000726 negative regulation of cardiac muscle cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell differentiation. GOC:BHF negative regulation of cardiomyocyte differentiation GOC:obol negative regulation of heart muscle cell differentiation GOC:obol Any process that activates or increases the frequency, rate or extent of cardiac muscle cell differentiation. vk 2011-06-08T10:51:15Z positive regulation of cardiomyocyte differentiation biological_process positive regulation of heart muscle cell differentiation GO:2000727 positive regulation of cardiac muscle cell differentiation Any process that activates or increases the frequency, rate or extent of cardiac muscle cell differentiation. GOC:BHF positive regulation of cardiomyocyte differentiation GOC:obol positive regulation of heart muscle cell differentiation GOC:obol Any process that modulates the frequency, rate or extent of stem cell differentiation. yaf 2011-06-14T02:05:16Z biological_process GO:2000736 regulation of stem cell differentiation Any process that modulates the frequency, rate or extent of stem cell differentiation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation. yaf 2011-06-14T02:05:20Z biological_process GO:2000737 negative regulation of stem cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation. GOC:obol Any process that activates or increases the frequency, rate or extent of stem cell differentiation. yaf 2011-06-14T02:05:23Z biological_process GO:2000738 positive regulation of stem cell differentiation Any process that activates or increases the frequency, rate or extent of stem cell differentiation. GOC:obol Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation involved in lung development. pr 2011-06-24T01:53:50Z biological_process GO:2000790 regulation of mesenchymal cell proliferation involved in lung development Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation involved in lung development. PMID:21513708 Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell proliferation involved in lung development. pr 2011-06-24T01:53:53Z biological_process GO:2000791 negative regulation of mesenchymal cell proliferation involved in lung development Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell proliferation involved in lung development. PMID:21513708 Any process that activates or increases the frequency, rate or extent of mesenchymal cell proliferation involved in lung development. pr 2011-06-24T01:53:56Z biological_process GO:2000792 positive regulation of mesenchymal cell proliferation involved in lung development Any process that activates or increases the frequency, rate or extent of mesenchymal cell proliferation involved in lung development. PMID:21513708 Any process that modulates the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis. pr 2011-06-25T07:22:38Z biological_process GO:2000794 regulation of epithelial cell proliferation involved in lung morphogenesis Any process that modulates the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis. PMID:21513708 Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis. pr 2011-06-25T07:22:42Z biological_process GO:2000795 negative regulation of epithelial cell proliferation involved in lung morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis. PMID:21513708 Any process that stops, prevents or reduces the frequency, rate or extent of myoblast proliferation. pr 2011-07-12T03:06:04Z biological_process GO:2000818 negative regulation of myoblast proliferation Any process that stops, prevents or reduces the frequency, rate or extent of myoblast proliferation. GOC:obol Any process that modulates the frequency, rate or extent of heart morphogenesis. vk 2011-07-19T10:08:58Z biological_process regulation of cardiac morphogenesis GO:2000826 regulation of heart morphogenesis Any process that modulates the frequency, rate or extent of heart morphogenesis. GOC:BHF regulation of cardiac morphogenesis GOC:obol Any process that modulates the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:46Z biological_process GO:2000831 regulation of steroid hormone secretion Any process that modulates the frequency, rate or extent of steroid hormone secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:50Z biological_process GO:2000832 negative regulation of steroid hormone secretion Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:51Z biological_process GO:2000833 positive regulation of steroid hormone secretion Any process that activates or increases the frequency, rate or extent of steroid hormone secretion. GOC:sl Any process that modulates the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:45Z biological_process GO:2000834 regulation of androgen secretion Any process that modulates the frequency, rate or extent of androgen secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:48Z biological_process GO:2000835 negative regulation of androgen secretion Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:51Z biological_process GO:2000836 positive regulation of androgen secretion Any process that activates or increases the frequency, rate or extent of androgen secretion. GOC:sl The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the renal system as it progresses from its formation to the mature state. yaf 2011-08-09T04:05:14Z biological_process mesenchymal cell differentiation involved in urinary system development mesenchymal cell differentiation involved in urinary tract development GO:2001012 mesenchymal cell differentiation involved in renal system development The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the renal system as it progresses from its formation to the mature state. GOC:mtg_kidney_jan10 GOC:obol GOC:yaf mesenchymal cell differentiation involved in urinary system development GOC:obol mesenchymal cell differentiation involved in urinary tract development GOC:obol Any process that modulates the frequency, rate or extent of skeletal muscle cell differentiation. yaf 2011-08-11T08:54:37Z biological_process GO:2001014 regulation of skeletal muscle cell differentiation Any process that modulates the frequency, rate or extent of skeletal muscle cell differentiation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle cell differentiation. yaf 2011-08-11T08:54:41Z biological_process GO:2001015 negative regulation of skeletal muscle cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle cell differentiation. GOC:obol Any process that activates or increases the frequency, rate or extent of skeletal muscle cell differentiation. yaf 2011-08-11T08:54:44Z biological_process GO:2001016 positive regulation of skeletal muscle cell differentiation Any process that activates or increases the frequency, rate or extent of skeletal muscle cell differentiation. GOC:obol Any process that modulates the frequency, rate or extent of mesenchymal cell apoptotic process. yaf 2011-09-08T02:49:59Z regulation of mesenchymal cell apoptosis biological_process GO:2001053 regulation of mesenchymal cell apoptotic process Any process that modulates the frequency, rate or extent of mesenchymal cell apoptotic process. GOC:mtg_apoptosis GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process. yaf 2011-09-08T02:50:05Z negative regulation of mesenchymal cell apoptosis biological_process GO:2001054 negative regulation of mesenchymal cell apoptotic process Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process. GOC:mtg_apoptosis GOC:obol Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process. yaf 2011-09-08T02:50:09Z positive regulation of mesenchymal cell apoptosis biological_process GO:2001055 positive regulation of mesenchymal cell apoptotic process Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process. GOC:mtg_apoptosis GOC:obol Any process that modulates the frequency, rate or extent of RNA biosynthetic process. dph 2011-10-17T11:36:25Z regulation of RNA anabolism regulation of RNA biosynthesis regulation of RNA formation regulation of RNA synthesis biological_process GO:2001141 regulation of RNA biosynthetic process Any process that modulates the frequency, rate or extent of RNA biosynthetic process. GOC:dph regulation of RNA anabolism GOC:obol regulation of RNA biosynthesis GOC:obol regulation of RNA formation GOC:obol regulation of RNA synthesis GOC:obol Any process that modulates the frequency, rate or extent of vasculogenesis. yaf 2011-11-15T01:22:31Z regulation of vascular morphogenesis biological_process GO:2001212 regulation of vasculogenesis Any process that modulates the frequency, rate or extent of vasculogenesis. GOC:obol regulation of vascular morphogenesis GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of vasculogenesis. yaf 2011-11-15T01:22:36Z negative regulation of vascular morphogenesis biological_process GO:2001213 negative regulation of vasculogenesis Any process that stops, prevents or reduces the frequency, rate or extent of vasculogenesis. GOC:obol negative regulation of vascular morphogenesis GOC:obol Any process that activates or increases the frequency, rate or extent of vasculogenesis. yaf 2011-11-15T01:22:39Z positive regulation of vascular morphogenesis biological_process GO:2001214 positive regulation of vasculogenesis Any process that activates or increases the frequency, rate or extent of vasculogenesis. GOC:obol positive regulation of vascular morphogenesis GOC:obol Any process that modulates the frequency, rate or extent of response to gamma radiation. yaf 2011-11-20T04:51:07Z biological_process regulation of response to gamma ray regulation of response to gamma-ray photon GO:2001228 regulation of response to gamma radiation Any process that modulates the frequency, rate or extent of response to gamma radiation. GOC:obol regulation of response to gamma ray GOC:obol regulation of response to gamma-ray photon GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of response to gamma radiation. yaf 2011-11-20T04:51:14Z biological_process negative regulation of response to gamma ray negative regulation of response to gamma-ray photon GO:2001229 negative regulation of response to gamma radiation Any process that stops, prevents or reduces the frequency, rate or extent of response to gamma radiation. GOC:obol negative regulation of response to gamma ray GOC:obol negative regulation of response to gamma-ray photon GOC:obol Any process that activates or increases the frequency, rate or extent of response to gamma radiation. yaf 2011-11-20T04:51:17Z biological_process positive regulation of response to gamma ray positive regulation of response to gamma-ray photon GO:2001230 positive regulation of response to gamma radiation Any process that activates or increases the frequency, rate or extent of response to gamma radiation. GOC:obol positive regulation of response to gamma ray GOC:obol positive regulation of response to gamma-ray photon GOC:obol Any process that modulates the frequency, rate or extent of apoptotic signaling pathway. pr 2011-11-24T01:20:49Z regulation of apoptotic signalling pathway biological_process GO:2001233 regulation of apoptotic signaling pathway Any process that modulates the frequency, rate or extent of apoptotic signaling pathway. GOC:mtg_apoptosis regulation of apoptotic signalling pathway GOC:mah Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway. pr 2011-11-24T01:20:54Z negative regulation of apoptotic signalling pathway biological_process GO:2001234 negative regulation of apoptotic signaling pathway Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway. GOC:mtg_apoptosis negative regulation of apoptotic signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway. pr 2011-11-24T01:20:58Z positive regulation of apoptotic signalling pathway biological_process GO:2001235 positive regulation of apoptotic signaling pathway Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway. GOC:mtg_apoptosis positive regulation of apoptotic signalling pathway GOC:mah Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:20Z negative regulation of chromosome organisation biological_process negative regulation of chromosome organization and biogenesis negative regulation of maintenance of genome integrity negative regulation of nuclear genome maintenance GO:2001251 negative regulation of chromosome organization Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. GOC:obol negative regulation of chromosome organisation GOC:obol negative regulation of chromosome organization and biogenesis GOC:obol negative regulation of maintenance of genome integrity GOC:obol negative regulation of nuclear genome maintenance GOC:obol Any process that activates or increases the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:26Z positive regulation of chromosome organisation biological_process positive regulation of chromosome organization and biogenesis positive regulation of maintenance of genome integrity positive regulation of nuclear genome maintenance GO:2001252 positive regulation of chromosome organization Any process that activates or increases the frequency, rate or extent of chromosome organization. GOC:obol positive regulation of chromosome organisation GOC:obol positive regulation of chromosome organization and biogenesis GOC:obol positive regulation of maintenance of genome integrity GOC:obol positive regulation of nuclear genome maintenance GOC:obol Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data ancestral group ancestry category A population with increased genetic homogeneity and reduced genetic variation due to cultural or geographic isolation founder population population isolate genetically isolated population General characterisation of the ancestry of a population or individual ancestry status Ancestry that is the result of cultural or geographic isolation. Generally characterised by increased genetic homogeneity and reduced genetic variation genetically isolated ancestry Ancestry which is an admixture of more than one defined ancestral population. The degree and type of admixture may vary within a population and the accuracy of classification requires well-defined reference samples admixed ancestry measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software information carrier In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. A quality of an information bearer that imparts the information content 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. James Malone PERSON: Chris Stoeckert OBI_0000142 information http://www.ebi.ac.uk/efo/EFO_0001435 true an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity information content entity IAO:0000030 Pier: 'data, information or knowledge'. OR 'representation information information content entity information content entity information entity 1 1 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters IAO:0000033 directive information entity directive information entity dot plot Dot plot of SSC-H and FSC-H. A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 IAO:0000104 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification plan specification measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos stationary movement behavior_ontology body part movement The act of moving any of the tissues and hard structures surrounding the mouth other than teeth, jaws or filter structures [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos mouth part movement other moved mouth parts behavior_ontology mouth movement The act of repeated grinding, tearing, and or crushing with teeth or jaws [NBO:SMAC] 2011-04-14T01:20:02Z George Gkoutos chew gnaw mastication behavior_ontology chewing "The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610] 2011-04-05T09:53:10Z George Gkoutos NBO:0000000 behavior behaviour behavior_ontology GO:0007610 behavior process "Movement behavior of the body or its parts." 2011-04-05T02:08:47Z George Gkoutos behavior_ontology kinesthetic behavior 2012-03-17T09:51:17Z gkoutos behavior_ontology jaw movement "Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GO:0050795] George Gkoutos GO:0050795 regulation of behavior GC_ID:1 PMID:30365038 PMID:32761142 ncbi_taxonomy all NCBITaxon:1 root all all GC_ID:1 hamsters ncbi_taxonomy Cricetinae hamsters GC_ID:1 ncbi_taxonomy Mesocricetus GC_ID:1 PMID:15371245 ncbi_taxonomy NCBITaxon:10066 Muridae Mus (commonly mice) is a small mammal belonging to the order of rodents. James Malone http://www.ebi.ac.uk/efo/EFO_0002644 GC_ID:1 MeSH:D051379 NCIt:C14238 SNOMEDCT:447482001 Mus mice mouse ncbi_taxonomy NCBITaxon:10088 Mus Mus <genus> Mus mice mouse Class imported / merged by efoimporter James Malone Mus formosanus Ryukyu mouse ricefield mouse ncbi_taxonomy NCBITaxon:10089 Mus caroli Mus formosanus Ryukyu mouse ricefield mouse Class imported / merged by efoimporter James Malone NCBITaxon:85055 GC_ID:1 NCIt:C45247 SNOMEDCT:447612001 Mus muscaris house mouse mice C57BL/6xCBA/CaJ hybrid mouse ncbi_taxonomy NCBITaxon:10090 Mus musculus Mus muscaris house mouse house mouse mice C57BL/6xCBA/CaJ hybrid mouse mouse Class imported / merged by efoimporter James Malone NCIt:C71624 Algerian mouse Mus musculus spretus western wild mouse ncbi_taxonomy NCBITaxon:10096 Mus spretus Algerian mouse Mus musculus spretus western wild mouse GC_ID:1 rat rats ncbi_taxonomy NCBITaxon:10114 Rattus rat rats Viruses Viruses GC_ID:1 ncbi_taxonomy Obtectomera NCBITaxon:1537974 GC_ID:1 ncbi_taxonomy Allolobophorinae Lumbricinae Allolobophorinae GC_ID:1 ncbi_taxonomy Lumbricus terrestris complex GC_ID:1 ncbi_taxonomy Lumbricus rubellus complex GC_ID:1 ncbi_taxonomy Palpata NCBITaxon:105389 Sedentaria Palpata GC_ID:1 ncbi_taxonomy NCBITaxon:105391 Canalipalpata GC_ID:1 ncbi_taxonomy NCBITaxon:110814 Xenoturbellida GC_ID:1 ncbi_taxonomy NCBITaxon:110815 Xenoturbella GC_ID:1 ncbi_taxonomy Sarsostraca GC_ID:1 ncbi_taxonomy Phyllopoda GC_ID:1 ncbi_taxonomy Anomopoda NCBITaxon:6795 GC_ID:1 ncbi_taxonomy Eubrachyura NCBITaxon:29963 NCBITaxon:6773 NCBITaxon:6803 GC_ID:1 ncbi_taxonomy Brachyrhyncha Heterotremata Brachyrhyncha GC_ID:1 fish fishes ncbi_taxonomy Agnatha Hyperotreti NCBITaxon:117565 Myxini fish fishes Agnatha Hyperotreti GC_ID:1 ncbi_taxonomy NCBITaxon:117570 Teleostomi Euteleostomi bony vertebrates NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy NCBITaxon:117571 Euteleostomi bony vertebrates NCBITaxon:27837 GC_ID:1 ncbi_taxonomy Adenophorea NCBITaxon:119089 Chromadorea Adenophorea GC_ID:1 ncbi_taxonomy NCBITaxon:1206794 Ecdysozoa GC_ID:1 ncbi_taxonomy NCBITaxon:1206795 Lophotrochozoa GC_ID:1 ncbi_taxonomy NCBITaxon:123365 Neoteleostei GC_ID:1 ncbi_taxonomy Eurypterygii NCBITaxon:123366 Eurypterygia Eurypterygii GC_ID:1 ncbi_taxonomy NCBITaxon:123367 Ctenosquamata GC_ID:1 ncbi_taxonomy Acanthomorpha NCBITaxon:123368 Acanthomorphata Acanthomorpha GC_ID:1 ncbi_taxonomy Euacanthomorpha NCBITaxon:123369 Euacanthomorphacea Euacanthomorpha GC_ID:1 ncbi_taxonomy NCBITaxon:124129 Acipenserinae GC_ID:1 ncbi_taxonomy NCBITaxon:124130 Acipenserini GC_ID:1 gamophytes ncbi_taxonomy Conjugatophyceae Gamophyceae Gamophyta Zygnematophyceae NCBITaxon:131209 Zygnemophyceae gamophytes Conjugatophyceae Gamophyceae Gamophyta Zygnematophyceae GC_ID:1 charophyte/embryophyte group ncbi_taxonomy Charophyta/Embryophyta group NCBITaxon:131221 Streptophytina charophyte/embryophyte group Charophyta/Embryophyta group GC_ID:1 ncbi_taxonomy NCBITaxon:1312402 Xenacoelomorpha GC_ID:1 ncbi_taxonomy biota NCBITaxon:131567 cellular organisms biota biota GC_ID:1 PMID:22839753 PMID:25450099 ncbi_taxonomy Archosauria-Testudines Testudines + Archosauria group NCBITaxon:1329799 Archelosauria Archosauria-Testudines Testudines + Archosauria group GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 Dipnotetrapodomorpha GC_ID:1 PMID:11062127 PMID:9342353 ncbi_taxonomy Eumycetozoa Zopf, 1884 Mycetozoa mycetozoans NCBITaxon:142796 Eumycetozoa Eumycetozoa Zopf, 1884 Mycetozoa mycetozoans GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria NCBITaxon:1437010 Boreoeutheria Boreotheria GC_ID:1 ncbi_taxonomy NCBITaxon:1437180 Acrogymnospermae GC_ID:1 PMID:25249442 ncbi_taxonomy Mesangiospermae GC_ID:1 PMID:26350789 ncbi_taxonomy Petrosaviidae GC_ID:1 ncbi_taxonomy NCBITaxon:1445966 Gnetidae GC_ID:1 ncbi_taxonomy Pinales GC_ID:1 ncbi_taxonomy NCBITaxon:147099 Acoelomorpha GC_ID:1 true yeasts ncbi_taxonomy NCBITaxon:147537 Saccharomycotina true yeasts GC_ID:1 ncbi_taxonomy Archiascomycota NCBITaxon:147554 Schizosaccharomycetes Archiascomycota GC_ID:1 jawless vertebrates ncbi_taxonomy Agnatha NCBITaxon:1476529 Cyclostomata jawless vertebrates Agnatha GC_ID:1 ncbi_taxonomy NCBITaxon:1489341 Osteoglossocephalai GC_ID:1 ncbi_taxonomy NCBITaxon:1489388 Euteleosteomorpha GC_ID:1 ncbi_taxonomy NCBITaxon:1489872 Percomorphaceae GC_ID:1 ncbi_taxonomy Carangimorpha Carangimorphariae Carangaria Carangimorpha Carangimorphariae GC_ID:1 ncbi_taxonomy Percomorpharia NCBITaxon:1489922 Eupercaria Percomorpharia GC_ID:1 ncbi_taxonomy NCBITaxon:1547233 Xenoturbellidae GC_ID:1 ncbi_taxonomy Galloanseri ducks, geese, chickens, fowl, quail, currasows and allies Galloanserae Galloanseri ducks, geese, chickens, fowl, quail, currasows and allies NCBITaxon:29008 GC_ID:1 ncbi_taxonomy Eisenia fetida andrei Eiseniella andrei Eisenia andrei Eisenia fetida andrei Eiseniella andrei GC_ID:1 ncbi_taxonomy NCBITaxon:186622 Acipenseroidei GC_ID:1 ncbi_taxonomy NCBITaxon:186623 Actinopteri GC_ID:1 ncbi_taxonomy NCBITaxon:186625 Clupeocephala GC_ID:1 ncbi_taxonomy Otophysa NCBITaxon:186626 Otophysi Otophysa GC_ID:1 ncbi_taxonomy Cypriniphysi NCBITaxon:186627 Cypriniphysae Cypriniphysi GC_ID:1 ncbi_taxonomy Ostarioclupeomorpha Otocephala NCBITaxon:186634 Otomorpha Ostarioclupeomorpha Otocephala GC_ID:1 mice and others ncbi_taxonomy Sciurognathi NCBITaxon:1963758 Myomorpha mice and others Sciurognathi GC_ID:1 ncbi_taxonomy Enchytraeida GC_ID:1 PMID:10874751 PMID:11557979 ncbi_taxonomy NCBITaxon:197562 Pancrustacea GC_ID:1 PMID:11557979 PMID:9727836 mandibulates ncbi_taxonomy NCBITaxon:197563 Mandibulata mandibulates Bacteria eubacteria GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:32628106 PMID:36748408 PMID:7520741 PMID:8123559 PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes NCBITaxon:2 Bacteria eubacteria Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes GC_ID:1 PMID:29367151 ncbi_taxonomy NCBITaxon:2058185 Dictyosteliaceae GC_ID:1 PMID:29367151 ncbi_taxonomy NCBITaxon:2058949 Dictyosteliales GC_ID:1 ncbi_taxonomy Homo/Pan/Gorilla group NCBITaxon:207598 Homininae Homo/Pan/Gorilla group Archaea GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:32628106 PMID:36748408 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes NCBITaxon:2157 Archaea Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes GC_ID:1 ncbi_taxonomy Multicrustacea GC_ID:1 ncbi_taxonomy Hirudinida GC_ID:1 ncbi_taxonomy NCBITaxon:2301116 Rhabditina GC_ID:1 ncbi_taxonomy NCBITaxon:2301119 Rhabditomorpha GC_ID:1 ncbi_taxonomy NCBITaxon:2605435 Evosea GC_ID:1 ncbi_taxonomy NCBITaxon:2611352 Discoba GC_ID:1 Xenopus ncbi_taxonomy NCBITaxon:262014 Xenopus <subgenus> Xenopus GC_ID:1 ncbi_taxonomy NCBITaxon:2684882 Zygnematophycidae GC_ID:1 ncbi_taxonomy Ochrophyta GC_ID:1 ncbi_taxonomy NCBITaxon:2697495 Spiralia GC_ID:1 ncbi_taxonomy SAR supergroup NCBITaxon:2698737 Sar SAR supergroup GC_ID:1 ncbi_taxonomy NCBITaxon:2743709 Danionidae GC_ID:1 ncbi_taxonomy NCBITaxon:2743711 Danioninae Eukaryota James Malone Tomasz Adamusiak eucaryotes eukaryotes http://www.ebi.ac.uk/efo/EFO_0001449 GC_ID:1 MeSH:D056890 NCIt:C25796 NIFSTD:birnlex_399 PMID:23020233 PMID:30257078 SNOMEDCT:415671008 Eucaryotae Eukarya eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes NCBITaxon:2759 Eukaryota eucaryotes eucaryotes eukaryotes eukaryotes eukaryotes Eucarya Eucarya Eucaryotae Eucaryotae Eukarya Eukarya Eukaryotae Eukaryotae eukaryotes eukaryotes GC_ID:1 ncbi_taxonomy Bovinae GC_ID:1 ncbi_taxonomy Crassiclitellata GC_ID:1 PMID:19761858 ncbi_taxonomy Conifers I GC_ID:1 brown algae ncbi_taxonomy Chromophycota Fucophyceae Phaeophyta algae brown algae Phaeophyceae brown algae Chromophycota Fucophyceae Phaeophyta algae brown algae GC_ID:1 ncbi_taxonomy Oryzomys GC_ID:1 ncbi_taxonomy Cancroidea GC_ID:1 ncbi_taxonomy NCBITaxon:30319 Pipoidea GC_ID:1 Ranoidea ncbi_taxonomy Ranoidea Rafinesque, 1814 Ranoidea <superfamily> Ranoidea Ranoidea Rafinesque, 1814 GC_ID:1 Anthophila ncbi_taxonomy Anthophila <bees> Anthophila GC_ID:1 ncbi_taxonomy Cyprinoidea NCBITaxon:30727 Cyprinoidei Cyprinoidea NCBITaxon:30946 GC_ID:1 ncbi_taxonomy Soleoidei Pleuronectoidei Soleoidei GC_ID:1 pufferfishes and others ncbi_taxonomy NCBITaxon:31022 Tetraodontiformes pufferfishes and others GC_ID:1 ncbi_taxonomy NCBITaxon:31028 Tetraodontoidei GC_ID:1 puffer fishes puffers ncbi_taxonomy NCBITaxon:31031 Tetraodontidae puffer fishes puffers GC_ID:1 ncbi_taxonomy Fugu NCBITaxon:31032 Takifugu Fugu GC_ID:1 tiger puffer torafugu ncbi_taxonomy Fugu rubripes Sphaeroides rubripes Tetraodon rubripes NCBITaxon:31033 Takifugu rubripes tiger puffer torafugu Fugu rubripes Sphaeroides rubripes Tetraodon rubripes GC_ID:1 PMID:11214318 PMID:11214319 PMID:12878460 ncbi_taxonomy Laurasiatheria Euarchontoglires GC_ID:1 PMID:11214319 PMID:12082125 PMID:12878460 PMID:15522813 ncbi_taxonomy NCBITaxon:314146 Euarchontoglires GC_ID:1 PMID:11214319 PMID:12082125 PMID:15522813 Rodents and rabbits ncbi_taxonomy NCBITaxon:314147 Glires Rodents and rabbits GC_ID:1 ncbi_taxonomy Anthropoidea NCBITaxon:314293 Simiiformes Anthropoidea GC_ID:1 ncbi_taxonomy Cercopithecoidea GC_ID:1 ape apes ncbi_taxonomy NCBITaxon:314295 Hominoidea ape apes GC_ID:1 ncbi_taxonomy NCBITaxon:3176 Zygnematales GC_ID:1 higher plants land plants plants ncbi_taxonomy land plants NCBITaxon:3193 Embryophyta higher plants land plants plants land plants NCBITaxon:3194 GC_ID:1 mosses ncbi_taxonomy Musci bryophytes mosses Bryophyta mosses Musci bryophytes mosses GC_ID:1 ncbi_taxonomy NCBITaxon:32341 Sophophora GC_ID:1 ncbi_taxonomy NCBITaxon:32346 melanogaster group GC_ID:1 ncbi_taxonomy NCBITaxon:32351 melanogaster subgroup GC_ID:1 ncbi_taxonomy NCBITaxon:32440 Chondrostei GC_ID:1 teleost fishes ncbi_taxonomy NCBITaxon:32443 Teleostei teleost fishes GC_ID:1 ncbi_taxonomy NCBITaxon:32517 Tetradontoidea GC_ID:1 ncbi_taxonomy NCBITaxon:32519 Ostariophysi Tetrapoda tetrapods GC_ID:1 tetrapods ncbi_taxonomy NCBITaxon:32523 Tetrapoda tetrapods Amniota amniotes GC_ID:1 amniotes ncbi_taxonomy NCBITaxon:32524 Amniota amniotes GC_ID:1 Theria ncbi_taxonomy NCBITaxon:32525 Theria <mammals> Theria GC_ID:1 diapsids ncbi_taxonomy Diapsida NCBITaxon:32561 Sauria diapsids Diapsida GC_ID:1 PMID:11062127 PMID:29367151 PMID:9342353 dictyostelid cellular slime molds ncbi_taxonomy Dictyostelida Dictyostelids Dictyosteliida cellular slime molds NCBITaxon:33083 Dictyostelia dictyostelid cellular slime molds Dictyostelida Dictyostelids Dictyosteliida cellular slime molds GC_ID:1 PMID:16248873 PMID:30257078 Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants ncbi_taxonomy Chlorobionta Chloroplastida green plants NCBITaxon:33090 Viridiplantae Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants Chlorobionta Chloroplastida green plants GC_ID:1 ncbi_taxonomy conifers NCBITaxon:3312 Coniferophyta conifers NCBITaxon:1445965 GC_ID:1 ncbi_taxonomy Coniferales Pinidae Coniferales Opisthokonta GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts NCBITaxon:33154 Opisthokonta Fungi/Metazoa group Fungi/Metazoa group opisthokonts opisthokonts GC_ID:1 pine family ncbi_taxonomy Pinaceae pine family Metazoa metazoans multicellular animals GC_ID:1 metazoans multicellular animals ncbi_taxonomy Animalia animals NCBITaxon:33208 Metazoa metazoans multicellular animals Animalia animals Bilateria GC_ID:1 ncbi_taxonomy NCBITaxon:33213 Bilateria GC_ID:1 ncbi_taxonomy NCBITaxon:33317 Protostomia GC_ID:1 ncbi_taxonomy NCBITaxon:33340 Neoptera GC_ID:1 ncbi_taxonomy Holometabola NCBITaxon:33392 Endopterygota Holometabola GC_ID:1 deuterostomes ncbi_taxonomy NCBITaxon:33511 Deuterostomia deuterostomes GC_ID:1 carnivores ncbi_taxonomy carnivores Carnivora carnivores carnivores GC_ID:1 alveolates ncbi_taxonomy NCBITaxon:33630 Alveolata alveolates GC_ID:1 heterokonts ncbi_taxonomy Chromophyta Heterokonta Straminipila Stramenopiles heterokonts Chromophyta Heterokonta Straminipila GC_ID:1 ncbi_taxonomy Euglenozoans NCBITaxon:33682 Euglenozoa Euglenozoans GC_ID:1 ncbi_taxonomy Chlamydospermopsida Gneticae NCBITaxon:3372 Gnetopsida Chlamydospermopsida Gneticae GC_ID:1 PMID:15371245 ncbi_taxonomy Cricetidae GC_ID:1 PMID:15019624 PMID:15371245 ncbi_taxonomy NCBITaxon:337687 Muroidea GC_ID:1 ncbi_taxonomy NCBITaxon:3378 Gnetales GC_ID:1 ncbi_taxonomy Felinae GC_ID:1 PMID:25249442 angiosperms flowering plants ncbi_taxonomy Angiospermae Magnoliophyta flowering plants NCBITaxon:3398 Magnoliopsida angiosperms flowering plants Angiospermae Magnoliophyta flowering plants GC_ID:1 ncbi_taxonomy NCBITaxon:34346 Schizosaccharomycetales GC_ID:1 bee bees ncbi_taxonomy bees Apoidea bee bees bees GC_ID:1 ncbi_taxonomy NCBITaxon:35493 Streptophyta GC_ID:1 ncbi_taxonomy Suiformes Suina Suiformes GC_ID:1 ncbi_taxonomy Pecora GC_ID:1 ncbi_taxonomy Ditrysia GC_ID:1 butterflies ncbi_taxonomy butterflies Papilionoidea butterflies butterflies GC_ID:1 ncbi_taxonomy NCBITaxon:376913 Haplorrhini GC_ID:1 ncbi_taxonomy Feliformia GC_ID:1 ncbi_taxonomy Caniformia GC_ID:1 ncbi_taxonomy Artemiidae GC_ID:1 glaucocystophytes ncbi_taxonomy Glaucophyceae Glaucophyta algae NCBITaxon:38254 Glaucocystophyceae glaucocystophytes Glaucophyceae Glaucophyta algae NCBITaxon:4478 NCBITaxon:4727 GC_ID:1 PMID:26350789 ncbi_taxonomy Poales NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 Murinae GC_ID:1 PMID:15019624 PMID:15371245 ncbi_taxonomy Sigmodontinae Mammalia mammals GC_ID:1 mammals ncbi_taxonomy mammals NCBITaxon:40674 Mammalia mammals mammals GC_ID:1 ncbi_taxonomy Glossata GC_ID:1 ncbi_taxonomy Neolepidoptera NCBITaxon:37583 GC_ID:1 ncbi_taxonomy Heteroneura NCBITaxon:167797 NCBITaxon:27906 NCBITaxon:29174 NCBITaxon:41329 NCBITaxon:54122 NCBITaxon:55674 NCBITaxon:55678 NCBITaxon:6422 GC_ID:1 pogonophores vestimentiferans ncbi_taxonomy Frenulata Lamellibrachiidae Obturata Oligobrachiidae Perviata Pogonophora Polybrachiidae Sclerolinidae Vestimentifera tube worms NCBITaxon:41324 Siboglinidae pogonophores vestimentiferans Frenulata Lamellibrachiidae Obturata Oligobrachiidae Perviata Pogonophora Polybrachiidae Sclerolinidae Vestimentifera tube worms GC_ID:1 ncbi_taxonomy Neopterygi NCBITaxon:41665 Neopterygii Neopterygi GC_ID:1 ncbi_taxonomy NCBITaxon:41666 Batrachia GC_ID:1 ncbi_taxonomy Protacanthopterygii GC_ID:1 ncbi_taxonomy Clitellata GC_ID:1 dinosaur dinosaurs ncbi_taxonomy NCBITaxon:436486 Dinosauria dinosaur dinosaurs GC_ID:1 ncbi_taxonomy NCBITaxon:436489 Saurischia GC_ID:1 ncbi_taxonomy NCBITaxon:436491 Theropoda GC_ID:1 ncbi_taxonomy NCBITaxon:436492 Coelurosauria NCBITaxon:43732 GC_ID:1 ncbi_taxonomy Asilomorpha NCBITaxon:43733 Muscomorpha Asilomorpha GC_ID:1 ncbi_taxonomy NCBITaxon:43738 Schizophora GC_ID:1 ncbi_taxonomy NCBITaxon:43741 Acalyptratae GC_ID:1 ncbi_taxonomy NCBITaxon:43746 Ephydroidea GC_ID:1 ncbi_taxonomy NCBITaxon:43845 Drosophilinae GC_ID:1 PMID:25249442 monocots monocotyledons ncbi_taxonomy Monocotyledoneae monocots Liliopsida monocots monocotyledons Monocotyledoneae monocots NCBITaxon:1661618 GC_ID:1 grass family ncbi_taxonomy Bambusaceae Gramineae Poaceae grass family Bambusaceae Gramineae GC_ID:1 PMID:15689432 PMID:16151185 PMID:17010206 PMID:17051209 PMID:17572334 ncbi_taxonomy NCBITaxon:451864 Dikarya GC_ID:1 ncbi_taxonomy NCBITaxon:451866 Taphrinomycotina GC_ID:1 ncbi_taxonomy NCBITaxon:46877 Drosophilini GC_ID:1 PMID:26350789 ncbi_taxonomy Commelinidae Commeliniflorae commelinids Commelinidae Commeliniflorae GC_ID:1 PMID:11062127 PMID:12684019 ncbi_taxonomy Mycota fungi NCBITaxon:4751 Fungi Mycota fungi GC_ID:1 ncbi_taxonomy NCBITaxon:480117 Cyclorrhapha GC_ID:1 ncbi_taxonomy NCBITaxon:480118 Eremoneura GC_ID:1 PMID:17572334 ascomycetes sac fungi ncbi_taxonomy ascomycete fungi NCBITaxon:4890 Ascomycota ascomycetes sac fungi ascomycete fungi GC_ID:1 ncbi_taxonomy Hemiascomycetes NCBITaxon:4891 Saccharomycetes Hemiascomycetes GC_ID:1 ncbi_taxonomy Endomycetales budding yeasts NCBITaxon:4892 Saccharomycetales Endomycetales budding yeasts NCBITaxon:221665 NCBITaxon:44280 GC_ID:1 ncbi_taxonomy NCBITaxon:4893 Saccharomycetaceae GC_ID:1 fission yeasts ncbi_taxonomy Schizosaccharomycetoideae NCBITaxon:4894 Schizosaccharomycetaceae fission yeasts Schizosaccharomycetoideae GC_ID:1 ncbi_taxonomy NCBITaxon:4895 Schizosaccharomyces NCBITaxon:45042 GC_ID:1 fission yeast ncbi_taxonomy Schizosaccharomyces malidevorans NCBITaxon:4896 Schizosaccharomyces pombe fission yeast Schizosaccharomyces malidevorans NCBITaxon:36915 GC_ID:1 ncbi_taxonomy Pachytichospora NCBITaxon:4930 Saccharomyces Pachytichospora NCBITaxon:41870 GC_ID:1 Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast ncbi_taxonomy Candida robusta Mycoderma cerevisiae Saccharomyces capensis Saccharomyces diastaticus Saccharomyces italicus Saccharomyces oviformis Saccharomyces uvarum var. melibiosus NCBITaxon:4932 Saccharomyces cerevisiae Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast Candida robusta Mycoderma cerevisiae Saccharomyces capensis Saccharomyces diastaticus Saccharomyces italicus Saccharomyces oviformis Saccharomyces uvarum var. melibiosus GC_ID:1 trouts, salmons & chars ncbi_taxonomy Salmoninae trouts, salmons & chars GC_ID:1 true insects ncbi_taxonomy insects NCBITaxon:50557 Insecta true insects insects GC_ID:1 PMID:23020233 PMID:30257078 ncbi_taxonomy NCBITaxon:554915 Amoebozoa NCBITaxon:6403 GC_ID:1 leeches ncbi_taxonomy Hirudinea leeches GC_ID:1 ncbi_taxonomy NCBITaxon:55879 Rhabditoidea GC_ID:1 ncbi_taxonomy NCBITaxon:55885 Peloderinae GC_ID:1 ncbi_taxonomy algae PX clade algae GC_ID:1 PMID:29367151 ncbi_taxonomy Hyalostilbum NCBITaxon:5782 Dictyostelium Hyalostilbum GC_ID:1 ncbi_taxonomy Coniferopsida Pinopsida Coniferopsida GC_ID:1 vascular plants ncbi_taxonomy vascular plants NCBITaxon:58023 Tracheophyta vascular plants vascular plants GC_ID:1 seed plants ncbi_taxonomy seed plants NCBITaxon:58024 Spermatophyta seed plants seed plants GC_ID:1 sponges ncbi_taxonomy Parazoa sponges NCBITaxon:6040 Porifera sponges Parazoa sponges GC_ID:1 ncbi_taxonomy NCBITaxon:6072 Eumetazoa GC_ID:1 cnidarians coelenterates ncbi_taxonomy Coelenterata cnidarians NCBITaxon:6073 Cnidaria cnidarians coelenterates Coelenterata cnidarians GC_ID:1 flatworm flatworms ncbi_taxonomy flatworms NCBITaxon:6157 Platyhelminthes flatworm flatworms flatworms GC_ID:1 nematode nematodes roundworm roundworms ncbi_taxonomy Nemata nematodes NCBITaxon:6231 Nematoda nematode nematodes roundworm roundworms Nemata nematodes NCBITaxon:33251 NCBITaxon:6308 GC_ID:1 ncbi_taxonomy Strongylida NCBITaxon:6236 Rhabditida Strongylida GC_ID:1 ncbi_taxonomy NCBITaxon:6237 Caenorhabditis GC_ID:1 ncbi_taxonomy Rhabditis elegans NCBITaxon:6239 Caenorhabditis elegans Rhabditis elegans NCBITaxon:54603 GC_ID:1 ncbi_taxonomy NCBITaxon:6243 Rhabditidae GC_ID:1 annelid worms ncbi_taxonomy segmented worms NCBITaxon:6340 Annelida annelid worms segmented worms GC_ID:1 polychaetes ncbi_taxonomy NCBITaxon:6341 Polychaeta polychaetes GC_ID:1 ncbi_taxonomy NCBITaxon:6362 Sabellida GC_ID:1 PMID:34811021 Oligochaeta ncbi_taxonomy Oligochaeta <segmented worms> Oligochaeta GC_ID:1 ncbi_taxonomy Enchytraeidae GC_ID:1 ncbi_taxonomy Enchytraeus GC_ID:1 earthworms ncbi_taxonomy Lumbricina earthworms GC_ID:1 ncbi_taxonomy Lumbricidae GC_ID:1 Eisenia ncbi_taxonomy Eisenia <segmented worms> Eisenia GC_ID:1 brandling worm common brandling worm common dung-worm red wiggler worm redworm tiger worm ncbi_taxonomy Eisenia foetida Eiseniella fetida Eisenia fetida brandling worm common brandling worm common dung-worm red wiggler worm redworm tiger worm Eisenia foetida Eiseniella fetida GC_ID:1 ncbi_taxonomy Lumbricus NCBITaxon:2175058 GC_ID:1 common earthworm ncbi_taxonomy Lumbricus terrestris common earthworm GC_ID:1 ncbi_taxonomy Hirudiniformes GC_ID:1 ncbi_taxonomy Hirudinidae GC_ID:1 molluscs mollusks ncbi_taxonomy molluscs Mollusca molluscs mollusks molluscs GC_ID:1 arthropods ncbi_taxonomy arthropods NCBITaxon:6656 Arthropoda arthropods arthropods GC_ID:1 crustaceans ncbi_taxonomy crustaceans Crustacea crustaceans crustaceans GC_ID:1 ncbi_taxonomy Branchiopoda GC_ID:1 fairy shrimps ncbi_taxonomy Anostraca fairy shrimps GC_ID:1 brine shrimps sea monkeys ncbi_taxonomy Artemia brine shrimps sea monkeys GC_ID:1 water flea water fleas ncbi_taxonomy Cladocera water flea water fleas NCBITaxon:77736 GC_ID:1 common water fleas ncbi_taxonomy Daphniopsis Daphnia common water fleas Daphniopsis GC_ID:1 ncbi_taxonomy Malacostraca GC_ID:1 ncbi_taxonomy Eucarida GC_ID:1 ncbi_taxonomy Decapoda GC_ID:1 ncbi_taxonomy Pleocyemata GC_ID:1 short-tailed crabs true crabs ncbi_taxonomy Brachyura short-tailed crabs true crabs GC_ID:1 rock crabs ncbi_taxonomy Cancridae rock crabs GC_ID:1 insects ncbi_taxonomy Atelocerata Tracheata Uniramia hexapods NCBITaxon:6960 Hexapoda insects Atelocerata Tracheata Uniramia hexapods GC_ID:1 butterflies and moths moths ncbi_taxonomy moths Lepidoptera butterflies and moths moths moths GC_ID:1 flies ncbi_taxonomy flies NCBITaxon:7147 Diptera flies flies GC_ID:1 ncbi_taxonomy NCBITaxon:716545 saccharomyceta GC_ID:1 ncbi_taxonomy NCBITaxon:7203 Brachycera GC_ID:1 ncbi_taxonomy Eumalacostraca GC_ID:1 pomace flies ncbi_taxonomy NCBITaxon:7214 Drosophilidae pomace flies NCBITaxon:7326 GC_ID:1 Drosophila fruit flies fruit fly ncbi_taxonomy NCBITaxon:7215 Drosophila <flies,genus> Drosophila fruit flies fruit fly NCBITaxon:2267365 GC_ID:1 fruit fly ncbi_taxonomy Sophophora melanogaster NCBITaxon:7227 Drosophila melanogaster fruit fly Sophophora melanogaster NCBITaxon:27522 NCBITaxon:27527 NCBITaxon:27531 GC_ID:1 hymenopterans ncbi_taxonomy hymenopterans Hymenoptera hymenopterans hymenopterans GC_ID:1 wasps, ants & bees ncbi_taxonomy wasps, ants & bees Apocrita wasps, ants & bees wasps, ants & bees GC_ID:1 Aculeata ncbi_taxonomy Aculeata <wasps, ants & bees> Aculeata GC_ID:1 bumble bees and honey bees ncbi_taxonomy Apidae bumble bees and honey bees GC_ID:1 Pterygota winged insects ncbi_taxonomy NCBITaxon:7496 Pterygota <insects> Pterygota winged insects GC_ID:1 chordates ncbi_taxonomy chordates NCBITaxon:7711 Chordata chordates chordates GC_ID:1 tunicates ncbi_taxonomy Urochordata tunicates NCBITaxon:7712 Tunicata tunicates Urochordata tunicates Vertebrata <vertebrates> Vertebrata vertebrates GC_ID:1 Vertebrata vertebrates ncbi_taxonomy vertebrates NCBITaxon:7742 Vertebrata <vertebrates> Vertebrata vertebrates vertebrates GC_ID:1 ncbi_taxonomy Myxinoidea hagfishes NCBITaxon:7761 Myxiniformes Myxinoidea hagfishes GC_ID:1 hagfishes ncbi_taxonomy NCBITaxon:7762 Myxinidae hagfishes NCBITaxon:77729 GC_ID:1 ncbi_taxonomy Daphniidae GC_ID:1 Gnathostomata jawed vertebrates ncbi_taxonomy NCBITaxon:7776 Gnathostomata <vertebrates> Gnathostomata jawed vertebrates GC_ID:1 cartilaginous fishes fish fishes ncbi_taxonomy cartilaginous fishes NCBITaxon:7777 Chondrichthyes cartilaginous fishes fish fishes cartilaginous fishes GC_ID:1 euphyllophytes ncbi_taxonomy NCBITaxon:78536 Euphyllophyta euphyllophytes GC_ID:1 ncbi_taxonomy NCBITaxon:7863 Holocephali GC_ID:1 chimaeras ncbi_taxonomy chimaeras NCBITaxon:7864 Chimaeriformes chimaeras chimaeras GC_ID:1 dipnoans fish fishes lungfishes ncbi_taxonomy Choanichthyes Dipneusti Dipnoi Osteichthyes lungfishes NCBITaxon:7878 Dipnomorpha dipnoans fish fishes lungfishes Choanichthyes Dipneusti Dipnoi Osteichthyes lungfishes GC_ID:1 fish fishes ray-finned fishes ncbi_taxonomy Actinopterygi Osteichthyes bony fishes NCBITaxon:7898 Actinopterygii fish fishes ray-finned fishes Actinopterygi Osteichthyes bony fishes GC_ID:1 sturgeons and paddlefish ncbi_taxonomy NCBITaxon:7899 Acipenseriformes sturgeons and paddlefish GC_ID:1 sturgeons ncbi_taxonomy NCBITaxon:7900 Acipenseridae sturgeons GC_ID:1 ncbi_taxonomy NCBITaxon:7901 Acipenser GC_ID:1 carps and others ncbi_taxonomy NCBITaxon:7952 Cypriniformes carps and others NCBITaxon:46777 NCBITaxon:487617 GC_ID:1 ncbi_taxonomy Brachydanio Celestichthys NCBITaxon:7954 Danio Brachydanio Celestichthys NCBITaxon:27702 NCBITaxon:37966 GC_ID:1 leopard danio zebra danio zebra fish zebrafish ncbi_taxonomy Brachydanio rerio Brachydanio rerio frankei Cyprinus rerio Danio frankei Danio rerio frankei NCBITaxon:7955 Danio rerio leopard danio zebra danio zebra fish zebrafish Brachydanio rerio Brachydanio rerio frankei Cyprinus rerio Danio frankei Danio rerio frankei GC_ID:1 salmons and trouts ncbi_taxonomy Salmoniformes salmons and trouts GC_ID:1 PMID:15062801 salmonids ncbi_taxonomy Salmonidae salmonids GC_ID:1 ncbi_taxonomy Parasalmo Oncorhynchus Parasalmo NCBITaxon:62064 NCBITaxon:82302 GC_ID:1 ncbi_taxonomy Acantholingua Salmothymus Salmo Acantholingua Salmothymus GC_ID:1 flatfishes ncbi_taxonomy Pleuronectiformes flatfishes GC_ID:1 righteye flounders ncbi_taxonomy Pleuronectidae righteye flounders GC_ID:1 ncbi_taxonomy NCBITaxon:8287 Sarcopterygii GC_ID:1 amphibians ncbi_taxonomy amphibians NCBITaxon:8292 Amphibia amphibians amphibians GC_ID:1 anurans frogs frogs and toads ncbi_taxonomy Salientia frogs & toads NCBITaxon:8342 Anura anurans frogs frogs and toads Salientia frogs & toads GC_ID:1 PMID:2385174 pipid frogs tongueless frogs ncbi_taxonomy NCBITaxon:8352 Pipidae pipid frogs tongueless frogs GC_ID:1 PMID:2385174 Xenopus ncbi_taxonomy NCBITaxon:8353 Xenopus <genus> Xenopus GC_ID:1 African clawed frog clawed frog common platanna platanna ncbi_taxonomy Bufo laevis NCBITaxon:8355 Xenopus laevis African clawed frog clawed frog common platanna platanna Bufo laevis GC_ID:1 PMID:2385174 ncbi_taxonomy Siluraninae NCBITaxon:8360 Xenopodinae Siluraninae NCBITaxon:685149 GC_ID:1 riparian frogs true frogs ncbi_taxonomy Ranidae riparian frogs true frogs GC_ID:1 ncbi_taxonomy Neobatrachia GC_ID:1 ncbi_taxonomy Diplostraca GC_ID:1 sauropsids ncbi_taxonomy NCBITaxon:8457 Sauropsida sauropsids GC_ID:1 ncbi_taxonomy NCBITaxon:8492 Archosauria GC_ID:1 ncbi_taxonomy NCBITaxon:85512 Dicondylia GC_ID:1 ncbi_taxonomy Artemia salina GC_ID:1 ncbi_taxonomy Amphiesmenoptera GC_ID:1 Mus ncbi_taxonomy NCBITaxon:862507 Mus <subgenus> Mus GC_ID:1 birds ncbi_taxonomy avian birds NCBITaxon:8782 Aves birds avian birds GC_ID:1 ncbi_taxonomy NCBITaxon:8783 Palaeognathae GC_ID:1 ostriches ncbi_taxonomy NCBITaxon:8798 Struthioniformes ostriches GC_ID:1 ncbi_taxonomy NCBITaxon:8799 Struthionidae GC_ID:1 ncbi_taxonomy NCBITaxon:8800 Struthio GC_ID:1 African ostrich ostrich ncbi_taxonomy Struthio camelus domesticus NCBITaxon:8801 Struthio camelus African ostrich ostrich Struthio camelus domesticus GC_ID:1 ncbi_taxonomy NCBITaxon:8825 Neognathae GC_ID:1 ducks, geese and swans ncbi_taxonomy Anseriformes ducks, geese and swans GC_ID:1 waterfowl ncbi_taxonomy Anatidae waterfowl GC_ID:1 ncbi_taxonomy NCBITaxon:88770 Panarthropoda GC_ID:1 pigeons and others ncbi_taxonomy NCBITaxon:8929 Columbiformes pigeons and others GC_ID:1 pigeons ncbi_taxonomy NCBITaxon:8930 Columbidae pigeons GC_ID:1 Craniata ncbi_taxonomy NCBITaxon:89593 Craniata <chordates> Craniata GC_ID:1 landfowls ncbi_taxonomy Galliformes landfowls NCBITaxon:9099 GC_ID:1 turkeys ncbi_taxonomy Phasianidae turkeys GC_ID:1 ncbi_taxonomy Gallus GC_ID:1 Gallus domesticus bantam chicken chickens ncbi_taxonomy Gallus gallus domesticus Phasianus gallus Gallus gallus Gallus domesticus bantam chicken chickens Gallus gallus domesticus Phasianus gallus GC_ID:1 ncbi_taxonomy Phasianinae GC_ID:1 ncbi_taxonomy Enchytraeus crypticus GC_ID:1 whales, hippos, ruminants, pigs, camels etc. ncbi_taxonomy Cetartiodactyla even-toed ungulates Artiodactyla whales, hippos, ruminants, pigs, camels etc. Cetartiodactyla even-toed ungulates GC_ID:1 ncbi_taxonomy NCBITaxon:9254 Prototheria GC_ID:1 egg-laying mammals ncbi_taxonomy monotremes NCBITaxon:9255 Monotremata egg-laying mammals monotremes GC_ID:1 echidnas ncbi_taxonomy NCBITaxon:9259 Tachyglossidae echidnas GC_ID:1 eutherian mammals placental mammals placentals ncbi_taxonomy Placentalia placentals NCBITaxon:9347 Eutheria eutherian mammals placental mammals placentals Placentalia placentals GC_ID:1 primate ncbi_taxonomy Primata primates NCBITaxon:9443 Primates primate Primata primates GC_ID:1 New World monkeys monkey monkeys ncbi_taxonomy Platyrrhini New World monkeys monkey monkeys GC_ID:1 ncbi_taxonomy NCBITaxon:9526 Catarrhini GC_ID:1 Old World monkeys monkey monkeys ncbi_taxonomy Cercopithecidae Old World monkeys monkey monkeys GC_ID:1 ncbi_taxonomy Cercopithecinae GC_ID:1 macaque macaques ncbi_taxonomy Macaca macaque macaques NCBITaxon:36502 GC_ID:1 Rhesus monkey rhesus macaque rhesus macaques rhesus monkeys ncbi_taxonomy Cercopithecus mulatta Macaca mulatta Rhesus monkey rhesus macaque rhesus macaques rhesus monkeys Cercopithecus mulatta GC_ID:1 great apes ncbi_taxonomy Pongidae NCBITaxon:9604 Hominidae great apes Pongidae GC_ID:1 humans ncbi_taxonomy NCBITaxon:9605 Homo humans Homo sapiens human human being GC_ID:1 human ncbi_taxonomy NCBITaxon:9606 Homo sapiens human GC_ID:1 dog, coyote, wolf, fox ncbi_taxonomy Canidae dog, coyote, wolf, fox GC_ID:1 ncbi_taxonomy Canis NCBITaxon:68731 NCBITaxon:9609 GC_ID:1 ncbi_taxonomy Fennecus Vulpes Fennecus GC_ID:1 cat family ncbi_taxonomy Felidae cat family GC_ID:1 ncbi_taxonomy Felis NCBITaxon:36475 GC_ID:1 PMID:17600185 PMID:8581300 PMID:8603894 cat cats domestic cat ncbi_taxonomy Felis domesticus Felis silvestris catus Felis catus cat cats domestic cat Felis domesticus Felis silvestris catus NCBITaxon:39423 GC_ID:1 boars pigs ncbi_taxonomy Suidae boars pigs GC_ID:1 ncbi_taxonomy Sus GC_ID:1 ncbi_taxonomy Ruminantia GC_ID:1 deer ncbi_taxonomy Cervidae deer GC_ID:1 ncbi_taxonomy Rangifer GC_ID:1 ncbi_taxonomy Odocoileinae GC_ID:1 ncbi_taxonomy Bovidae GC_ID:1 oxen, cattle ncbi_taxonomy Bos oxen, cattle NCBITaxon:272461 GC_ID:1 bovine cattle cow dairy cow domestic cattle domestic cow ox ncbi_taxonomy Bos bovis Bos primigenius taurus Bos taurus bovine cattle cow dairy cow domestic cattle domestic cow ox Bos bovis Bos primigenius taurus GC_ID:1 ncbi_taxonomy Ovis NCBITaxon:9936 GC_ID:1 domestic sheep lambs sheep wild sheep ncbi_taxonomy Ovis ammon aries Ovis orientalis aries Ovis ovis Ovis aries domestic sheep lambs sheep wild sheep Ovis ammon aries Ovis orientalis aries Ovis ovis GC_ID:1 ncbi_taxonomy Caprinae GC_ID:1 ncbi_taxonomy rabbits & hares Lagomorpha rabbits & hares GC_ID:1 rodent ncbi_taxonomy rodents NCBITaxon:9989 Rodentia rodent rodents planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) CHMO:0001840 OBI:0000011 completely executed planned process planned process planned process regulator role Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator OBI regulator role regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role classified data set A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. CHMO:0000000 CHMO:0001133 measurement method OBI:0000070 assay A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. obi:pppb material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ James Malone modified from original OBI definition PERSON: Philippe Rocca-Serra Tomasz Adamusiak modified from original OBI definition adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process http://www.ebi.ac.uk/efo/EFO_0000664 true MeSH:D011153 NIFSTD:sao2254405550 SNOMEDCT:385436007 population population organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization plan protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. A protocol is an information entity which is a set of instructions that describe an how an experiment is done. a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. James Malone Jie Zheng PlanAndPlannedProcess Branch Tomasz Adamusiak OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol http://www.ebi.ac.uk/efo/EFO_0001442 true MO:214 NCIt:C42651 SNOMEDCT:260686004 method method used in an experiment plan specification protocol protocol interpreting data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data light emission function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. Bill Bug Daniel Schober Frank Gibson Melanie Courtot light emission function excitation function A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. Bill Bug Daniel Schober Frank Gibson Melanie Courtot excitation function regulatory agency The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective manufacturing A planned process with the objective to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role clustered data set A clustered data set is the output of a K means clustering data transformation A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective support vector machine A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. James Malone Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine decision tree induction objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software peak matching Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching k-nearest neighbors A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. James Malone k-NN PERSON: James Malone k-nearest neighbors CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART statistical model validation Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation manufacturer A person or organization that has a manufacturer role. manufacturer service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. CHMO:0000998 OBI:0000968 device A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. obi:obi dose An organism has been injected 1ml of vaccine A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. dose questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) A device which has a function to emit light. Person:Helen Parkinson OBI light emission device X-ray source A device that is used to generate X-rays. PERSON: Erik Segerdell x-ray generator http://en.wikipedia.org/wiki/X-ray_generator CHMO:0000944 X-ray generator OBI:0001138 X-ray source A device that is used to generate X-rays. obi:es conclusion based on data The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification 1 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens histologic grade according to AJCC 7th edition G1:Well differentiated G4: Undifferentiated A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade according to AJCC 7th edition histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System histologic grade for ovarian tumor A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system histologic grade for ovarian tumor according to the World Health Organization A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to the World Health Organization pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for colon and rectum according to AJCC 7th edition pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for lung according to AJCC 7th edition pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for kidney according to AJCC 7th edition pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for ovary according to AJCC 7th edition pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for colon and rectum according to AJCC 7th edition pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for kidney according to AJCC 7th edition pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for ovary according to AJCC 7th edition pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for colon according to AJCC 7th edition pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for lung according to AJCC 7th edition pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for kidney according to AJCC 7th edition pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for ovary according to AJCC 7th edition clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB clinical tumor stage group according to AJCC 7th edition International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification performance status value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status NCI BBRB performance status value specification Eastern Cooperative Oncology Group score value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI NCI BBRB Eastern Cooperative Oncology Group score value specification Karnofsky score vaue specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI NCI BBRB Karnofsky score vaue specification altitude measurement datum A length measurement datum between a point at sea or ground level and some point above it. Chris Stoeckert Adapted from https://www.merriam-webster.com/dictionary/altitude altitude measurement datum material supplier A person or organization that provides material supplies to other people or organizations. Rebecca Jackson https://github.com/obi-ontology/obi/issues/1289 material supplier organism Drosophila melanogaster animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. E.g Drosophila melanogaster 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch James Malone Jie Zheng Tomasz Adamusiak WEB: http://en.wikipedia.org/wiki/Organism http://www.ebi.ac.uk/efo/EFO_0000634 true MO:508 NCIt:C14250 NIFSTD:birnlex_376 SNOMEDCT:410607006 species organism organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation leave one out cross validation method The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method k-means clustering A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). Elisabetta Manduchi James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering hierarchical clustering A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering hierarchical clustering dimensionality reduction A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction principal components analysis dimensionality reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot principal components analysis dimensionality reduction data visualization Generation of a heatmap from a microarray dataset A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. James Malone PERSON: James Malone partitioning data transformation partitioning objective A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery data transformation class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective class prediction objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction objective cross validation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective clustered data visualization A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization planned irradiation PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370. A planned process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays, X-rays, charged particles or neutrons) or non-ionizing radiation (such as UV light or microwaves) Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) planned irradiation light source A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A time quality inhering in a bearer by virtue of how long the bearer has existed. age A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATO:0002015 composed of compositionality content structure, composition quality PATO:0000025 For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATOC:GVG A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration concentration of A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced impenetrability toughness hardness morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0001647 relational shape quality quality PATO:0000052 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATOC:GVG quality PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 deviation (from_normal) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet length A 1-D extent quality which is equal to the distance between two points. length A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent. quality PATO:0000136 closure A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent. PATOC:CJM PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. location placement relational spatial quality position A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0001452 conformation relational structural quality quality PATO:0000141 structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATOC:GVG conformation VT:1000738 A physical quality of the thermal energy of a system. temperature A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics. quality PATO:0000150 texture A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics. PATOC:GVG A quality in which events occur in sequence. time An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. viability A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. quality PATO:0000261 maturity A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. Merriam-Webster:Merriam-Webster An age which is relatively high. old An age which is relatively low. young A hardness quality of being rigid and resistant to pressure. firm impenetrable tough hard A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course. quality PATO:0000389 acute A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course. dictionary:reference A branchiness quality inhering in a bearer by virtue of the bearer's having branches. ramified ramiform quality PATO:0000402 branched A branchiness quality inhering in a bearer by virtue of the bearer's having branches. WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature. quality plate-like PATO:0000407 flat A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature. web:http://www.merriam-webster.com/ A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. quality round rounded PATO:0000411 circular A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. thefreedictionary.com:thefreedictionary.com A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. quality average PATO:0000461 normal A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. PATOC:GVG A duration quality of a process which is relatively high. PATO:0000715 high time increased period increased time quality chronic prolonged period slow time PATO:0000498 increased duration A duration quality of a process which is relatively high. PATOC:GVG A size quality which is relatively high. PATO:0001202 quality big enlarged expanded great large PATO:0000586 increased size A size quality which is relatively high. PATOC:GVG A size quality which is relatively low. hypoplasia underdeveloped reduced small tiny decreased size A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view. quality blocked PATO:0000608 closed A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view. answers.com:answers.com A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. ellipse-shaped ellipsoid elliptical quality oval ovoid PATO:0000947 elliptic A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. PATOC:GVG An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. quality PATO:0000957 opacity An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. PATOC:GVG A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. non-transparent quality clouding cloudy PATO:0000963 opaque A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. PATOC:GVG A optical quality inhering in a bearer by virtue of the bearer's lacking opacity. clear hyaline quality PATO:0000964 transparent A optical quality inhering in a bearer by virtue of the bearer's lacking opacity. PATOC:GVG A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices. porosity A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices. porous A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow. quality PATO:0000992 viscosity A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow. PATOC:GVG A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity. quality PATO:0000998 viscous A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity. PATOC:GVG physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way. quality PATO:0001031 elasticity A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way. merriam-webster:merriam-webster A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. elongated An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way. quality PATO:0001171 elastic An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way. merriam-webster:merriam-webster A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis. quality PATO:0001185 larval A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis. Wikipedia:http://en.wikipedia.org/wiki/Larval A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. linear A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG physical object quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. electromagnetic (EM) radiation quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. quality PATO:0001300 optical quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. PATOC:GVG A temperature which is relatively low. cold low temperature decreased temperature A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATO:0000081 period quality time PATO:0001309 duration A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATOC:mellybelly A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology. amorphous A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. quality PATO:0001374 ploidy A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. Wikipedia:http://en.wikipedia.org/wiki/Ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. quality PATO:0001375 haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. quality PATO:0001377 polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. quality PATO:0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Euploid A monadic quality of continuant that exists at the cellular level of organisation. quality PATO:0001396 cellular quality A monadic quality of continuant that exists at the cellular level of organisation. PATOC:GVG A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. quality PATO:0001397 cellular potency A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. PATOC:GVG A cellular potency that is the capacity to produce only one differentiated cell type. quality PATO:0001400 Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells. unipotent A cellular potency that is the capacity to produce only one differentiated cell type. Wikipedia:http://en.wikipedia.org/wiki/Unipotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. quality PATO:0001401 Less potent than multipotent, often thought of as precursor or progenitor cell status. oligopotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. PATOC:MAH A cellular potency that is the capacity to form multiple differentiated cell types. quality PATO:0001402 multipotent A cellular potency that is the capacity to form multiple differentiated cell types. Wikipedia:http://en.wikipedia.org/wiki/Multipotent A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. quality PATO:0001404 nucleate quality A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. quality PATO:0001405 anucleate A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. quality PATO:0001406 binucleate A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. quality PATO:0001407 mononucleate A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. Biology-online:Biology-online A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body. quality PATO:0001408 ciliatedness A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body. Wikipedia:http://en.wikipedia.org/wiki/Ciliated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. quality PATO:0001410 striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. Biology-online:Biology-online A structural quality inhering in a bearer by virtue of the bearer's having distinct structure. structured A structural quality inhering in a bearer by virtue of the bearer's lacking distinct structure. unstructured A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. dead A concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base. medium acidity An medium acidity quality inhering in a solution by virtue of the bearer's a high concentration of H+ ions. acidic A position which is relatively high. high position increased position A positional which is relatively low. low position decreased position A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction. sloped A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking. flexibility A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. stiff stiffness inflexible A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. solidity quality PATO:0001546 quality of a solid A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. Chemistry:http://chemistry.about.com/od/chemistryglossary/a/soliddefinition.htm A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. gaseous quality PATO:0001547 quality of a gas A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. Chemistry:http://chemistry.about.com/od/chemistryglossary/a/gasdefinition.htm PATOC:GVG A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. liquidity quality PATO:0001548 quality of a liquid A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. url:http://www.chemistry-dictionary.com/definition/liquid.php A mass which is higher than normal or average. high mass large mass increased mass A physical quality that is the ability to contract or shrink. quality PATO:0001579 contractility A physical quality that is the ability to contract or shrink. WordNet:WordNet A contractility which is relatively high. high contractility quality PATO:0001580 increased contractility A contractility which is relatively high. PATO:GVG A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. quality PATO:0001591 curvature A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. WordNet:WordNet A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution. osmolarity A osmolarity which is relatively high. high osmolarity increased osmolarity A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface. elevation An elevation which is relatively high. high elevation elevated increased elevation An elevation which is relatively low. low elevation decreased elevation A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. quality PATO:0001690 This refers to the disposition of the bearer. contractile A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. PATOC:GVG A viscosity which relatively high. high viscosity quality PATO:0001693 increased viscosity A viscosity which relatively high. PATOC:GVG An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process. shedability A quality inhering in a plant by virtue of the bearer's disposition to shed foliage. deciduous (plant) A quality inhering in a plant by virtue of the bearer's disposition to retain foliage. evergreen (plant) A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. liquid quality PATO:0001735 liquid configuration A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids. solid quality PATO:0001736 solid configuration A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids. PATOC:GVG A quality of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited. quality PATO:0001739 Radiation quality is often expressed in terms of the linear energy transfer of the ionising particles that deliver the absorbed dose, but this is an over simplification. radiation quality A quality of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited. DOI:10.20348/STOREDB/1173/1250 https://orcid.org/0000-0002-5111-7263 Radiation quality is often expressed in terms of the linear energy transfer of the ionising particles that deliver the absorbed dose, but this is an over simplification. DOI:10.2307/3570787 A quality of a substance inhering in a bearer by virtue of it being currently or previously exposed to electromagnetic radiation, radiation exposed quality PATO:0001744 This may refer to incident external irradiation or internal radiation from an ingested or otherwise internal source. irradiated A quality of a substance inhering in a bearer by virtue of it being currently or previously exposed to electromagnetic radiation, ISSN:9781496335418 https://orcid.org/0000-0002-5111-7263 A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave. quality PATO:0001748 invaginated A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave. PATOC:GVG A composition quality inhering in a bearer by virtue of the bearer's containing granules. granular A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid. wetness A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid. wet A wetness quality inhering in a bearer by virtue of the bearer's not being covered by a liquid. dry A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions). pH acidity A shape quality in a bearer by virtue of the bearer's curving inward. quality PATO:0001857 concave A shape quality in a bearer by virtue of the bearer's curving inward. WordNet:WordNet A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. quality PATO:0001863 chronic A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. PATOC:cjm A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATO:0001203 rod-like rod-shaped tubulate quality PATO:0001873 cylindrical A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATOC:MAH A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. quality PATO:0001908 multinucleate A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. frozen A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance. sacular quality PATO:0001987 saccular A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance. PATOC:MAH An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. quality PATO:0001992 cellularity An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. PATOC:GVG A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. quality PATO:0001993 multicellular A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. PATOC:GVG A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality A quality that inheres in an entire organism or part of an organism. PATOC:CJM Surface shape that refers to the inward or outward curvature of the surface. quality PATO:0002005 concavity Surface shape that refers to the inward or outward curvature of the surface. PATOC:MAH A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. quality 2-D projection cross-sectional PATO:0002006 2-D shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. PATOC:CJM A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 Use this term or an is_a child of this term when the entire shape of the object is known. convex 3-D shape A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. PATOC:CJM A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity. quality PATO:0002009 branchiness A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity. PATOC:MAH A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas. quality PATO:0002014 structure, cavities A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas. PATOC:GVG A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. quality PATO:0002039 biconcave A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. PATOC:GVG A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure. 2009-02-15T08:11:41Z dendriform dendroid dendroidal quality PATO:0002045 dendritic A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure. PATOC:cvs george 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within. 2009-09-18T02:19:20Z quality PATO:0002078 hollow A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within. url:http://www.merriam-webster.com/dictionary/hollow An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions. 2009-10-05T12:05:23Z quality PATO:0002094 basophilic An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. 2009-10-06T04:37:14Z quality PATO:0002124 laminar A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. PATOC:GVG sloped downward A positional quality inhering in a bearer by virtue the bearer's being changed in position. displaced A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. relational molecular quality molecular quality A quality inhering in a bearer by virtue of its constitution. 2010-03-15T04:35:27Z quality PATO:0002198 quality of a substance A quality inhering in a bearer by virtue of its constitution. PATOC:GVG A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical. 2010-07-13T04:22:30Z quality PATO:0002226 subcylindrical A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical. url:http://www.thefreedictionary.com/Subcylindrical A quality inhering in a bearer by virtue of the bearer's being roundish, flattish shape, possibly with a slightly angled edge. plate-like platelike A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane. 2010-08-16T03:59:34Z quality compressed PATO:0002254 Becoming flat but not necessarily completely flat. flattened A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane. PATOC:CVS Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels. 2010-09-01T10:27:48Z quality channeled creased PATO:0002255 grooved Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels. PATOC:JE A shape that inheres in a 3 dimensional entity. 2010-10-05T12:31:16Z quality PATO:0002266 3-D shape A shape that inheres in a 3 dimensional entity. PATOC:OREGON An elasticity which is relatively high. 2011-03-30T11:50:21Z quality PATO:0002287 increased elasticity An elasticity which is relatively high. PATOC:GVG A cylindrical shape that is hollow. 2011-06-08T06:33:50Z tube like tube-shaped tubulate quality PATO:0002299 tubular A cylindrical shape that is hollow. PATOC:GVG A quality that has a value that is increased compared to normal or average. 2011-06-16T06:39:43Z quality PATO:0002300 increased quality A quality that has a value that is increased compared to normal or average. PATOC:GVG A quality that has a value that is decreased compared to normal or average. decreased quality A quality of an object that has a value that is decreased compared to normal or average. decreased object quality A quality of a process that has a value that is increased compared to normal or average. 2011-06-16T06:53:08Z quality PATO:0002304 increased process quality A quality of a process that has a value that is increased compared to normal or average. PATOC:GVG A quality of an object that has a value that is increased compared to normal or average. 2011-06-16T06:54:01Z quality PATO:0002305 increased object quality A quality of an object that has a value that is increased compared to normal or average. PATOC:GVG A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. 2011-09-09T04:50:10Z quality PATO:0002309 Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). fiber shaped A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. PATOC:DC A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt 2011-10-12T12:45:16Z Lamé curve quality PATO:0002318 superelliptic A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt wiktionary:superellipse A quality inhering in a bearer by virtue of the bearer's upper parts die back to the rootstock at the end of the growing season. herbaceous An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions. 2012-12-17T03:01:19Z eosinophilic quality PATO:0002418 Eosin stains acidophilic structures, hence eosinophilic is the same as acidophilic. acidophilic An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions. PATOC:GVG Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry. 2012-12-17T03:11:10Z quality PATO:0002422 Acinus is Latin for berry. acinar Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry. wikipedia:https://en.wikipedia.org/wiki/Acinus A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen. 2013-09-15T11:34:15Z quality PATO:0002462 collagenous A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen. PATOC:WD A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching. 2013-09-15T11:48:26Z quality PATO:0002468 distensible A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. 2013-09-15T12:29:15Z quality PATO:0002478 transversely striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. PATOC:DS A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. 2013-10-21T05:44:34Z quality PATO:0002505 nucleated A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. PATOC:GVG A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other. 2014-12-12T08:43:17Z quality PATO:0010001 disconnected A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other. GOC:dos A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array. quality PATO:0015006 A complete coverage of this domain would subclasses homopolymeric, copolymeric, crystalline. polymeric A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array. GOC:DOS https://github.com/pato-ontology/pato/issues/78 A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen. quality PATO:0015008 distensibility A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen. GOC:CJM A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content. humidity An increase in humidity. humid increased humidity The propensity of a material to undergo combustion. Combustion encompasses smouldering and flaming combustion. Combustibility is usually applied to solids. combustibility An increase in combustibility. combustible increased combustibility A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. http://orcid.org/0000-0001-7258-9596 quality PATO:0070047 polychromatophilic An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. GOC:add A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength. quality PATO:0070060 quality of interaction of a substance with electromagnetic radiation A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength. https://orcid.org/0000-0002-5111-7263 2 Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. group of organism organism collection May be of the same or different species. collection of organisms This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. A collection of organisms, all of the same species, that live in the same place. ISBN:0878932739 It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. population of organisms A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 envoPolar Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. ecological community A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species single-species collection of organisms A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". multi-species collection of organisms A material entity that is one or more organisms, viruses or viroids. organismal entity 2 A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. pair of interacting organisms A plant structure (PO:0005679) which is a whole organism. genet (broad) ramet (broad) PO_GIT:538 PO_GIT:69 planta entera (Spanish, exact) 植物体全体 (Japanese, exact) bush (narrow) frutex (narrow) frutices (narrow) gametophyte (narrow) herb (narrow) liana (narrow) prothalli (narrow) prothallium (narrow) prothallus (narrow) seedling (narrow) shrub (narrow) sporophyte (narrow) suffrutex (narrow) suffrutices (narrow) tree (narrow) vine (narrow) woody clump (narrow) plant_anatomy clonal colony (related) colony (related) PO:0000003 Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). whole plant A plant structure (PO:0005679) which is a whole organism. POC:curators planta entera (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物体全体 (Japanese, exact) NIG:Yukiko_Yamazaki frutex (narrow) FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba frutices (narrow) FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b prothalli (narrow) FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0 prothallus (narrow) FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8 suffrutex (narrow) FNA:99508f62-7116-4e2b-90c0-19ff55ebd967 suffrutices (narrow) FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2 woody clump (narrow) FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0 A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127). PO_GIT:234 &#225pice del epiblasto (epiblastema) (Spanish, exact) シュート頂、茎頂 (Japanese, exact) plant_anatomy PO:0000037 shoot axis apex A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127). POC:curators &#225pice del epiblasto (epiblastema) (Spanish, exact) POC:Maria_Alejandra_Gandolfo シュート頂、茎頂 (Japanese, exact) NIG:Yukiko_Yamazaki A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division. zona perif&#233rica (Spanish, exact) 周辺帯 (Japanese, exact) plant_anatomy peripheral meristem (related) PO:0000225 peripheral zone A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division. ISBN:0521288959 TAIR_curator:Leonore_Reiser zona perif&#233rica (Spanish, exact) POC:Maria_Alejandra_Gandolfo 周辺帯 (Japanese, exact) NIG:Yukiko_Yamazaki A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. CL:0000034 PO_GIT:272 c&#233lula meristem&#225tica (Spanish, exact) stem cell (exact) 分裂組織細胞 (Japanese, exact) plant_anatomy PO:0004010 meristematic cell A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. ISBN:0471245208 POC:Laurel_Cooper c&#233lula meristem&#225tica (Spanish, exact) POC:Maria_Alejandra_Gandolfo 分裂組織細胞 (Japanese, exact) NIG:Yukiko_Yamazaki A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005). PO_GIT:467 portion of root primordium tissue (exact) primordio de ra&#237z (Spanish, exact) root primordia (exact, plural) 根原基（可視的） (Japanese, exact) plant_anatomy PO:0005029 A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147). root primordium A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005). ISBN:0521288959 POC:curators primordio de ra&#237z (Spanish, exact) POC:Maria_Alejandra_Gandolfo 根原基（可視的） (Japanese, exact) NIG:Yukiko_Yamazaki A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148). filoma (Spanish, exact) フィロム、葉(的）器官 (Japanese, exact) plant_anatomy PO:0006001 phyllome A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148). POC:curators filoma (Spanish, exact) POC:Maria_Alejandra_Gandolfo フィロム、葉(的）器官 (Japanese, exact) NIG:Yukiko_Yamazaki A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006). PO_GIT:472 PO_GIT:583 meristema del epiblasto (epiblastema) (Spanish, exact) シュート分裂組織 (Japanese, exact) plant_anatomy PO:0006079 shoot system meristem A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006). Gramene:Pankaj_Jaiswal POC:Laurel_Cooper meristema del epiblasto (epiblastema) (Spanish, exact) POC:Maria_Alejandra_Gandolfo シュート分裂組織 (Japanese, exact) NIG:Yukiko_Yamazaki A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679). PO_GIT:125 portion of protoderm tissue (exact) protodermis (Spanish, exact) 前表皮、原表皮 (Japanese, exact) plant_anatomy dermatogen cell (related) PO:0006210 A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state. protoderm A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679). ISBN:0471245208 POC:Laurel_Cooper protodermis (Spanish, exact) POC:Maria_Alejandra_Gandolfo 前表皮、原表皮 (Japanese, exact) NIG:Yukiko_Yamazaki A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003). PO_GIT:390 plant_structure_development_stage Solanaceae whole plant growth stages (SGN:0000001) (related) cereal plant growth stage ontology (GRO:0007199) (related) maize growth stage (GRO:0007002) (related) plant growth stages in Arabidopsis (TAIR:0000021) (related) rice growth stage (GRO:0007040) (related) sorghum growth stage (GRO:0007124) (related) wheat, barley and oat growth stage (GRO:0007156) (related) PO:0007033 whole plant development stage A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003). POC:curators A cell which is a plant structure (PO:0009011). cell (broad) GO:0005623 PO_GIT:56 c&#233lula vegetal (Spanish, exact) 植物細胞 (Japanese, exact) plant_anatomy PO:0009002 Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. plant cell A cell which is a plant structure (PO:0009011). GO:0005623 POC:curators c&#233lula vegetal (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物細胞 (Japanese, exact) NIG:Yukiko_Yamazaki A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. PO:0003006 PO_GIT:578 ra&#237z (Spanish, exact) radices (exact, plural) radix (exact) 根 (Japanese, exact) aerial root (narrow) climbing root (narrow) plant_anatomy PO:0009005 Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034). root A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. ISBN:978-0879015329 ISBN:9780964022157 NYBG:Brandon_Sinn NYBG:Dario_Cavaliere POC:Laurel_Cooper POC:curators ra&#237z (Spanish, exact) POC:Maria_Alejandra_Gandolfo radices (exact, plural) FNA:3c46e84c-23e4-416b-91cd-2f7c42e4b13d radix (exact) FNA:e6315684-fc99-4976-b39d-b356c4b7e7fd 根 (Japanese, exact) NIG:Yukiko_Yamazaki climbing root (narrow) FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. PO_GIT:135 sistema de epiblasto (epiblastema) (Spanish, exact) シュート系、苗条系 (Japanese, exact) tree crown (narrow) plant_anatomy Poaceae crown (related) shoot (related) thalli (related) thallus (related) PO:0009006 The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system. shoot system A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. POC:Laurel_Cooper POC:curators sistema de epiblasto (epiblastema) (Spanish, exact) POC:Maria_Alejandra_Gandolfo シュート系、苗条系 (Japanese, exact) NIG:Yukiko_Yamazaki thalli (related) FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85 thallus (related) FNA:02756ad4-a09c-48d7-8754-903254e557a9 A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. portion of tissue (broad) tissue (broad) PO_GIT:59 porci&#243n de un tejido vegetal (Spanish, exact) 植物組織の一部 (Japanese, exact) plant_anatomy plant tissue (related) PO:0009007 A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. portion of plant tissue A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. POC:curators TAIR_curator:Leonore_Reiser porci&#243n de un tejido vegetal (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物組織の一部 (Japanese, exact) NIG:Yukiko_Yamazaki A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. organ (broad) PO_GIT:55 &#243rgano vegetal (Spanish, exact) 植物 器官 (Japanese, exact) plant_anatomy compound plant organ (related) simple plant organ (related) PO:0009008 Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). plant organ A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. POC:curators &#243rgano vegetal (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物 器官 (Japanese, exact) NIG:Yukiko_Yamazaki simple plant organ (related) PATO:01503 A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. PO_GIT:57 estructura vegetal (Spanish, exact) 植物 構造 (Japanese, exact) plant_anatomy PO:0009011 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. plant structure A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. CARO:0000003 POC:curators estructura vegetal (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物 構造 (Japanese, exact) NIG:Yukiko_Yamazaki 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. PO:cooperl A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. PO:0007021 PO_GIT:185 etapa de desarrollo de estructura vegetal (Spanish, exact) plant growth and development stage (exact) plant_structure_development_stage Arabidopsis growth (related) PO:0009012 Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'. plant structure development stage A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. BFO:0000003 GO:0032502 POC:curators etapa de desarrollo de estructura vegetal (Spanish, exact) POC:Maria_Alejandra_Gandolfo Arabidopsis growth (related) TAIR:0000205 A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. PO_GIT:472 meristem (exact) meristema (Spanish, exact) meristematic tissue (exact) 分裂組織 (Japanese, exact) plant_anatomy PO:0009013 portion of meristem tissue A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. APweb:Glossary Gramene:Pankaj_Jaiswal meristema (Spanish, exact) POC:Maria_Alejandra_Gandolfo 分裂組織 (Japanese, exact) NIG:Yukiko_Yamazaki A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025). promeristem (broad) PO_GIT:579 AM (exact) meristema apical (Spanish, exact) 頂端分裂組織 (Japanese, exact) plant_anatomy primary meristem (related) PO:0020144 apical meristem A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025). Gramene:Pankaj_Jaiswal POC:Laurel_Cooper POC:curators meristema apical (Spanish, exact) POC:Maria_Alejandra_Gandolfo 頂端分裂組織 (Japanese, exact) NIG:Yukiko_Yamazaki A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232). promeristem (broad) PO_GIT:472 SAM (exact) meristema apical del epiblasto (epiblastema) (Spanish, exact) 茎頂分裂組織 (Japanese, exact) plant_anatomy primary shoot meristem (related) PO:0020148 shoot apical meristem A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232). POC:Laurel_Cooper UMSL_curator:fz meristema apical del epiblasto (epiblastema) (Spanish, exact) POC:Maria_Alejandra_Gandolfo 茎頂分裂組織 (Japanese, exact) NIG:Yukiko_Yamazaki An axial plant organ (PO:0009008). rwalls 2010-07-01T03:44:41Z eje de la planta (Spanish, exact) plant axes (exact, plural) 植物軸（軸柱） (Japanese, exact) plant_anatomy PO:0025004 Includes roots and shoots. plant axis An axial plant organ (PO:0009008). POC:curators eje de la planta (Spanish, exact) POC:Maria_Alejandra_Gandolfo plant axes (exact, plural) FNA:2355281f-ab10-4ae2-a3d8-672cace068a8 植物軸（軸柱） (Japanese, exact) NIG:Yukiko_Yamazaki A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). rwalls 2010-02-09T04:12:11Z PO_GIT:63 estructura vegetal colectiva de &#243rgano (Spanish, exact) 集合植物器官構造 (Japanese, exact) plant_anatomy PO:0025007 Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. collective plant organ structure A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). POC:curators estructura vegetal colectiva de &#243rgano (Spanish, exact) POC:Maria_Alejandra_Gandolfo 集合植物器官構造 (Japanese, exact) NIG:Yukiko_Yamazaki A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof. rwalls 2010-07-01T02:11:26Z root (broad) PO_GIT:136 sistema de ra&#237z (Spanish, exact) 根系 (Japanese, exact) plant_anatomy PO:0025025 Generally the below ground portion of a vascular plant. root system A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof. POC:Laurel_Cooper POC:curators root (broad) FNA:b7ce680b-c6ed-4d2e-81e6-66970f7deff9 sistema de ra&#237z (Spanish, exact) POC:Maria_Alejandra_Gandolfo 根系 (Japanese, exact) NIG:Yukiko_Yamazaki A plant axis (PO:0025004) that is part of a shoot system (PO:0009006). rwalls 2010-07-01T03:46:35Z caullome (exact) eje del epiblasto (epiblastema) (Spanish, exact) シュート軸 (Japanese, exact) plant_anatomy shoot (related) PO:0025029 Often bears leaves and branches. In vascular plants, has at least one node and one internode. shoot axis A plant axis (PO:0025004) that is part of a shoot system (PO:0009006). POC:curators eje del epiblasto (epiblastema) (Spanish, exact) POC:Maria_Alejandra_Gandolfo シュート軸 (Japanese, exact) NIG:Yukiko_Yamazaki A phyllome (PO:0006001) that is not associated with a reproductive structure. rwalls 2010-07-12T01:31:44Z PO_GIT:274 PO_GIT:301 hoja (Spanish, exact) 葉 (Japanese, exact) plant_anatomy PO:0025034 leaf A phyllome (PO:0006001) that is not associated with a reproductive structure. POC:curators hoja (Spanish, exact) POC:Maria_Alejandra_Gandolfo 葉 (Japanese, exact) NIG:Yukiko_Yamazaki A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). rwalls 2010-11-15T09:10:22Z PO_GIT:186 portion of primordial tissue (exact) portion of primordium tissue (exact) primordia (exact, plural) primordio (Spanish, exact) 原基（可視的） (Japanese, exact) plant_anatomy PO:0025127 A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. primordium A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). POC:curators primordio (Spanish, exact) POC:Maria_Alejandra_Gandolfo 原基（可視的） (Japanese, exact) NIG:Yukiko_Yamazaki A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001). rwalls 2010-11-15T09:27:11Z PO_GIT:466 phyllome primordia (exact, plural) portion of phyllome primordium tissue (exact) primordio del filoma (Spanish, exact) フィロム原基（可視的） (Japanese, exact) plant_anatomy PO:0025128 The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop. phyllome primordium A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001). PMID:11572953 POC:curators primordio del filoma (Spanish, exact) POC:Maria_Alejandra_Gandolfo フィロム原基（可視的） (Japanese, exact) NIG:Yukiko_Yamazaki An anatomical entity that is or was part of a plant. rwalls 2010-11-15T11:41:38Z PO_GIT:224 entidad anat&#243mica vegetal (Spanish, exact) 植物 解剖学（形態）的実体 (Japanese, exact) plant_anatomy PO:0025131 Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. plant anatomical entity cjm An anatomical entity that is or was part of a plant. BFO:0000004 CARO:0000000 POC:curators entidad anat&#243mica vegetal (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物 解剖学（形態）的実体 (Japanese, exact) NIG:Yukiko_Yamazaki Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. CAROC:Brownsville2014 A maximal whole plant development stage. rwalls 2011-10-19T10:54:37Z PO_GIT:230 vida de la planta entera (Spanish, exact) 植物体の一生 (Japanese, exact) plant_structure_development_stage PO:0025337 There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage. life of whole plant stage A maximal whole plant development stage. POC:curators vida de la planta entera (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物体の一生 (Japanese, exact) NIG:Yukiko_Yamazaki A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128). Laurel_Cooper 2012-02-07T08:20:10Z phyllome meristem (broad) PO_GIT:427 フィロム原基 (Japanese, exact) plant_anatomy PO:0025430 The phyllome anlagen is only detectable by gene expression, not morphology. phyllome anlagen A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128). POC:Laurel_Cooper POC:curators フィロム原基 (Japanese, exact) NIG:Yukiko_Yamazaki A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029). Laurel_Cooper 2012-02-08T01:00:56Z PO_GIT:427 precursor de ra&#237 (Spanish, exact) 根原基 (Japanese, exact) plant_anatomy PO:0025433 Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042). root anlagen A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029). POC:curators precursor de ra&#237 (Spanish, exact) POC:Maria_Alejandra_Gandolfo 根原基 (Japanese, exact) NIG:Yukiko_Yamazaki A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. Laurel_Cooper 2012-06-11T14:57:00Z PO_GIT:480 estructura vegetal con m&#250ltiples tejidos (Spanish, exact) 複数の組織からなる植物構造 (Japanese, exact) plant_anatomy PO:0025496 Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. multi-tissue plant structure A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. CARO:0000055 POC:curators estructura vegetal con m&#250ltiples tejidos (Spanish, exact) POC:Maria_Alejandra_Gandolfo 複数の組織からなる植物構造 (Japanese, exact) NIG:Yukiko_Yamazaki A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). Laurel_Cooper 2012-06-11T15:09:20Z PO_GIT:479 estructura vegetal colectiva (Spanish, exact) 集合的植物構造 (Japanese, exact) plant_anatomy PO:0025497 This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). collective plant structure A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). POC:curators estructura vegetal colectiva (Spanish, exact) POC:Maria_Alejandra_Gandolfo 集合的植物構造 (Japanese, exact) NIG:Yukiko_Yamazaki A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). Laurel_Cooper 2014-05-13T16:51:47Z PO_GIT:586 plant_anatomy PO:0025606 A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). native plant cell A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). POC:Laurel_Cooper A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death. rwalls 2010-07-15T02:56:11Z PO_GIT:139 PO_GIT:68 fase esporof&#237tica (Spanish, exact) sporophytic development stage (exact) sporophytic phase (exact) sporphyte phase (exact) 胞子体発生過程 (Japanese, exact) plant_structure_development_stage PO:0028002 A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis. sporophyte development stage A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death. POC:curators fase esporof&#237tica (Spanish, exact) POC:Maria_Alejandra_Gandolfo 胞子体発生過程 (Japanese, exact) NIG:Yukiko_Yamazaki An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein protein PR:000000001 The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. PRO:DAN PRO:WCB natural protein PRO:DAN native protein IEDB:BP A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. IUPHARobj:2764 PIRSF:PIRSF016630 B-lymphocyte surface antigen B4 CD19 T-cell surface antigen Leu-12 differentiation antigen CD19 protein PR:000001002 Category=gene. Requested by=CL. CD19 molecule A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. PMID:15778510 CD19 PRO:DNx A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. PIRSF:PIRSF028749 CD34 hematopoietic progenitor cell antigen CD34 protein PR:000001003 Category=gene. Requested by=CL. CD34 molecule A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. PMID:16720896 PMID:8983065 CD34 PRO:DNx A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. PIRSF:PIRSF001977 CD4 T-cell differentiation antigen L3T4 T-cell surface antigen T4/Leu-3 T-cell surface glycoprotein CD4 protein PR:000001004 Category=gene. Requested by=CL. CD4 molecule A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. PMID:15326605 CD4 PRO:DNx An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage. PIRSF:PIRSF002497 integrin alpha with I domain protein PR:000001005 Category=family. integrin alpha with A domain An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage. PIRSF:PIRSF002497 An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. IUPHARobj:2452 CD11 antigen-like family member B CD11b CR-3 alpha chain ITGAM cell surface glycoprotein MAC-1 subunit alpha leukocyte adhesion receptor MO1 neutrophil adherence receptor protein CD11B CR3A PR:000001012 Category=gene. Requested by=CL. integrin alpha-M An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. UniProtKB:P11215 ITGAM PRO:DNx CD11B CR3A A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. PIRSF:PIRSF001993 CD3 subunit with Ig-like domain protein PR:000001018 Category=family. CD3 subunit with immunoglobulin domain A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. PMID:16473826 PMID:1724736 A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. IUPHARobj:2742 CD3E CD3e T-cell surface antigen T3/Leu-4 epsilon chain protein T3E PR:000001020 Category=gene. Requested by=CL. CD3 epsilon A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. PRO:CNA CD3E PRO:DNx T3E A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain. PIRSF:PIRSF002507 protein PR:000001022 Category=family. neural cell adhesion molecule A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain. PRO:CNA A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration. PIRSF:PIRSF501037 protein PR:000001023 Category=family. neural cell adhesion molecule NCAM A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration. PMID:17975827 A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. IUPHARobj:2769 CD56 N-CAM-1 NCAM-1 NCAM1 protein NCAM PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. PRO:CNA NCAM1 PRO:DNx NCAM A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. IUPHARobj:2600 PIRSF:PIRSF001984 CD2 LFA-2 LFA-3 receptor T-cell surface antigen CD2 T-cell surface antigen T11/Leu-5 T-cell surface glycoprotein CD2 erythrocyte receptor ly-37 lymphocyte antigen 37 rosette receptor protein SRBC PR:000001083 Category=gene. Requested by=CL. CD2 molecule A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. PRO:CNA CD2 PRO:DNx SRBC A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. CD8A CD8a T-cell surface glycoprotein Lyt-2 T-lymphocyte differentiation antigen T8/Leu-2 protein Lyt-2 Lyt2 MAL PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. PMID:11114424 PRO:CNA Wikipedia:CD8 CD8A PRO:DNx Lyt-2 Lyt2 MAL A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. IUPHARobj:2628 PIRSF:PIRSF001995 B-cell differentiation antigen Ly-44 B-cell surface antigen CD20 B-lymphocyte antigen CD20 B-lymphocyte surface antigen B1 Bp35 MS4A1 leukocyte surface antigen Leu-16 lymphocyte antigen 44 protein CD20 Ly-44 Ms4a2 PR:000001289 Category=gene. Requested by=CL. membrane-spanning 4-domains subfamily A member 1 A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. PRO:WCB MS4A1 PRO:DNx CD20 Ly-44 Ms4a2 A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues. PIRSF:PIRSF002504 protein PR:000001327 Category=family. cadherin A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues. PRO:WCB A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. 7B4 antigen CD144 CDH5 VE-cadherin vascular endothelial cadherin protein PR:000001444 Category=gene. Requested by=CL. cadherin-5 A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. PRO:WCB CDH5 PRO:DNx A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. CD5 Lyt-1 ly-1 lymphocyte antigen 1 lymphocyte antigen T1/Leu-1 protein LEU1 PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. PRO:WCB CD5 PRO:DNx LEU1 A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. IUPHARobj:1698 PIRSF:PIRSF001960 CD127 CDw127 IL-7 receptor subunit alpha IL-7R subunit alpha IL-7R-alpha IL-7RA IL7R protein PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. PRO:WCB IL7R PRO:DNx A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. PIRSF:PIRSF002017 CD14 monocyte differentiation antigen CD14 myeloid cell-specific leucine-rich glycoprotein protein PR:000001889 Category=gene. Requested by=CL. CD14 molecule A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. PRO:WCB CD14 PRO:DNx A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. p90 CD71 T9 TFRC TfR TfR1 protein TR Trfr PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. PRO:WCB p90 PRO:DNx TFRC PRO:DNx Trfr A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein PR:000001971 Category=family. vascular endothelial growth factor receptor A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PRO:WCB A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. IUPHARobj:1813 CD309 FLK-1 KDR VEGFR-2 fetal liver kinase 1 kinase NYK kinase insert domain receptor protein-tyrosine kinase receptor flk-1 protein FLK1 VEGFR2 PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. PRO:WCB KDR PRO:DNx FLK1 VEGFR2 A protein that is the translation product of any of the LY6 genes (LY6A-LY6I). PIRSF:PIRSF002021 protein PR:000002976 Category=family. Ly-6-like protein A protein that is the translation product of any of the LY6 genes (LY6A-LY6I). PRO:CNA An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. Ly-6G Ly-6G.1 Ly6g protein PR:000002978 Category=gene. Requested by=CL. lymphocyte antigen 6G An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. PRO:CNA Ly6g PRO:DNx A protein that is a translation product of the Ly76 gene in mouse. mLy76 ter-119 ter119 protein PR:000002981 Category=organism-gene. Requested by=CL. lymphocyte antigen 76 (mouse) A protein that is a translation product of the Ly76 gene in mouse. PMID:10848813 PRO:DAN mLy76 PRO:DNx A protein that is a translation product of the human FGF8 gene or a 1:1 ortholog thereof. FGF-8 FGF8 androgen-induced growth factor protein AIGF HBGF-8 heparin-binding growth factor 8 PR:000007499 Category=gene. fibroblast growth factor 8 A protein that is a translation product of the human FGF8 gene or a 1:1 ortholog thereof. PRO:DNx FGF8 PRO:DNx AIGF An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof. insulin INS protein PR:000009054 Category=gene. insulin gene translation product An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof. PRO:DNx insulin PRO:DAN INS PRO:DNx A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof. HHG-1 SHH Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains ShhNC protein Hhg1 PR:000014841 Category=gene. sonic hedgehog protein A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof. PRO:DNx SHH PRO:DNx Hhg1 A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. T-cell leukemia/lymphoma protein 5 TAL-1 TAL1 bHLHa17 class A basic helix-loop-helix protein 17 stem cell protein protein BHLHA17 SCL TCL5 PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. PRO:DNx TAL1 PRO:DNx BHLHA17 SCL TCL5 2 An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. peptide polypeptide protein PR:000018263 Category=polymer. amino acid chain An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. PRO:DAN PRO:JSG peptide PRO:DAN polypeptide PRO:DAN A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif. protein PR:000025796 Category=family. Integrins are heterodimeric complexes of an alpha and a beta subunit. They are a structurally elaborate family of adhesion molecules that transmit signals bidirectionally across the plasma membrane by undergoing large-scale structural rearrangements. By regulating cell-cell and cell-matrix contacts, integrins participate in a wide-range of biological interactions including development, tissue repair, angiogenesis, inflammation and hemostasis. [PMID:10402956, PMID:11988479, PMID:9676575]. integrin alpha A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif. PMID:19693543 A protein that is encoded in the genome of Mus musculus. mouse protein protein PR:000029032 Mus musculus protein A protein that is encoded in the genome of Mus musculus. PRO:DAN mouse protein PRO:DAN A protein that is encoded in the genome of Homo sapiens. human protein protein PR:000029067 Homo sapiens protein A protein that is encoded in the genome of Homo sapiens. PRO:DAN human protein PRO:DAN A protein that is encoded in the genome of some Eukaryota. Eukaryota protein protein PR:000036194 eukaryotic protein A protein that is encoded in the genome of some Eukaryota. PRO:DAN Eukaryota protein PRO:DAN A protein that is a translation product of a gene that encodes a standalone Insulin (Pfam:PF00049) domain preceded by a signal peptide. fam:INS protein PR:000045358 Category=family. insulin family protein A protein that is a translation product of a gene that encodes a standalone Insulin (Pfam:PF00049) domain preceded by a signal peptide. PRO:DAN fam:INS PRO:DAN A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein PR:000050567 Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). protein-containing material entity A material entity that minimally consists of a protein. PRO:DAN protein PRO:DAN protein aggregate PRO:DAN protein complex PRO:DAN protein-containing complex PRO:DAN An insulin gene translation product that is encoded in the genome of human. UniProtKB:P01308 hINS protein PR:P01308 Category=organism-gene. insulin gene translation product (human) An insulin gene translation product that is encoded in the genome of human. PRO:DAN UniProtKB:P01308 hINS PRO:DNx A CD4 molecule that is encoded in the genome of human. UniProtKB:P01730 T-cell surface antigen T4/Leu-3 (human) hCD4 protein CD4 PR:P01730 Category=organism-gene. T-cell surface glycoprotein CD4 (human) A CD4 molecule that is encoded in the genome of human. PRO:DNx UniProtKB:P01730 T-cell surface antigen T4/Leu-3 (human) UniProtKB:P01730 hCD4 PRO:DNx CD4 UniProtKB:P01730 A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse. UniProtKB:P01731 CD8a (mouse) T-cell surface glycoprotein Lyt-2 (mouse) mCD8A protein Cd8a Lyt-2 Lyt2 PR:P01731 Category=organism-gene. T-cell surface glycoprotein CD8 alpha chain (mouse) A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse. OMA:P01731 PRO:DNx CD8a (mouse) UniProtKB:P01731 T-cell surface glycoprotein Lyt-2 (mouse) UniProtKB:P01731 mCD8A PRO:DNx Cd8a UniProtKB:P01731 Lyt-2 UniProtKB:P01731 Lyt2 UniProtKB:P01731 A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human. UniProtKB:P01732 CD8a (human) T-lymphocyte differentiation antigen T8/Leu-2 (human) hCD8A protein CD8A MAL PR:P01732 Category=organism-gene. T-cell surface glycoprotein CD8 alpha chain (human) A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human. PRO:CNA UniProtKB:P01732 CD8a (human) UniProtKB:P01732 T-lymphocyte differentiation antigen T8/Leu-2 (human) UniProtKB:P01732 hCD8A PRO:DNx CD8A UniProtKB:P01732 MAL UniProtKB:P01732 A transferrin receptor protein 1 that is encoded in the genome of human. TR (human) p90 (human) Reactome:R-HSA-434196 Reactome:R-HSA-434330 Reactome:R-HSA-8869124 Reactome:R-HSA-8961829 Reactome:R-HSA-917983 UniProtKB:P02786 CD71 (human) T9 (human) TfR (human) TfR1 (human) Trfr (human) hTFRC protein TFRC PR:P02786 Category=organism-gene. transferrin receptor protein 1 (human) A transferrin receptor protein 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P02786 TR (human) UniProtKB:P02786 p90 (human) UniProtKB:P02786 Reactome:R-HSA-434196 PR:P02786 located_in GO:0030659 Reactome:R-HSA-434330 PR:P02786 located_in GO:0000139 Reactome:R-HSA-8869124 PR:P02786 located_in GO:0030665 Reactome:R-HSA-8961829 PR:P02786 located_in GO:0010008 Reactome:R-HSA-917983 PR:P02786 located_in GO:0005886 CD71 (human) UniProtKB:P02786 T9 (human) UniProtKB:P02786 TfR (human) UniProtKB:P02786 TfR1 (human) UniProtKB:P02786 Trfr (human) UniProtKB:P02786 hTFRC PRO:DNx TFRC UniProtKB:P02786 An integrin alpha-M that is encoded in the genome of mouse. UniProtKB:P05555 CD11 antigen-like family member B (mouse) CD11b (mouse) CR-3 alpha chain (mouse) cell surface glycoprotein MAC-1 subunit alpha (mouse) leukocyte adhesion receptor MO1 (mouse) mITGAM protein Itgam PR:P05555 Category=organism-gene. integrin alpha-M (mouse) An integrin alpha-M that is encoded in the genome of mouse. PRO:DNx UniProtKB:P05555 CD11 antigen-like family member B (mouse) UniProtKB:P05555 CD11b (mouse) UniProtKB:P05555 CR-3 alpha chain (mouse) UniProtKB:P05555 cell surface glycoprotein MAC-1 subunit alpha (mouse) UniProtKB:P05555 leukocyte adhesion receptor MO1 (mouse) UniProtKB:P05555 mITGAM PRO:DNx Itgam UniProtKB:P05555 A T-cell surface glycoprotein CD5 that is encoded in the genome of human. UniProtKB:P06127 hCD5 lymphocyte antigen T1/Leu-1 (human) protein CD5 LEU1 PR:P06127 Category=organism-gene. T-cell surface glycoprotein CD5 (human) A T-cell surface glycoprotein CD5 that is encoded in the genome of human. PRO:WCB UniProtKB:P06127 hCD5 PRO:DNx lymphocyte antigen T1/Leu-1 (human) UniProtKB:P06127 CD5 UniProtKB:P06127 LEU1 UniProtKB:P06127 A CD4 molecule that is encoded in the genome of mouse. UniProtKB:P06332 CD4 (mouse) T-cell differentiation antigen L3T4 (mouse) T-cell surface antigen T4/Leu-3 (mouse) mCD4 protein Cd4 PR:P06332 Category=organism-gene. T-cell surface glycoprotein CD4 (mouse) A CD4 molecule that is encoded in the genome of mouse. OMA:P06332 PRO:DNx CD4 (mouse) UniProtKB:P06332 T-cell differentiation antigen L3T4 (mouse) UniProtKB:P06332 T-cell surface antigen T4/Leu-3 (mouse) UniProtKB:P06332 mCD4 PRO:DNx Cd4 UniProtKB:P06332 A CD2 molecule that is encoded in the genome of human. UniProtKB:P06729 LFA-2 (human) LFA-3 receptor (human) T-cell surface antigen T11/Leu-5 (human) erythrocyte receptor (human) hCD2 rosette receptor (human) protein CD2 SRBC PR:P06729 Category=organism-gene. T-cell surface antigen CD2 (human) A CD2 molecule that is encoded in the genome of human. PRO:CNA UniProtKB:P06729 LFA-2 (human) UniProtKB:P06729 LFA-3 receptor (human) UniProtKB:P06729 T-cell surface antigen T11/Leu-5 (human) UniProtKB:P06729 erythrocyte receptor (human) UniProtKB:P06729 hCD2 PRO:DNx rosette receptor (human) UniProtKB:P06729 CD2 UniProtKB:P06729 SRBC UniProtKB:P06729 A CD3 epsilon that is encoded in the genome of human. UniProtKB:P07766 CD3e (human) T-cell surface antigen T3/Leu-4 epsilon chain (human) hCD3E protein CD3E T3E PR:P07766 Category=organism-gene. T-cell surface glycoprotein CD3 epsilon chain (human) A CD3 epsilon that is encoded in the genome of human. PRO:CNA UniProtKB:P07766 CD3e (human) UniProtKB:P07766 T-cell surface antigen T3/Leu-4 epsilon chain (human) UniProtKB:P07766 hCD3E PRO:DNx CD3E UniProtKB:P07766 T3E UniProtKB:P07766 A CD14 molecule that is encoded in the genome of human. UniProtKB:P08571 hCD14 myeloid cell-specific leucine-rich glycoprotein (human) protein CD14 PR:P08571 Category=organism-gene. monocyte differentiation antigen CD14 (human) A CD14 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P08571 hCD14 PRO:DNx myeloid cell-specific leucine-rich glycoprotein (human) UniProtKB:P08571 CD14 UniProtKB:P08571 A CD2 molecule that is encoded in the genome of mouse. UniProtKB:P08920 CD2 (mouse) LFA-2 (mouse) LFA-3 receptor (mouse) T-cell surface antigen T11/Leu-5 (mouse) lymphocyte antigen 37 (mouse) mCD2 protein Cd2 Ly-37 PR:P08920 Category=organism-gene. T-cell surface antigen CD2 (mouse) A CD2 molecule that is encoded in the genome of mouse. OMA:P08920 PRO:DNx CD2 (mouse) UniProtKB:P08920 LFA-2 (mouse) UniProtKB:P08920 LFA-3 receptor (mouse) UniProtKB:P08920 T-cell surface antigen T11/Leu-5 (mouse) UniProtKB:P08920 lymphocyte antigen 37 (mouse) UniProtKB:P08920 mCD2 PRO:DNx Cd2 UniProtKB:P08920 Ly-37 UniProtKB:P08920 A CD14 molecule that is encoded in the genome of mouse. UniProtKB:P10810 CD14 (mouse) mCD14 myeloid cell-specific leucine-rich glycoprotein (mouse) protein Cd14 PR:P10810 Category=organism-gene. monocyte differentiation antigen CD14 (mouse) A CD14 molecule that is encoded in the genome of mouse. OMA:P10810 PRO:WCB CD14 (mouse) UniProtKB:P10810 mCD14 PRO:DNx myeloid cell-specific leucine-rich glycoprotein (mouse) UniProtKB:P10810 Cd14 UniProtKB:P10810 An integrin alpha-M that is encoded in the genome of human. UniProtKB:P11215 CD11 antigen-like family member B (human) CR-3 alpha chain (human) cell surface glycoprotein MAC-1 subunit alpha (human) hITGAM leukocyte adhesion receptor MO1 (human) neutrophil adherence receptor (human) protein CD11B CR3A ITGAM PR:P11215 Category=organism-gene. integrin alpha-M (human) An integrin alpha-M that is encoded in the genome of human. PRO:DNx UniProtKB:P11215 CD11 antigen-like family member B (human) UniProtKB:P11215 CR-3 alpha chain (human) UniProtKB:P11215 cell surface glycoprotein MAC-1 subunit alpha (human) UniProtKB:P11215 hITGAM PRO:DNx leukocyte adhesion receptor MO1 (human) UniProtKB:P11215 neutrophil adherence receptor (human) UniProtKB:P11215 CD11B UniProtKB:P11215 CR3A UniProtKB:P11215 ITGAM UniProtKB:P11215 A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of human. UniProtKB:P11836 B-lymphocyte surface antigen B1 (human) Bp35 (human) hMS4A1 leukocyte surface antigen Leu-16 (human) membrane-spanning 4-domains subfamily A member 1 (human) protein CD20 MS4A1 PR:P11836 Category=organism-gene. B-lymphocyte antigen CD20 (human) A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P11836 B-lymphocyte surface antigen B1 (human) UniProtKB:P11836 Bp35 (human) UniProtKB:P11836 hMS4A1 PRO:DNx leukocyte surface antigen Leu-16 (human) UniProtKB:P11836 membrane-spanning 4-domains subfamily A member 1 (human) UniProtKB:P11836 CD20 UniProtKB:P11836 MS4A1 UniProtKB:P11836 A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse. UniProtKB:P13379 CD5 (mouse) Lyt-1 (mouse) lymphocyte antigen 1 (mouse) mCD5 protein Cd5 Ly-1 PR:P13379 Category=organism-gene. T-cell surface glycoprotein CD5 (mouse) A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse. OMA:P13379 PRO:DNx CD5 (mouse) UniProtKB:P13379 Lyt-1 (mouse) UniProtKB:P13379 lymphocyte antigen 1 (mouse) UniProtKB:P13379 mCD5 PRO:DNx Cd5 UniProtKB:P13379 Ly-1 UniProtKB:P13379 A neural cell adhesion molecule 1 that is encoded in the genome of human. UniProtKB:P13591 CD56 (human) N-CAM-1 (human) NCAM-1 (human) hNCAM1 protein NCAM NCAM1 PR:P13591 Category=organism-gene. neural cell adhesion molecule 1 (human) A neural cell adhesion molecule 1 that is encoded in the genome of human. PRO:CNA UniProtKB:P13591 CD56 (human) UniProtKB:P13591 N-CAM-1 (human) UniProtKB:P13591 NCAM-1 (human) UniProtKB:P13591 hNCAM1 PRO:DNx NCAM UniProtKB:P13591 NCAM1 UniProtKB:P13591 A neural cell adhesion molecule 1 that is encoded in the genome of mouse. UniProtKB:P13595 CD56 (mouse) N-CAM-1 (mouse) NCAM-1 (mouse) mNCAM1 protein Ncam Ncam1 PR:P13595 Category=organism-gene. neural cell adhesion molecule 1 (mouse) A neural cell adhesion molecule 1 that is encoded in the genome of mouse. OMA:P13595 PRO:DNx CD56 (mouse) UniProtKB:P13595 N-CAM-1 (mouse) UniProtKB:P13595 NCAM-1 (mouse) UniProtKB:P13595 mNCAM1 PRO:DNx Ncam UniProtKB:P13595 Ncam1 UniProtKB:P13595 A CD19 molecule that is encoded in the genome of human. UniProtKB:P15391 B-lymphocyte surface antigen B4 (human) T-cell surface antigen Leu-12 (human) differentiation antigen CD19 (human) hCD19 protein CD19 PR:P15391 Category=organism-gene. B-lymphocyte antigen CD19 (human) B-lymphocyte surface antigen B4 (human) UniProtKB:P15391 T-cell surface antigen Leu-12 (human) UniProtKB:P15391 differentiation antigen CD19 (human) UniProtKB:P15391 hCD19 PRO:DNx CD19 UniProtKB:P15391 An interleukin-7 receptor subunit alpha that is encoded in the genome of human. UniProtKB:P16871 CD127 (human) CDw127 (human) IL-7 receptor subunit alpha (human) IL-7R subunit alpha (human) IL-7R-alpha (human) IL-7RA (human) hIL7R protein IL7R PR:P16871 Category=organism-gene. interleukin-7 receptor subunit alpha (human) An interleukin-7 receptor subunit alpha that is encoded in the genome of human. PRO:WCB UniProtKB:P16871 CD127 (human) UniProtKB:P16871 CDw127 (human) UniProtKB:P16871 IL-7 receptor subunit alpha (human) UniProtKB:P16871 IL-7R subunit alpha (human) UniProtKB:P16871 IL-7R-alpha (human) UniProtKB:P16871 IL-7RA (human) UniProtKB:P16871 hIL7R PRO:DNx IL7R UniProtKB:P16871 An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse. UniProtKB:P16872 CD127 (mouse) IL-7 receptor subunit alpha (mouse) IL-7R subunit alpha (mouse) IL-7R-alpha (mouse) IL-7RA (mouse) mIL7R protein Il7r PR:P16872 Category=organism-gene. interleukin-7 receptor subunit alpha (mouse) An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse. OMA:P16872 PRO:DNx CD127 (mouse) UniProtKB:P16872 IL-7 receptor subunit alpha (mouse) UniProtKB:P16872 IL-7R subunit alpha (mouse) UniProtKB:P16872 IL-7R-alpha (mouse) UniProtKB:P16872 IL-7RA (mouse) UniProtKB:P16872 mIL7R PRO:DNx Il7r UniProtKB:P16872 A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human. Reactome:R-HSA-8956511 UniProtKB:P17542 Stem cell protein (human) T-cell leukemia/lymphoma protein 5 (human) TAL-1 (human) class A basic helix-loop-helix protein 17 (human) hTAL1 protein BHLHA17 SCL TAL1 TCL5 PR:P17542 Category=organism-gene. T-cell acute lymphocytic leukemia protein 1 (human) A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human. PRO:DNx UniProtKB:P17542 Reactome:R-HSA-8956511 PR:P17542 located_in GO:0005654 Stem cell protein (human) UniProtKB:P17542 T-cell leukemia/lymphoma protein 5 (human) UniProtKB:P17542 TAL-1 (human) UniProtKB:P17542 class A basic helix-loop-helix protein 17 (human) UniProtKB:P17542 hTAL1 PRO:DNx BHLHA17 UniProtKB:P17542 SCL UniProtKB:P17542 TAL1 UniProtKB:P17542 TCL5 UniProtKB:P17542 A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse. UniProtKB:P19437 B-cell differentiation antigen Ly-44 (mouse) CD20 (mouse) lymphocyte antigen 44 (mouse) mMS4A1 membrane-spanning 4-domains subfamily A member 1 (mouse) protein Cd20 Ly-44 Ms4a1 Ms4a2 PR:P19437 Category=organism-gene. B-lymphocyte antigen CD20 (mouse) A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse. OMA:P19437 PRO:DNx B-cell differentiation antigen Ly-44 (mouse) UniProtKB:P19437 CD20 (mouse) UniProtKB:P19437 lymphocyte antigen 44 (mouse) UniProtKB:P19437 mMS4A1 PRO:DNx membrane-spanning 4-domains subfamily A member 1 (mouse) UniProtKB:P19437 Cd20 UniProtKB:P19437 Ly-44 UniProtKB:P19437 Ms4a1 UniProtKB:P19437 Ms4a2 UniProtKB:P19437 A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse. UniProtKB:P22091 Stem cell protein (mouse) TAL-1 (mouse) mTAL1 protein Scl Tal-1 Tal1 PR:P22091 Category=organism-gene. T-cell acute lymphocytic leukemia protein 1 homolog (mouse) A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse. OMA:P22091 PRO:DNx Stem cell protein (mouse) UniProtKB:P22091 TAL-1 (mouse) UniProtKB:P22091 mTAL1 PRO:DNx Scl UniProtKB:P22091 Tal-1 UniProtKB:P22091 Tal1 UniProtKB:P22091 A CD3 epsilon that is encoded in the genome of mouse. UniProtKB:P22646 CD3e (mouse) T-cell surface antigen T3/Leu-4 epsilon chain (mouse) mCD3E protein Cd3e PR:P22646 Category=organism-gene. T-cell surface glycoprotein CD3 epsilon chain (mouse) A CD3 epsilon that is encoded in the genome of mouse. OMA:P22646 PRO:DNx CD3e (mouse) UniProtKB:P22646 T-cell surface antigen T3/Leu-4 epsilon chain (mouse) UniProtKB:P22646 mCD3E PRO:DNx Cd3e UniProtKB:P22646 A CD19 molecule that is encoded in the genome of mouse. UniProtKB:P25918 CD19 (mouse) differentiation antigen CD19 (mouse) mCD19 protein Cd19 PR:P25918 Category=organism-gene. B-lymphocyte antigen CD19 (mouse) A CD19 molecule that is encoded in the genome of mouse. OMA:P25918 PRO:DNx CD19 (mouse) UniProtKB:P25918 differentiation antigen CD19 (mouse) UniProtKB:P25918 mCD19 PRO:DNx Cd19 UniProtKB:P25918 A CD34 molecule that is encoded in the genome of human. UniProtKB:P28906 hCD34 protein CD34 PR:P28906 Category=organism-gene. hematopoietic progenitor cell antigen CD34 (human) hCD34 PRO:DNx CD34 UniProtKB:P28906 A cadherin-5 that is encoded in the genome of human. UniProtKB:P33151 7B4 antigen (human) CD144 (human) VE-cadherin (human) hCDH5 vascular endothelial cadherin (human) protein CDH5 PR:P33151 Category=organism-gene. cadherin-5 (human) A cadherin-5 that is encoded in the genome of human. PRO:WCB UniProtKB:P33151 7B4 antigen (human) UniProtKB:P33151 CD144 (human) UniProtKB:P33151 VE-cadherin (human) UniProtKB:P33151 hCDH5 PRO:DNx vascular endothelial cadherin (human) UniProtKB:P33151 CDH5 UniProtKB:P33151 A lymphocyte antigen 6G that is encoded in the genome of mouse. UniProtKB:P35461 Ly-6G (mouse) Ly-6G.1 (mouse) mLy6g protein Ly6g PR:P35461 Category=organism-gene. lymphocyte antigen 6G (mouse) A lymphocyte antigen 6G that is encoded in the genome of mouse. PRO:CNA UniProtKB:P35461 Ly-6G (mouse) UniProtKB:P35461 Ly-6G.1 (mouse) UniProtKB:P35461 mLy6g PRO:DNx Ly6g UniProtKB:P35461 A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse. UniProtKB:P35918 CD309 (mouse) FLK-1 (mouse) VEGFR-2 (mouse) fetal liver kinase 1 (mouse) kinase NYK (mouse) mKDR protein-tyrosine kinase receptor flk-1 (mouse) protein Flk-1 Flk1 Kdr PR:P35918 Category=organism-gene. vascular endothelial growth factor receptor 2 (mouse) A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse. OMA:P35918 PRO:DNx CD309 (mouse) UniProtKB:P35918 FLK-1 (mouse) UniProtKB:P35918 VEGFR-2 (mouse) UniProtKB:P35918 fetal liver kinase 1 (mouse) UniProtKB:P35918 kinase NYK (mouse) UniProtKB:P35918 mKDR PRO:DNx protein-tyrosine kinase receptor flk-1 (mouse) UniProtKB:P35918 Flk-1 UniProtKB:P35918 Flk1 UniProtKB:P35918 Kdr UniProtKB:P35918 A vascular endothelial growth factor receptor 2 that is encoded in the genome of human. DTO:03100560 UniProtKB:P35968 CD309 (human) FLK-1 (human) VEGFR-2 (human) fetal liver kinase 1 (human) hKDR kinase insert domain receptor (human) protein-tyrosine kinase receptor flk-1 (human) protein FLK1 KDR VEGFR2 PR:P35968 Category=organism-gene. vascular endothelial growth factor receptor 2 (human) A vascular endothelial growth factor receptor 2 that is encoded in the genome of human. PRO:WCB UniProtKB:P35968 CD309 (human) UniProtKB:P35968 FLK-1 (human) UniProtKB:P35968 VEGFR-2 (human) UniProtKB:P35968 fetal liver kinase 1 (human) UniProtKB:P35968 hKDR PRO:DNx kinase insert domain receptor (human) UniProtKB:P35968 protein-tyrosine kinase receptor flk-1 (human) UniProtKB:P35968 FLK1 UniProtKB:P35968 KDR UniProtKB:P35968 VEGFR2 UniProtKB:P35968 A fibroblast growth factor 8 that is encoded in the genome of mouse. UniProtKB:P37237 AIGF (mouse) FGF-8 (mouse) androgen-induced growth factor (mouse) mFGF8 protein Aigf Fgf8 HBGF-8 (mouse) heparin-binding growth factor 8 (mouse) PR:P37237 Category=organism-gene. fibroblast growth factor 8 (mouse) A fibroblast growth factor 8 that is encoded in the genome of mouse. OMA:P37237 PRO:DNx AIGF (mouse) UniProtKB:P37237 FGF-8 (mouse) UniProtKB:P37237 androgen-induced growth factor (mouse) UniProtKB:P37237 mFGF8 PRO:DNx Aigf UniProtKB:P37237 Fgf8 UniProtKB:P37237 HBGF-8 (mouse) UniProtKB:P37237 heparin-binding growth factor 8 (mouse) UniProtKB:P37237 A fibroblast growth factor 8 that is encoded in the genome of human. HBGF-8 (human) heparin-binding growth factor 8 (human) UniProtKB:P55075 FGF-8 (human) androgen-induced growth factor (human) hFGF8 protein AIGF FGF8 PR:P55075 Category=organism-gene. fibroblast growth factor 8 (human) A fibroblast growth factor 8 that is encoded in the genome of human. PRO:DNx UniProtKB:P55075 HBGF-8 (human) UniProtKB:P55075 heparin-binding growth factor 8 (human) UniProtKB:P55075 FGF-8 (human) UniProtKB:P55075 androgen-induced growth factor (human) UniProtKB:P55075 hFGF8 PRO:DNx AIGF UniProtKB:P55075 FGF8 UniProtKB:P55075 A cadherin-5 that is encoded in the genome of mouse. UniProtKB:P55284 CD144 (mouse) VE-cadherin (mouse) mCDH5 vascular endothelial cadherin (mouse) protein Cdh5 PR:P55284 Category=organism-gene. cadherin-5 (mouse) A cadherin-5 that is encoded in the genome of mouse. OMA:P55284 PRO:DNx CD144 (mouse) UniProtKB:P55284 VE-cadherin (mouse) UniProtKB:P55284 mCDH5 PRO:DNx vascular endothelial cadherin (mouse) UniProtKB:P55284 Cdh5 UniProtKB:P55284 A sonic hedgehog protein that is encoded in the genome of human. UniProtKB:Q15465 HHG-1 (human) Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (human) ShhNC (human) hSHH protein SHH PR:Q15465 Category=organism-gene. sonic hedgehog protein (human) A sonic hedgehog protein that is encoded in the genome of human. PRO:DNx UniProtKB:Q15465 HHG-1 (human) UniProtKB:Q15465 Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (human) UniProtKB:Q15465 ShhNC (human) UniProtKB:Q15465 hSHH PRO:DNx SHH UniProtKB:Q15465 A sonic hedgehog protein that is encoded in the genome of mouse. UniProtKB:Q62226 HHG-1 (mouse) SHH (mouse) Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (mouse) ShhNC (mouse) mSHH protein Hhg1 Shh PR:Q62226 Category=organism-gene. sonic hedgehog protein (mouse) A sonic hedgehog protein that is encoded in the genome of mouse. OMA:Q62226 PRO:DNx HHG-1 (mouse) UniProtKB:Q62226 SHH (mouse) UniProtKB:Q62226 Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (mouse) UniProtKB:Q62226 ShhNC (mouse) UniProtKB:Q62226 mSHH PRO:DNx Hhg1 UniProtKB:Q62226 Shh UniProtKB:Q62226 A transferrin receptor protein 1 that is encoded in the genome of mouse. UniProtKB:Q62351 CD71 (mouse) TfR (mouse) TfR1 (mouse) mTFRC protein TR (mouse) Tfrc Trfr PR:Q62351 Category=organism-gene. transferrin receptor protein 1 (mouse) A transferrin receptor protein 1 that is encoded in the genome of mouse. OMA:Q62351 PRO:DNx CD71 (mouse) UniProtKB:Q62351 TfR (mouse) UniProtKB:Q62351 TfR1 (mouse) UniProtKB:Q62351 mTFRC PRO:DNx TR (mouse) UniProtKB:Q62351 Tfrc UniProtKB:Q62351 Trfr UniProtKB:Q62351 A CD34 molecule that is encoded in the genome of mouse. UniProtKB:Q64314 CD34 (mouse) mCD34 protein Cd34 PR:Q64314 Category=organism-gene. hematopoietic progenitor cell antigen CD34 (mouse) A CD34 molecule that is encoded in the genome of mouse. OMA:Q64314 PRO:DNx CD34 (mouse) UniProtKB:Q64314 mCD34 PRO:DNx Cd34 UniProtKB:Q64314 Ionizing radiation classified by the material entity which generates or emits it. ionizing radiation categorized by source Radiation originating outside the Earth's atmosphere. space radiation One of the principal sources of ground radiation is radon gas. Radiation produced on Earth or on another planetary body by natural or artificial means. ground radiation Material presenting, when irradiated, interaction properties similar to those of soft tissue. ICRP glossary (http://icrpaedia.org/Tissue_equivalent_material) tissue equivalent material Atomic nuclei, each with 26 protons and 30 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Fe-56 ion radiation Atomic nuclei, each with 6 protons and 6 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator C-12 ion radiation Atomic nuclei, each with 14 protons and 14 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Si-28 ion radiation Atomic nuclei, each with 2 protons and 2 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator He-4 ion radiation Atomic nuclei, each with 10 protons and 10 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Ne-20 ion radiation An atomic nucleus, fully stripped of its orbital electrons, and containing 2, 3, 4, 5, or 6 protons. light ion Ionization chambers and silicon solid state detectors can be used as active dosimeters. A radiation measuring device which records dose at the time of detection, with data available in real time active dosimeter Thermoluminescent dosimeters and plastic nuclear track detectors are passive detectors. A radiation measuring device which integrates the amount of radiation to which it is exposed. Passive detectors are interrogated at a later time to determine the dose. passive dosimeter The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra background ionizing radiation The effective dose was calculated to be 300 mSv. The sum of the equivalent doses to all organs in the body, each adjusted to account for the sensitivity of the organ to radiation. Effective dose is calculated for the whole body. Effective dose is expressed in millisieverts (mSv). effective dose The samples were exposed to a mixed radiation field consisting of several ions at different energies. The process of exposing the same sample to more than one type and/or energy of radiation, in sequence or simultaneously. mixed field|mixed radiation field mixed radiation Radiation classified by where the exposure to the radiation is occurring. radiation environment That part of the Earth exposed to the Earth atmosphere. earth surface The region between the Earth's surface and an altitude of approximately 100 km earth atmosphere LEO The region of outer space between the Earth's atmosphere and the innermost Earth radiation belt LEO low earth orbit BLEO That part of outer space beyond the Earth's radiation belts. BLEO beyond low earth orbit fractionated A radiation dose administered in two or more exposures at specified time intervals fractionated radiation exposure A unit of absorbed dose equal to 1/1000 of a rad mrad millirad The equivalent dose was calculated to be 300 mSv. The product of the mean absorbed dose in an organ or tissue and the radiation weighting factor (w_R )of the radiation type of interest equivalent dose The total dose was administered in five dose fractions. The absorbed radiation dose administered in a single one of a series comprising a fractionated radiation exposure dose fraction Penetrating ionizing radiation, both particulate and electromagnetic, that originates in outer space cosmic radiation Galactic cosmic radiation is one of the principal sources of radiation dose outside low-earth orbit Galactic cosmic radiation consists of high-energy charged particles originating from outside the solar system galactic cosmic radiation Solar cosmic radiation contributes to the radiation dose to humans in space. Solar cosmic radiation is high-energy charged particles that originate from the sun. solar cosmic radiation The dose rate was 0.5 mGy/min. The measurement datum representing a dose to an organism or object per unit time. dose rate The Apollo spacecraft took 24 astronauts to the Moon between 1968 and 1972. Vehicles, crewed or uncrewed, which are designed to orbit about the Earth or another celestial body or be placed into a trajectory to another celestial body or location in space. NASA Thesaurus, 1988 spacecraft a self-contained unit of a spacecraft spacecraft module ISS module The experiment was conducted in the International Space Station module Columbus The experiment was conducted on the Russian module of the ISS. A self-contained unit of the International Space Station. international space station module Mir was a space station that operated in low Earth orbit from 1986 to 2001, operated by the Soviet Union and later by Russia. A spacecraft capable of supporting a human crew in orbit for an extended period of time. It lacks major propulsion or landing systems. Stations must have docking ports to allow other spacecraft to dock to transfer crew and supplies. Wikipedia space station The HIMAC accelerator has a beamline dedicated for radiation biology experiments. The path leading from a particle accelerator to an experimental station used in experiments in particle physics, materials science, chemistry, and molecular biology, or in irradiation tests or to produce isotopes. Wikipedia particle accelerator beamline Radiation produced by a particle accelerator. particle accelerator radiation Radiation produced by a nuclear reactor. nuclear reactor radiation Cs-137 gamma High energy photons emitted during nuclear decay of the Cesium-137 isotope. Cs-137 cesium-137 gamma radiation Co-60 gamma High energy photons emitted during nuclear decay of the Cobalt-60 isotope. Co-60 cobalt-60 gamma radiation Co-57 gamma High energy photons emitted during nuclear decay of the Cobalt-57 isotope. obo:RBO_00000060 Co-57 cobalt-57 gamma radiation Isotopes that exhibit radioactivity and undergo radioactive decay. (From Grant & Hackh's Chemical Dictionary, 5th ed & McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) http://purl.bioontology.org/ontology/MESH/D011868 radionuclide A series of radioactive elements from ACTINIUM, atomic number 89, to and including LAWRENCIUM, atomic number 103 http://purl.bioontology.org/ontology/MESH/D008671 actinide A trivalent radioactive element and the prototypical member of the actinide family. It has the atomic symbol Ac, and atomic number 89. Its principal isotope is 227 and it decays primarily by beta-emission. http://purl.bioontology.org/ontology/MESH/D000186 actinium A completely man-made radioactive actinide with atomic symbol Am, and atomic number 95. Its valence can range from +3 to +6. Because of its nonmagnetic ground state, it is an excellent superconductor. It is also used in bone mineral analysis and as a radiation source for radiotherapy http://purl.bioontology.org/ontology/MESH/D000576 americium A man-made radioactive actinide with atomic symbol Cf, atomic number 98, and atomic weight 251. Its valence can be +2 or +3. Californium has medical use as a radiation source for radiotherapy http://purl.bioontology.org/ontology/MESH/D002142 californium A radioactive element of the actinide metals family. It has the atomic symbol Np, and atomic number 93. http://purl.bioontology.org/ontology/MESH/D009405 neptunium A naturally radioactive element of the actinide metals series. It has the atomic symbol Pu, and atomic number 94. Plutonium is used as a nuclear fuel, to produce radioisotopes for research, in radionuclide batteries for pacemakers, and as the agent of fission in nuclear weapons. http://purl.bioontology.org/ontology/MESH/D011005 plutonium A radioactive element of the actinide series of metals. It has an atomic symbol Th, atomic number 90, and atomic weight 232.04. It is used as fuel in nuclear reactors to produce fissionable uranium isotopes. Because of its radioopacity, various thorium compounds are used to facilitate visualization in roentgenography. http://purl.bioontology.org/ontology/MESH/D013910 thorium A radioactive element of the actinide series of metals. It has an atomic symbol U, atomic number 92, and atomic weight 238.03. U-235 is used as the fissionable fuel in nuclear weapons and as fuel in nuclear power reactors. http://purl.bioontology.org/ontology/MESH/D014501 uranium UV Electromagnetic radiation with photon energies approximately 3-120 eV. High energy UV radiation can be ioinizing. UV radiation http://son.nasa.gov/tass/content/electrospectrum.htm ultraviolet radiation radioprotector E.G. amifostine. A substance present at the time of irradiation that mitigates or prevents the biological effects of irradiation. Richard T. Hoppe, Theodore Locke Phillips, Mack Roach, Leibel and Phillips Textbook of Radiation Oncology (Third Edition), W.B. Saunders, (2010), ISBN 9781416058977, https://doi.org/10.1016/B978-1-4160-5897-7.00093-7. radioprotectant Radionuclide chelators are small organic molecules or in some cases larger peptides that chemically sequester the radionuclide ion by forming a complex that determines the thermodynamic stability and kinetic inertness of the radionuclide. radionuclide chelator A co-carcinogen is generally a chemical that promotes the effects of a carcinogen in the production of cancer. In some circumstances exposure to radiation or physical trauma is considered to be co-carcinogenic. co-carcinogen Radiation response modifiers are agents that alter tumor or normal tissue response to radiation, such as radiation sensitizers and radiation protectors. Citrin DE, Mitchell JB. Altering the response to radiation: sensitizers and protectors. Semin Oncol. 2014 Dec;41(6):848-59. doi: 10.1053/j.seminoncol.2014.09.013. Epub 2014 Oct 7. PMID: 25499642; PMCID: PMC4270009. radiation response modifier Radiation response modifiers that are peptides. Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577 peptide radiation response modifier Radiation response modifiers that are small molecules. small molecule radiation response modifier A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers. Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1 nuclear industry worker astronaut military medical professional dentist radiologist The theme or modality of an experimental, theoretical, critical or summative study involving radiation, radioactive materials including their impacts on orgnisms and society. radiobiology investigation radiobiology study type An epidemiological study is the study (scientific, systematic, and data-driven) of the distribution (frequency, pattern) and determinants (causes, risk factors) of health-related states and events (not just diseases) in specified populations (neighborhood, school, city, state, country, global) https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section1.html epidemiological study A study of the impact of radiation on the composition of or processes within the natural or anthropogenic environment. environmental study A owl:deprecated A study who endpoint is the lifespan of the organism under investifgation. lifespan study A study of the effect of agents including radiation, seperately or together, on the incidence or type of neoplasia or pre-neoplasia. carcinogenesis study A study in which the structural or processual damage to normal tissue caused by radiation is assessed. Often by histopathology or molecular profiling. tissue damage study A study of the mechanism or effects of radiation on dna damage and its repair. dna damage and repair study A study of the effects of internal or external radiation on cellular or organismal physiology. physiological study A study of the effects of radiation on the integrity, composition and quality of adult, fetal or embryonic anatomical structures. anatomical study A study of the effects of external irradiation on an organism. external exposure study A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. internal contamination study A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. mixed exposure route study A study of the effects of external irradiation on an organism where the most of the dose is given in a single or small number of fractions closely in time. acute external exposure study A study of the effects of external irradiation on an organism where the dose is given over a protracted time period either continuously or in many fractions. Often these are lose dose studies. chronic external exposure study A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. The dose is delivered over a long period of time, often continuously and generlly at low dose. For example long term Radon exposure by inhalation. chronic internal contamination study A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. Most of the dose is given over a short period of time and is generally unfractionated, such as in brachytherapy. acute internal contamination study A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. Acute exposure involves usually a single exposure over a short period of time with no fractionation. acute mixed exposure route study A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. Chronic exposure involves usually a continuous or highly fractionated exposure over a long period of time. chronic mixed exposure route study A study of the effects of radiation on gene expression. gene expression study A study of the effects of radiation on the proteome or individual proteins. proteomics study A study that aims at the discovery of protein, RNA or other molecular entities or modifcations that can act as reliable surrogates for the prediction or measurement of the effects of radiation or the response of the organism to radiation. marker discovery study A study that aims at the discovery, development or assessment of efficacy of therapeutic agents or processes designed to mitigate or cure the effects of radiation exposure. therapeutics study A owl:deprecated A study that uses survival as an endpoint. Generally applicable to animal studies rather than human studies which would use the "lifespan" measure (RBO:00000085) survival study A study of the effects of radiation on the metabolome or individual metabolites. metabolomics study A study of the contributing factors consequences and prevention of nuclear accidents nuclear accident study A owl:deprecated A study of the toxicity of chemical or biological agents on cells or whole organisms. toxicity study A study of the effects of radiation on the endocrine system or of endocrine hormones on the effects of radiation. endocrine study A study of the effects of radiation on the offspring of an irradiated animal or plant. transgenerational study offspring study A study of the distribution and metabolism orf drugs or biologicals used for therapeutic purposes. pharmacokinetics biokinetics study A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society. occupational role Neutrons or charged particles, such as protons or alpha particles that produce ionizing events densely spaced on a molecular scale (e.g., >10 keV-micron^[-1]. NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf NCIT:C17052 high linear energy transfer radiation X and gamma rays or light charged particles such as electrons that produce sparse ionizing events far apart on a molecular scale. NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf NCIT:C17052 low LET|low-LET low linear energy transfer radiation Electromagnetic radiation having sufficient energy to remove one or more electrons from an atom ionizing electromagnetic radiation radiation dosimeter A device that is used to measure the amount of ionizing radiation exposure or absorption. radiation dosimeter NCIT NCIT:C150121 dosimeter radiation dosimeter device Particle or electromagnetic radiation with sufficient energy to liberate one or more electrons from an atom. ionising radiation NCIT:C17052 ionising radiation ionizing radiation charged particle Charged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator) charged particle NCIT:C18982 charged particle radiation NCIT:C19015 risk estimate NCIT:C19662 lifetime risk estimate electromagnetic radiation with photon energies greater than approximately 100 keV http://son.nasa.gov/tass/content/electrospectrum.htm NCIT:C44386 gamma radiation A device used to impart kinetic energy to subatomic particles by means of electric and magnetic fields NCIT:C94854 particle accelerator A device in which nuclear fission may be initiated and controlled in a self-sustaining chain reaction to generate energy or produce useful radiation. MESH:D009688 nuclear reactor GO:0008150 biological process owl:deprecated GO:0009987 cellular process owl:deprecated Atomic nuclei, each with 8 protons and 8 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator O-16 ion radiation Atomic nuclei, each with 18 protons and 22 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Ar-40 ion radiation Atomic nuclei, each with 22 protons and 26 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Ti-48 ion radiation Atomic nuclei, each with 36 protons and 48 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Kr-84 ion radiation Atomic nuclei, each with 41 protons and 52 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Nb-93 ion radiation Atomic nuclei, each with 47 protons and 60 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Ag-107 ion radiation Atomic nuclei, each with 54 protons and 75 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Xe-129 ion radiation Atomic nuclei, each with 73 protons and 108 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Ta-181 ion radiation Atomic nuclei, each with 79 protons and 118 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator Au-197 ion radiation Atomic nuclei, each with 7 protons and 7 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator N-14 ion radiation The process by which an entity is exposed to electromagnetic or acoustic radiation radiation energy internally or externally. 0000-0002-5111-7263 Irradiation radiation exposure Unplanned exposure to radiation of any type in any environment or otherwise planned process. 0000-0002-5111-7263 Accidental irradiation accidental radiation exposure Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally or externally. 0000-0002-5111-7263 Planned irradiation planned radiation exposure Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a diagnosis of disease. 0000-0002-5111-7263 Diagnostic irradiation medical diagnostic radiation exposure Exposure to naturally occurring radiation (NORM) of any type in any environment . 0000-0002-5111-7263 Environmental irradiation exposure to naturally ocurring radioactive material Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a cure or mitigation of disease. 0000-0002-5111-7263 Therapeutic irradiation medical therapeutic radiation exposure Unplanned exposure to anthropogenic radiation of any type in any environment ; for example radiation from nuclear waste, nuclear industry discharge or weapons. 0000-0002-5111-7263 Accidental man-made radiation exposure accidental non-medical anthropogenic radiation exposure Exposure to ionising radiation created by a man-made machine or exposure to a fixed source. For example a cobalt source, an X ray machine, an acceleratororf a nucler weapon. 0000-0002-5111-7263 Exposure to human generated radiation anthropogenic radiation exposure Planned exposure to radiation generated through a device or exposure to a source emitting ionising radiation 0000-0002-5111-7263 planned anthropogenic radiation exposure Accidental or incidental exposure to radiation from a man made process or machine. Covers both radiation accidents and routine occupational exposure. 0000-0002-5111-7263 accidental anthropogenic radiation exposure Accidental exposure occurring during medical therapy or diagnostics, for example medical radiation accidents or overdoses. 0000-0002-5111-7263 accidental medical anthropogenic radiation exposure Incidental exposure to naturally occurring radiation in a natural or anthropogenic environment, such as geographical areas with high background levels of radiation or specific locations such as Uranium mines. 0000-0002-5111-7263 unplanned naturally occurring radiation exposure TRUE Deliberate or knowing exposure to naturally occurring radiation in a natural or anthropogenic environment, such as a radon spa. 0000-0002-5111-7263 planned naturally occurring radiation exposure Studies relating to human society and the interrelation of social and educational factors with individual thought and behaviour including mental illness. 0000-0002-5111-7263 social and psychosocial study Studies on the distribution of information or opinion by technological means of communication that reach large numbers of people. 0000-0002-5111-7263 http://purl.biolontology.org/ontology/CSP/1580-0981 mass media study Studies on the civil, legal, and political preparedness for accidental or deliberate release of radioactive materials or radiation into the environment. 0000-0002-5111-7263 preparedness study Studies in which research is conducted with human subjects or on material of human origin in which the investigator directly interacts with human subjects, including the dveelopment of new technologies, understanding of the mechanisms of disease, therapy, clinical trials, epidemiology behaviousrand health services research. 0000-0002-5111-7263 http://purl.bioontology.org/ontology/CSP/4006-0105 clinical study Study of the laws, statutes, ordinances, government or international treaty regulations or authoritative guidelines, as well as for legal controversy and court decisions, relating to the regulation of radiation safety, movement and containment of radioactive materials and the consequences for human health or the natural environment of radioactive contamination. 0000-0002-5111-7263 legal and governance study Studies relating to organisations and processes concerned with freedom from or resilience towards potential harm caused by hostile intent or circumstances (for example terrorism and illegal release of radioactive substances or radiation) towards the natural environment or human population, and the enforcement of relevant laws and international treaties. 0000-0002-5111-7263 security and law enforcement study A study whose intention is to discover knowledge concerning the origins, nature diagnosis or therapy for neoplastic disease and cancer. This includes studies in humans, model organisms, the laboratory and in silico. This class includes experimental and epidemiological studies specifically aimed at cancer. 0000-0002-5111-7263 cancer study The specific manner, characteristic, pattern of application, or the employment of any technology, approach or formal procedure to implement the study plan to generate a study type. 0000-0002-5111-7263 study modality Studies of the presence of radiation of any type in the natural or anthropogenic environment and its impact on animals, plants, and microorganisms. This includes studies measuring nuclide transfer in the environment, and interaction with meteorological phenomena. This excludes occupational exposure and the human working environment. 0000-0002-5111-7263 environmental study Studies concerned with the regulation, monitoring and operation of the nuclear industry. For example nuclear power station and reprocessing plants, isotope purification and manufactore, weapons manufacture and testing. This includes occupation health studies, impact of accidental or deliberate release on the natural or man made environment and impact on organisms specifically affected directly or indirectly by contamination. 0000-0002-5111-7263 nuclear industry study Research done in a laboratory. A laboratory study may use special equipment and cells or animals to investigate the effects of an experimental perturbation, discover fundamental molecular mechanisms, assay biological substances, or find out if a drug, procedure, or treatment is likely to be useful in humans. A laboratory investigation is often characterised by a hypothesis and is carried out with controls. 0000-0002-5111-7263 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28278 laboratory study Study of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ethicolegal constructs surrounding radiation and radiation safety and regulation. 0000-0002-5111-7263 http://purl.bioontology.org/ontology/CSP/2482-9501 attitudinal study Study concerning exchange or transmission of thoughts, messages, or information between people or between authorities and the general public (for example educational information, risk communication, safety communication) concerning exposure to and use of radiation. 0000-0002-5111-7263 communication study A study focussed on a set of people with some shared characteristic. The substance of shared element varies widely, from geography to a situation to interest to lives and values. The term is widely used to evoke sense of collectivity. For example communities collectively exposed to radioactive environmental contamination. 0000-0002-5111-7263 community study The study of political involvement in radiation and nuclear regulation, military use, and safety as shown by inclusion in political manifestos and messaging by established or informal groups and its impact on voting patterns and democracy. 0000-0002-5111-7263 political and psephological study A study measuring "psychological" aspects of a person such as knowledge, skills, abilities, attitudes, or personality using defined scales. 0000-0002-5111-7263 psychometric study A study of human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology. 0000-0002-5111-7263 behavioural study A study dealing with group relationships, patterns of collective behavior, and social organization. 0000-0002-5111-7263 sociological study Studies involving fields of inquiry into human constructs and concerns as opposed to natural processes . These are traditionally the study of literature, philosophy, and religion. Included in this definition are sociological studies, especially those concerned with the social impact of the humanities. 0000-0002-5111-7263 social science and humanities study Specifically an attitudinal study looking at how perception, for example of risk, and expectations affect behaviour. 0000-0002-5111-7263 perceptions, expectations and behaviours study Sociological, attitudinal, ethocolegal and regulatory approaches to governance of radiation and radioactive substance use. 0000-0002-5111-7263 holistic approaches to governance study Studies on policy concerning socially and ethically responsible research and innovation 0000-0002-5111-7263 responsible research and innovation study Studies of the engagement between an organisational entity and those groups or individuals potentially or actually impacted by the actions of that entity over a range of activities and approaches. 0000-0002-5111-7263 stakeholder engagement study Study concerning the modes, efficacy and response to communication of risk and health impacts of radiation in all aspects. 0000-0002-5111-7263 risk and health communication study Studies concenring the attitudes to and practices of radiological protection in defined groups of people. For example the nuclear industry of a country or within a specific laboratory. 0000-0002-5111-7263 radiological protection culture study Genetic study done at the population level or among population groups, generally to find the cause, incidence or spread of a disease or to see the response to a treatment, nutrition or environment. 0000-0002-5111-7263 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16160 genetic population study A type of study in which participants are enrolled into the study before they develop the disease or outcome in question. 0000-0002-5111-7263 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142646 prospective study Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ) An observational study that is also considered to be a Patient Registry. 0000-0002-5111-7263 http://purl.obolibrary.org/obo/NCIT_C129000 registry study A study looking backwards in time using observations collected predominantly prior to subject selection and enrolment 0000-0002-5111-7263 retrospective study A study of the number of new cases of a given disease during a given period in a specified population. It also is used for the rate at which new events occur in a defined population. this class also includes PREVALENCE, which refers to all cases in the population at a given time. 0000-0002-5111-7263 incidence or prevalence study Studies concerning the optimisation of situation awareness through gathering and analysing information, and methodologies for making decisions on that awareness, such as estimating the path of a radioactive fallout with respect to weather and population density and making a decision to evacuate a population. 0000-0002-5111-7263 situation awareness and decision support study A study concerning the protection of the population from unexpected radioactive discharge or contamination, such as a dirty bomb, and civil safetyy coningency plans, such as deployment of emergency services and evacuation. 0000-0002-5111-7263 civil protection study Studies on planning for unexpected natural or man-made radiological catastrophe of substantial extent causing significant property damage or destruction, loss of life or sometimes permanent changes to the natural environment. Broader scope than civil protection as may relate to livestock, food and water shortage, disease outbreak and extensive traumas caused by precipitating or consequential damage. 0000-0002-5111-7263 disaster planning study Studies on plannig for or analysing a nuclear accident with release of airborn or waterborn contamination into the environment. Narrower than Disaster planning study but may be used to qualify an annotation to Disaster planning study if the source of contamination is a nuclear accident. A nuclear accident is not necessarily a disaster. 0000-0002-5111-7263 nuclear accident study A controlled study designed to assess the safety and efficacy of new drugs, devices, treatments, or preventive measures in humans by comparing two or more interventions or regimens 0000-0002-5111-7263 http://purl.bioontology.org/ontology/CSP/0690-6917 clinical trial study Study of the effects of radiation used in a medical therapeutic or diagnostic context. Inlcudes radiation accidents in this context, excludes occupational exposure for health professionals. 0000-0002-5111-7263 medical radiological safety study A study concerned with health and safety policy development, implementation and practice in the workplace including investigating accidents at work, and chronic occupational exposure. Includes monitoring compliance with health and safety legislation and study of the promotion and maintenance of physical and mental health in the work environment. 0000-0002-5111-7263 occupational health study Study on the efficacy, outcomes and adverse consequences of exposure to medical diagnostic procedures using internal or external irradiation. 0000-0002-5111-7263 radiation based diagnostics study Study of the efficacy, outcomes and adverse consequences of exposure to therapeutic use of ionizing and nonionizing radiation including RADIONUCLIDE THERAPY, therapeutic radiation with visible, laser, or ultraviolet light. Includes technical development of protocols and equipment. 0000-0002-5111-7263 radiotherapy study A study involvingdevelopment of agents or procedures intended to produce an effect that is intended to mitigate or stop a pathologic process. 0000-0002-5111-7263 therapeutics study A study of the macroscopic and microscopic anatomical changes in diseased tissue. 0000-0002-5111-7263 http://purl.bioontology.org/ontology/CSP/1448-3909 histopathologic study Study of legal and statutory instruments and legislation designed to regulate the safety, use and transport of radioactive materials, release of such materials into the environment, or external radiation. 0000-0002-5111-7263 radiation legislation study Study of the policy approaches and their implementation concerned with harmonising regulatory guidelines and legislation dealing with radiation and radioactive substances between legislatures, generally internationally. 0000-0002-5111-7263 regulatory harmonisation study Study of the development, implementation and monitoring of nuclear non proliferation treaties between states. 0000-0002-5111-7263 nuclear proliferation treaty study Studies concerning intentional release of organisms (germs), toxic chemicals, or radioactive substances with intent to harm or kill people or the environment, or to inflict panic within a population. 0000-0002-5111-7263 http://purl.bioontology.org/ontology/CSP/5000-0002 bioterrorism study Study of strategies and their implementation towards defence against radiation used as a weapon conducted by military powers and institutions. May also include civil defence where the military has a significant operational role, but not disaster preparedness. 0000-0002-5111-7263 military defence study Study of biological processes that involve adding/removing chemical moieties to/from DNA, including methylation, phosphorylation, dephosphorylation, etc. Includes interventional DNA modification. 0000-0002-5111-7263 dna modification study Study of biological processes that involve adding/removing chemical moieties to/from histones, including methylation, acetylation,phosphorylation, dephosphorylation, etc. 0000-0002-5111-7263 histone modification study Study conducted by means of structured or unstructured interviews of persons of interest. 0000-0002-5111-7263 interview study A study of genetic variation and the inheritance of a trait or traits within a population or an individual including examination of genetic material for the presence or absence of cytogenetic or molecular genetic abnormalities. 0000-0002-5111-7263 genetic study A radiographic study used to evaluate a specific anatomic location for a specific purpose. This may include the assessment of imaging modalities and the development of new techniques. Includes PET, MRI, CT and related techniques. 0000-0002-5111-7263 imaging study Study concerned with the construction, analysis, evaluation, refinement etc. of mathematical or statistical models of the properties or behaviour of a set of entities, such as molecules, physiological processes, environmental processes such as nuclide transfer, such that functions are developed to reliably predict the behaviour of those entities. 0000-0002-5111-7263 mathematical modelling study A study usually conducted in a laboratory where non human animals are used to model aspects of a disease process or its therapy to provide insights into human biology or pathobiology. 0000-0002-5111-7263 model organism study Study concerning the development, use, calibration or standardisation of technologies for the qualitative or quantitative measurement of radiation and radionuclides. 0000-0002-5111-7263 monitoring technologies and metrology study Study of the chemistry of radioactive materials including radioactive tracer studies of metabolic processes 0000-0002-5111-7263 radiochemistry study Study of the development and implementation of public policy towards issues involving radiation 0000-0002-5111-7263 policy development study Study of the effects of acoustic radiation on cellular and organismal physiology and the effects of acoustic radiation emitted in response to exposure to ionising radiation. 0000-0002-5111-7263 acoustic radiation study Study of radiation levels and effects in the human built environment. 0000-0002-5111-7263 environmental study_ abiotic_anthropogenic Study of radiation levels and effects in the natural environment. 0000-0002-5111-7263 natural environment study The development and use of mathematical models and systems analysis for the description of naturally occurring non-human populations, and applications to measuring the effects of radiological contamination. 0000-0002-5111-7263 ecological population modelling study The study of environmental contamination with radiation and radioactive substances and the toxic effects on the ecosystem either through chemical toxicity or radiation exposure. 0000-0002-5111-7263 ecotoxicology study The study of environmental contamination with radon and the toxic effects on biota including humans. Both natural and anthropogenic environments. Includes radiometrics, safety policies and mitigation technologies. 0000-0002-5111-7263 environmental radon study Mathematical modelling of radionuclide transfer and dispersal processes in water, earth or air, either directly or through the mediation of biota. 0000-0002-5111-7263 radionuclide dispersal modelling study Study of the ocurrence, levels and effects of naturally occurring radioactive materials such as Radon. 0000-0002-5111-7263 naturally occurring radioactive materials study Study involving the measurement of radiation levels, or concentration of radionuclides, in the natural or man made environment. Usually in a time series. 0000-0002-5111-7263 environmental radiation monitoring study Study concerned with the measurement of transfer of radionuclides to biota from the environment. 0000-0002-5111-7263 environmental radionuclide transfer study Any study concenrd with the prevalence or effects on non-ionising radiations such as UV, acoustic, or RF. 0000-0002-5111-7263 non ionising electromagnetic radiation study Study concerning the safety, regulation, activities and engineering of nuclear installations including power stations, waste processing plant, radionuclide generation and purification plant, and military nuclear establishments. May include occupational health studies if broader than just occupationaal health in scope. 0000-0002-5111-7263 nuclear installation study Study of the process of generation of nuclear waste, its monitoring, regulation, disposal and inadvertent discharge. 0000-0002-5111-7263 nuclear waste study Study of the engineering of nuclear installations such as power plants. 0000-0002-5111-7263 nuclear engineering study Study of the process, regulation and monitoring of mines where exposure to naturally occurring radiation presents an occupational hazard for workers or the process itself, for example run off water or spoil, constitutes an environmental hazard. 0000-0002-5111-7263 mining study A study using cells derived from an organism grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent. 0000-0002-5111-7263 cell culture study A study using an organ, part of an organ or an organoid culture, derived from an organism and grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent. The system differs from cell culture in the generation or maintenance of multiple cell types with the spatial and functional relationship between them derived from or reflecting the normal organisation in vivo. 0000-0002-5111-7263 organ culture study Any study involving the manipulation, measurement, or characterisation of DNA or RNA in a cell or organism. 0000-0002-5111-7263 molecular genetic study Elucidation of the physical structure of a macromolecule, protein, carbohydrate, DNA or RNA, its analysis and manipulation based on structure/function considerations. 0000-0002-5111-7263 molecular structural study A study using an intact organism, plant, animal, or microorganism 0000-0002-5111-7263 whole organism study Study of the cellular phenomenon which radiation energy is not been directly deposited in cells by transfer of medium, proximity/justaposition, or other means, but results in their behaving as if they had been irradiated. 0000-0002-5111-7263 bystander effect study A study of heritable phenotype changes that do not involve alterations in the DNA sequence. This may be in intact organisms or in cells and includes population analysis of epigenetic phenomena and molecular analysis of gene expression and epigenetic modifications of chromatin such as DNA methylation and histone acetylation. 0000-0002-5111-7263 epigenetic study Study of the frequency of induction , nature and consequences of the production of genetic or epigenetic alterations by any technique, including chemicals, radiation, recombination, or other molecular biology methods. 0000-0002-5111-7263 mutagenesis study Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or regulation of the nuclear industries. 0000-0002-5111-7263 attitudinal study of nuclear industry risk perception Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic ionising radiation in the environment. 0000-0002-5111-7263 attitudinal study towards ionising radiation in the environment Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic non-ionising radiation in the natural environment. 0000-0002-5111-7263 attitudinal study towards non-ionising radiation in the environment Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety and efficacy in a clinical context where radiation is used for diagnostic or therapeutic procedures.. 0000-0002-5111-7263 attitudinal study towards medical radiation procedures Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety towards natural or anthropogenic non-ionising radiation in the occupational environment. 0000-0002-5111-7263 attitudinal study towards radiation in the occupational environment Study of social and individual trust in the position and activities of legal or other competent advisory or regulatory authorities. 0000-0002-5111-7263 authority trust study Study on the modality, efficacy and responses to communcation of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context. 0000-0002-5111-7263 risk communication study Study on the modality, efficacy and responses to communication of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context. 0000-0002-5111-7263 public communication study Study on the modality, efficacy and responses to communication of information or advice to populations on any aspect of radiation, conceived of as an educational programme, and including a wider scope than just safety and risk. For example basic nuclear physics, emergency action advice. 0000-0002-5111-7263 public education study Study involving attitudes, health status, social organisation of defined communities identified by common characteristics such as occupation type, geography, gender identity, with respect to radiation. 0000-0002-5111-7263 social affairs and community health study Studies involving creation and assessment of plans for the future physical arrangement, well being, efficiency and condition of a community. It may have the goals of improving health, promoting efficiency in the provision of services and resources on a comprehensive basis for a whole community. In the context of radiation this may be concerned with community planning for dealing with mitigation measures for local NORM, or organised community-wide continegency measures for nuclear accident or recovery from such. 0000-0002-5111-7263 community planning study Study concerned with eliciting information in a structured way concerning issues of interest from members of a community defined by common characteristics, for example occupation, geographical location, personal history or gender. 0000-0002-5111-7263 community survey study A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology at the level of slected individuals. May be carried out by observation or as individual responses to a questioannaire or interview in the case of humans where the person records their own assessment of their behaviour. 0000-0002-5111-7263 individual behaviour study A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology within substantial populations of individuals. Likely to be carried out by mass observation or indirect inference. 0000-0002-5111-7263 population behaviour study Mathematical modelling for theraputic regime optimisation and for optimal tumor response, for example modelling spatiotemporal dynamics of tumor and blood volume fraction, and predicting response to radiation therapy. Also studies for beam modelling and multiimaging techniques. 0000-0002-5111-7263 radiotherapeutic modelling study Study of the radiolonuclide components and emissions from building materials 0000-0002-5111-7263 building materials radiological safety study Studies on radiological safety within buildings. Primary purpose os for buildings not specifially designed to hold radioactive materials but anaylyis and mitigation of risks from radioactive exposure from the local environment or materials. 0000-0002-5111-7263 building radiological safety study Study of the weather and atmospheric dynamics mainly with respect to dissemination of radionuclides. 0000-0002-5111-7263 meteorology study Study of non-living objects in the environment, such as soils or rocks. 0000-0002-5111-7263 environmental study_abiotic Study of non-human biota in the natural environment. 0000-0002-5111-7263 environmental study_biota ( non human) Study which may include human and non-human biota in the environment. 0000-0002-5111-7263 environmental study_panbiota (all) Study of the measurement, effects and regulation of wireless communication signals, for example mobile phone radiation and microwave communication. 0000-0002-5111-7263 wireless communication radiation study The sample was irradiated with Cs-137 gamma ray photons. Photons having energies that are greater than tens of thousands of electron volts (eV). Britannica.com gamma ray photon The sample was irradiated with x-ray photons. A photon with energies from about 100 eV (electron volts) to 1 MeV (million electron volts). Britannica.com x-ray photon Irradiation of the sample was with x-ray photons. An energy transfer process in which energy in the form of particles or waves is transferred from one entity to another 0000-0003-1741-8297 Jack Miller obo:RBO_0002000 irradiation TRUE 1 A process involving the emission of energy from an atomic nucleus resulting in change in the character of the nucleus radioactive decay Irradiation that is not the result of a planned process unplanned irradiation Unplanned irradiation that is of anthropogenic origin unplanned anthropogenic irradiation Unplanned irradiation that is non-anthropogenic in origin unplanned naturally occurring radiation exposure Environmental monitoring that includes continual assay for radiation dose or quality. environmental radiation monitoring Monitoring within an environment which was not man-made. natural environment monitoring Monitoring within a man-made or constructed environment anthropogenic environment monitoring Monitoring for radiation dose or quality within a man-made or constructed environment such as a building or a vehicle. anthropogenic environment radiation monitoring Monitoring for radiation dose or quality within a natural environment. natural environment radiation monitoring Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means heavy ion radiation Atomic nuclei, variously defined as having atomic number 2, 3, 4, 5 or 6 and kinetic energy imparted by natural or artificial means light ion radiation A particle with a positive or negative electric charge charged particle An atomic nucleus with 26 protons and 30 neutrons Fe-56 ion;Fe-56 nucleus;Fe-56 Iron-56 nucleus An atomic nucleus with 14 protons and 14 neutrons Si-28 ion;Si-28 nucleus;Si-28 Silicon-28 nucleus An atomic nucleus with 6 protons and 6 neutrons C-12 ion;C-12 nucleus;C-12 Carbon-12 nucleus An atomic nucleus with 2 protons and 2 neutrons He-4 ion;He-4 nucleus;He-4 Helium-4 nucleus An atomic nucleus with 10 protons and 10 neutrons Ne-20 ion;Ne-20 nucleus;Ne-20 Neon-20 nucleus space flight Activity carried out by crewed or robotic vehicles outside the Earth's atmmosphere. spaceflight Space flight space flight The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium. Jack Miller absorbed radiation dose The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium per unit time. Jack Miller absorbed radiation dose rate The kinetic energy carried by a particle or photon of ionizing radiation. Jack Miller ionizing radiation energy x-ray Electromagnetic radiation with photon energies approximately between 0.1 and 120 keV. The upper end of the x-ray spectrum overlaps with the lower end of the gamma ray spectrum. Jack Miller x-ray http://son.nasa.gov/tass/content/electrospectrum.htm x-ray radiation A material entity which emits radiation Jack Miller radiation source sham irradiation Sham irradiation refers to a procedure in which participants or subjects in an experiment are exposed to simulated radiation, mimicking precisely the conditions of actual irradiation. The purpose of using sham irradiation is to create a control group that experiences the non-specific effects of the experimental setup, while excluding the specific effects associated with radiation exposure. Jack Miller sham sham irradiation fractionation protocol A protocol for administering a total radiation dose in two or more increments separated by a specified time interval Jack Miller fractionation protocol radiation fractionation protocol cis-lunar space The region of space between the Earth and the Moon Jack Miller cis-lunar space lunar orbit A region of space defined by a regular, repeating path of a specified object about Earth's moon Jack Miller lunar orbit lunar surface The area of the lunar landmass exposed to space Jack Miller lunar surface cis-Mars space The region of space between the Earth and Mars Jack Miller cis-mars space Mars orbit A region of space defined by a regular, repeating path of a specified object about Mars Jack Miller mars orbit Mars surface The area of the Mars landmass exposed to the Martian atmosphere Jack Miller mars surface interplanetary space The region of space in the Solar System between planets Jack Miller interplanetary space planet surface The outermost solid or liquid area of a planet Jack Miller planet surface non-irradiated An organism or material entity kept unexposed to radiation, for purposes of comparison to a similar organism or material entity that has been exposed to radiation Jack Miller non-irradiated ground analog experiment A study at a ground facility designed so as to replicate one or more conditions in space (e.g. radiation, microgravity, isolation) Jack Miller ground analog ground analog study ground control An study at a ground facility designed so as to replicate conditions in space (e.g. radiation, microgravity, isolation) with the exception of one condition, so as to ascertain the effects of that condition on an organism or instrument Jack Miller ground control ground control study irradiation protocol A protocol for administering radiation to a sample Jack Miller irradiation protocol radiation fraction One of the series of individual doses administered to a sample in a fractionated irradiation. Jack Miller fraction radiation fraction radiation fraction interval Time between fractions in a fractionated irradiation. Jack Miller radiation fraction interval high altitude The region of the atmosphere above 8000 feet above sea level. Altitudes above 12000 feet are sometimes referred to as very high altitude, and above 18000 feet as extremely high altitude. Jack Miller https://www.medicinenet.com/high_altitude/definition.htm high altitude sham The class should be used in cases where it is clear that the control sample was treated in precisely the same way as the experimental samples or sham irradiation is specified. It is therefore a more restricted quality definition than "non-irradiated". It is likely to be used more often with external radiation exposure or exposure to a beam, and with a biological rather than abiotic sample. A quality of a biotic or abiotic sample or individual which is part of an experiment that tests the effects of radiation on organisms or materials by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. In sham irradiation the precise treatment of the sample must be identical to that of the experimental samples and should be made explicit in the description of the method. Jack Miller sham-irradiated parabolic flight An aircraft which flies a series of parabolic arcs to simulate micrgravity. Jack Miller Vomit Comet parabolic flight aircraft An aircraft which flies at altitudes greater than commercial aircraft altitudes for research purposes. Jack Miller high altitude research aircraft UAV An research aircraft designed to operate without crew members, either autonomously or under control from a ground station Jack Miller UAV uncrewed aerial vehicle HZE Fully ionized atomic nucleus with 2 or more protons and energies in excess of tens of MeV per nucleon Jack Miller HZE highly charged energetic nuclei highly charged energetic nucleus A study of a response to radiation conditioned by prior administration of radiation of a different type and/or at a different dose or dose rate Jack Miller adaptive adaptive radiation response study The total dose administered in a series of radiation fractions divided by the elapsed time between the beginning of the first exposure fraction and the end of the last exposure fraction Jack Miller average fractionated dose rate A device which exposes samples to gamma radiation. Jack Miller gamma irradiator charge The electric charge of a particle used in an irradiation Jack Miller particle charge The measurement of the amount of radiation taken up by a sample. Jack Miller radiation dosimetry A microbeam is a narrow beam of radiation, of micrometer or sub-micrometer dimensions. Together with integrated imaging techniques, microbeams allow precisely defined quantities of damage to be introduced at precisely defined locations. Jack Miller Wikipedia microbeam An atomic nucleus with 41 protons and 52 neutrons Nb-93 ion;Nb-93 nucleus;Nb-93 Niobium-93 nucleus An atomic nucleus with 47 protons and 60 neutrons Ag-107 ion;Ag-107 nucleus;Ag-107 Silver-107 nucleus An atomic nucleus with 54 protons and 75 neutrons Xe-129 ion;Xe-129 nucleus;Xe-129 Xenon-129 nucleus An atomic nucleus with 73 protons and 108 neutrons Ta-181 ion;Ta-181 nucleus;Ta-181 Tantalum-181 nucleus An atomic nucleus with 79 protons and 118 neutrons Au-197 ion;Au-197 nucleus;Au-197 Gold-197 nucleus An atomic nucleus with 7 protons and 7 neutrons N-14 ion;N-14 nucleus;N-14 Nitrogen-14 nucleus An atomic nucleus with 8 protons and 8 neutrons O-16 ion;O-16 nucleus;O-16 Oxygen-16 nucleus An atomic nucleus with 18 protons and 22 neutrons Ar-40 ion;Ar-40 nucleus;Ar-40 Argon-40 nucleus An atomic nucleus with 22 protons and 26 neutrons Ti-48 ion;Ti-48 nucleus;Ti-48 Titanium-48 nucleus An atomic nucleus with 36 protons and 48 neutrons Kr-84 ion;Kr-84 nucleus;Kr-84 Krypton-84 nucleus mGy/sec A derived absorbed dose unit which is equal to one milligray absorbed per second mGy/sec UO:0010065 miligray per second TRUE Indirect cellular response to stimulus This could be used to describe a tissue response to immune stimulation, so for example an IL2 response of endothelial cells in response to lymphocytes stimulated by pathogen. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus which acts on another cell and not on the responding cell. The process begins with detection of the stimulus by a cell and ends with a change in state or activity of a different cell Paul Schofield indirect cellular response to stimulus The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield indirect cellular response to radiation Directly describes the bystander effect (Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) but can alo sbe used to describe phenomena related to the abscopal effect, manifest in whole organisms where irradiation of one part of the organism causes changes in another un-irradiated component. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to ionising radiation which acts on another cell and not on the responding cell. The process begins with detection of the ionising radiation by one cell or cells and ends with a change in state or activity of a different cell or cells. Paul Schofield indirect cellular response to ionising radiation A device for exposing materials or biological organisms to ionizing radiation for research or therapeutic purposes. ionizing radiation device High-altitude balloons are crewed or uncrewed balloons, usually filled with helium or hydrogen, that are released into the stratosphere, generally attaining between 18 and 37 km (11 and 23 mi; 59,000 and 121,000 ft) above sea level. Jack Miller Wikipedia high-altitude balloon spaceflight Travel beyond the Earth's atmosphere Jack Miller space flight non-targeted effects of ionising radiation Non-targeted effects of ionising radiation are characterised by cellular responses that occur in cells in which energy from ionizing radiation has not been deposited. The distinct classes of non-targeted effects include Genomic Instability, and Bystander effect which latter includes Abscopal effects and Bystander-mediated adaptive response. These can also arise non-clonally in the progeny of irradiated somatic or germ cells, resulting in radiation-induced genomic instability and transgenerational genomic instability respectively. (Kadhim M, Salomaa S, Wright E, et al. Non-targeted effects of ionising radiation--implications for low dose risk. Mutat Res. 2013;752(2):84-98. doi:10.1016/j.mrrev.2012.12.001) Paul Schofield ORCID: 0000-0002-5111-7263 NTE non-targeted effects non-targeted effects of ionising radiation That energy which is transferred in space and time as part of the process of radiation (ENVO:01001023). radiation Uncharged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator) neutral particle radiation An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at nm scale nanodosimetry assay An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006. Usually a track structure assay at micrometre scale microdosimetry assay Nuclear decay in which an alpha particle is emitted. https://goldbook.iupac.org/terms/view/A00005 http://purl.obolibrary.org/obo/REX_0000017 alpha-decay alpha decay Radioactive decay in which a beta particle is emitted or in which orbital electron capture occurs. http://goldbook.iupac.org/B00572.html http://purl.obolibrary.org/obo/REX_0000007 beta-decay beta decay Processes in which electrons or components of the atomic nucleus are participants. subatomic process Measurement of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers nanodosimetric measurement datum In microdosimetry the specific energy, z, is the energy deposited by radiation ( in one or more deposition events) in a specified micrometric (or smaller) site divided my the mass of the site. Measured in Gy. specific energy measurement datum The path of a particle in matter, delineated by sites where the particle deposits energy. particle track A pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers. nanodosimetry The complete set of spatial coordinates of energy deposition events along a particle track in matter particle track structure A group of ionization events closely related in time and space, occurring in a specified target volume and originating from a single primary ionizing particle. ionization cluster Measurement of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers. microdosimetric measurement datum A volume of matter characterised by linear dimensions of the order of 0.5- 10's of microns, referred to as the "site" in microdosimetry. micrometric volume A control specimen role of a biotic or abiotic sample or individual describes a specimen by its purpose, and therefore treatment, within a planned experimental process that tests hypotheses by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. The quality of control inhering in the sample role exists as a result of the historical treatment of the sample. In a controlled experiment, two or more virtually identical experiments are conducted, but the factor being tested is varied in only one of them. This serves to isolate any causal phenomena. A control may have been subject to treatments during the experiment that might alter its state or behaviour and is therefore distinguishable from the sample as initial input into the experiment. However such treatments should in all cases but that of the variable under scrutiny, be the same as the experimental sample. http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C64355 control specimen role Sham irradiation in which an identical irradiation protocol (with the exception of the administration of the radiation exposure) is not followed in every respect. Use approximate sham irradiation when at least one aspect of the irradiation (with the exception of the administration of the radiation exposure) is not followed precisely. For example, Not placing an organism or sample in a beam line for the same length of time as the irradiated organism(s) or sample(s) were left in the beam. approximate sham irradiation Experimental internal radiation exposure of rodents to radon gas through inhalation. Exposure to an inhaled, ingested, injected or implanted source of radiation of any origin as part of a planned or accidental process. internal radiation exposure Mice exposed to external radiation from a Sr source. Exposure to an external source of radiation of any origin or type. https://orcid.org/0000-0002-5111-7263 external radiation exposure Sham irradiation in which an identical irradiation protocol is followed in every respect, with the exception of the administration of the radiation exposure. Use complete sham irradiation when all steps of an irradiation protocol are followed for sham control group (with the exception of administration of the radiation exposure). complete sham irradiation Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally by the ingestion, inhalation or implantation of a source of radiation. https://orcid.org/0000-0002-5111-7263 Research subjects participating in a clinical trial using an internally implanted radiation source have an internal experimental radiation exposure internal experimental radiation exposure The direct or indirect transfer of energy from radiation to a medium through ionisation or excitation of the atoms of the medium. energy deposition event track formation A mixed irradiation study typically involves exposing a sample or system to a combination of different types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 mixed irradiation study A mixed ion and photon irradiation study typically involves exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 mixed ion and photon irradiation study A mixed ion and photon simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 mixed ion and photon simultaneous irradiation study A mixed ion and photon sequential irradiation study typically involves sequentially exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 mixed ion and photon sequential irradiation study A multiple ion irradiation study typically involves exposing a sample or system to a combination of different types of charged particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 multiple ion mixed irradiation study multiple ion irradiation study A multiple ion simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of ions. This could include exposure to various forms of particle radiation, for example ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 multiple ion simultaneous irradiation study A multiple ion sequential irradiation study involves exposing a sample or system to a combination of different ions. This could include exposure to various forms of particle radiation such as ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation. http://orcid.org/0000-0002-5111-7263 https://orcid.org/0000-0001-9227-0670 multiple ion sequential irradiation study ALARA One of the measures to ensure ALARA is to minimize the time spent working around radioactive materials. A principle of radiation protection philosophy that requires that exposures to ionizing radiation be kept as low as reasonably achievable, economic and social factors being taken into account. The protection from radiation exposure is ALARA when the expen Jack Miller ALARA NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) ALARA as low as reasonably achievable Attenuation in concrete or leadshielding is a common method of radiation protection on Earth, but is impractical in space due to mass constraints. The reduction of radiation intensity upon passage of radiation through matter Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) radiation attenuation Biodosimetry was used to measure the exposure of some victims of the Chernobyl nuclear accident. Use of a biological response as an indicator of a dose of an effective agent (e.g., the extent of decline in peripheral blood lymphocytes of humans exposed to ionizing radiation can be used as an indicator of the absorbed dose to the whole body from that Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) biodosimetry The bystander effect can be studied by identifying cells that were traversed by a charged particle. The term used to describe the effects on cells in proximity to irradiated cells, but through which radiation has not passed. In experimental radiation biology, the bystander effect can be investigated by targeting individual cells, or by using doses low enough that the probability for a given cell to be hit by a particle is less than one. Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) bystander effect Delta ray energies increase with the velocity of the incident particle. Highly energetic electrons produced during inelastic collisions between ionizing radiation and atomic electrons. In a small proportion of collisions, the ejected electron receives a considerable amount of energy (i.e., >1,000 eV), allowing it to travel a Jack Miller delta electron NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) delta electron delta ray The average annual dose equivalent for crew members on the ISS is approximately 300 mSv. The product of the absorbed dose (D) at a point and the quality factor (Q) at that point for the radiation type (i.e., H = DQ). The unit of H is J-kg^[-1] with the special name sievert (Sv) Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) dose equivalent The increased risk from induced cancer due to exposure when the effects over an entire lifetime are accounted for. Individuals who would have died of cancer anyway but die early because of exposure are not included Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) excess lifetime risk of cancer The sample was irradiated with fast neutrons. Neutrons of energies above a few hundred kiloelectron volts (keV) Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) fast neutron The value of the fluence was approximately 1 particle per cm2. The number of particles or photons per unit of cross-sectional area perpendicular to the direction of the particle (units of m^2 or cm^2) (i.e., particles-m^[-2] or particles-cm^[-2]). Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) fluence The flux of cosmic ray muons per cm2 at the surface of the Earth is approximately 1.0. The quotient of dN by dt, where dN is the increment of the particle number in the time interval dt. The unit for flux is reciprocal second (s^[-1].) Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) flux An atomic nucleus, fully stripped of its orbital electrons, containing 2 or more protons. Nuclei containing between 2 protons (helium) and 6 protons (carbon) are sometimes referred to as light ions. Jack Miller In RBO--needs def from NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) heavy ion Biological effects are a function of LET. The energy deposited by an ionizing charged particle or photon in any medium per unit path length. Jack Miller LET NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) LET linear energy transfer Radiation protection standards take into account organ dose as well as whole body dose. The mean absorbed radiation dose in a specified tissue or organ of the human body. Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) organ dose Neutrons have a high quality factor compared to photons. Dimensionless factor developed for purposes of radiation protection and assessing health risks in general terms that accounts for the relative biological effectiveness of different radiations in producing stochastic effects and is used to relate absorbed Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) quality factor The samples received a dose of 1 Gy. (The use of the gray unit implies that "dose" refers to a measured quantity, typically absorbed dose or organ dose.) The samples received a dose of 1 Sv. (The use of the sievert unit implies that "dose" refers to a der A measurement datum of the quantity of radiation absorbed by a substance or organism. The term "radiation dose" may for example refer to absorbed dose, organ dose, dose equivalent or equivalent dose, depending upon context and weighting factor(s). Jack Miller radiation dose Radiation quality is often expressed in terms of the linear energy transfer of the ionising particles that deliver the absorbed dose. Rossi, Harald H. Specification of Radiation Quality. Radiation Research, vol. 10, no. 5, Radiation Research Society, 1959, pp. 522 31, https://doi.org/10.2307/3570787. But this is an over simplification. Is a quality of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited. Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) and see https://melodi-online.eu/wp-content/uploads/2021/04/02-What-is-radiation-quality-Goodhead.pdf radiation quality TRUE Radiation weighting factors may change as more data on biological effects are obtained. A factor used to allow for differences in the biological effectiveness between different radiations when calculating equivalent dose (H_T) (see equivalent dose). These factors are independent of the tissue or organ irradiated. Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) radiation weighting factor Neutrons have been found to have a higher RBE than electrons. Factor used to compare the biological effectiveness of absorbed doses from different types of ionizing radiation, determined experimentally. RBE is the ratio of the absorbed dose of a reference radiation to the absorbed dose of the radiation in question r Jack Miller RBE NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) RBE relative biological effectiveness Tissue equivalent materials can be used to study radiation effects at depth in the human body. Denotes a substance with absorbing and scattering properties for a given radiation that sufficiently match those of a particular biological tissue. Jack Miller NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) tissue equivalence A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system A role realized by a participant in a process such that the participant causes the process. agent role A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. SO editors NCIt:C16612 SNOMEDCT:67271001 gene An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. BFO:0000003 uberon UBERON:0000000 processual entity An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. span:ProcessualEntity FBbt:00005157 chemosensory sensory organ uberon UBERON:0000005 chemosensory organ FBbt:00005157 chemosensory sensory organ FBbt:00005157 The clusters of hormone-producing cells that are scattered throughout the pancreas. Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG] A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986) AAO:0010406 BTO:0000991 CALOHA:TS-0741 EFO:0000856 EMAPA:32927 EV:0100130 FMA:16016 GAID:324 MA:0000127 MAT:0000076 MESH:D007515 MIAA:0000076 NCIT:C12608 UMLS:C0022131 VHOG:0000646 Wikipedia:Islets_of_Langerhans XAO:0000159 pancreatic insula pancreatic islet uberon island of Langerhans island of pancreas islets of Langerhans UBERON:0000006 islet of Langerhans http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png PMID:16417468 PMID:16417468 PMID:16417468 The clusters of hormone-producing cells that are scattered throughout the pancreas. MA:0000127 MESH:A03.734.414 MP:0005215 Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] 2012-06-20 AAO:0010406 AAO AAO:BJB Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG] 2012-09-17 VHOG:0000646 VHOG PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995) http://bgee.unil.ch/ A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986) PMID:16417468 UMLS:C0022131 ncithesaurus:Islet_of_Langerhans island of Langerhans BTO:0000991 island of pancreas BTO:0000991 A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. submucosal BTO:0002107 FMA:85391 FMA:85392 NCIT:C13167 SCTID:68439008 UMLS:C0225344 Wikipedia:Submucosa organ submucosa region of submucosa submucosa of organ submucosa of region of organ uberon submucous layer tela submucosa tunica submucosa UBERON:0000009 submucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. Wikipedia:Submucosa UMLS:C0225344 ncithesaurus:Submucosa organ submucosa FMA:85391 region of submucosa FMA:85392 submucosa of organ FMA:85391 submucosa of region of organ FMA:85392 submucous layer BTO:0002107 tela submucosa BTO:0002107 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] PNS AAO:0000429 BAMS:PNS BILA:0000081 BIRNLEX:1111 BTO:0001028 CALOHA:TS-0808 EFO:0000891 EHDAA2:0001445 EHDAA:2893 EMAPA:16665 EV:0100335 FBbt:00005098 FMA:9903 GAID:715 MA:0000218 MAT:0000338 MESH:D017933 MIAA:0000338 NCIT:C12465 SCTID:362292005 TAO:0000142 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 Wikipedia:Peripheral_nervous_system XAO:0000178 ZFA:0000142 neuronames:3232 pars peripherica systema nervosum periphericum uberon UBERON:0000010 peripheral nervous system http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png cjm A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. GO:0007422 Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000142 TAO ZFIN:curator Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] 2012-06-20 AAO:0000429 AAO AAO:BJB The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) http://neurolex.org/wiki/Cumbo_terms (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] 2012-09-17 VHOG:0000399 VHOG DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006) http://bgee.unil.ch/ PNS FBbt:00005098 UMLS:C0206417 BIRNLEX:1111 ncithesaurus:Peripheral_Nervous_System UMLS:C1305921 BIRNLEX:1111 pars peripherica FMA:9903 FMA:TA Wikipedia:Peripheral_nervous_system systema nervosum periphericum FMA:9903 FMA:TA Wikipedia:Peripheral_nervous_system The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest) AAO:0010487 BIRNLEX:2516 BTO:0001832 CALOHA:TS-2050 EFO:0000893 EHDAA2:0001971 EHDAA:3769 EMAPA:16985 FMA:9906 GAID:710 MA:0000225 MESH:D013564 MIAA:0000100 NCIT:C12795 SCTID:362484004 TAO:0001576 UMLS:C0039044 UMLS:C1269646 VHOG:0000384 Wikipedia:Sympathetic_nervous_system ZFA:0001576 pars sympathica divisionis autonomici systematis nervosi sympathetic nervous system sympathetic part of autonomic division of nervous system uberon pars sympathica divisionis autonomici systematis nervosi UBERON:0000013 sympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png cjm FMA MA ZFA-modified-from-isa The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. GO:0048485 Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] 2012-06-20 AAO:0010487 AAO AAO:BJB The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000384 VHOG http://bgee.unil.ch/ The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] 2012-09-17 VHOG:0000384 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463 http://bgee.unil.ch/ UMLS:C0039044 BIRNLEX:2516 ncithesaurus:Sympathetic_Nervous_System UMLS:C1269646 BIRNLEX:2516 pars sympathica divisionis autonomici systematis nervosi FMA:9906 FMA:TA pars sympathica divisionis autonomici systematis nervosi Wikipedia:Sympathetic_nervous_system Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive EHDAA2:0001844 EHDAA:6530 EMAPA:17525 EV:0100152 FMA:86166 GAID:933 MA:0000151 MAT:0000284 MESH:D012867 MIAA:0000284 SCTID:20795001 VHOG:0000860 Wikipedia:Skin portion of skin region of skin skin skin region skin zone uberon UBERON:0000014 zone of skin http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg FMA Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Wikipedia:Skin http://orcid.org/0000-0002-6601-2165 (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] 2012-09-17 VHOG:0000860 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) http://bgee.unil.ch/ skin MA:0000151 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 FMA:50705 anatomical boundary uberon UBERON:0000015 Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. non-material anatomical boundary CARO A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CARO:0000010 anatomical boundary CARO:0000010 The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. create a separate class for distributed pancreas, eg cyclostomes? The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG] The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys BTO:0000650 CALOHA:TS-1302 EFO:0002542 EMAPA:35305 EV:0100129 FMA:16018 MA:0001582 MESH:D007515 NCIT:C32509 SCTID:361339003 TAO:0001260 VHOG:0000049 Wikipedia:Islets_of_Langerhans ZFA:0001260 endocrine pancreas pars endocrina pancreatis uberon endocrine part of pancreas islets of Langerhans part of pancreas UBERON:0000016 endocrine pancreas ZFA AAO FMA XAO GO GO GO The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. GO:GO http://orcid.org/0000-0002-6601-2165 The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG] 2012-09-17 VHOG:0000049 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Pancreas The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO] 2012-08-14 TAO:0001260 TAO ZFIN:curator In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000049 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) http://bgee.unil.ch/ endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys PMID:20959416 MESH:D007515 https://github.com/biopragmatics/biomappings endocrine part of pancreas BTO:0000650 The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] AAO:0010407 BTO:0000434 CALOHA:TS-1241 EMAPA:35328 EV:0100093 FMA:16017 MA:0002415 MESH:D046790 NCIT:C32546 SCTID:248202004 TAO:0001249 UMLS:C0553695 VHOG:0000048 Wikipedia:Exocrine_component_of_pancreas XAO:0000137 ZFA:0001249 exocrine pancreas pars exocrina pancreatis uberon exocrine component of pancreas exocrine part of pancreas UBERON:0000017 exocrine pancreas The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. GOC:GO http://orcid.org/0000-0002-6601-2165 The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] 2012-08-14 TAO:0001249 TAO ZFIN:curator The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] 2012-09-17 VHOG:0000048 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Pancreas In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000048 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) http://bgee.unil.ch/ MESH:D046790 https://github.com/biopragmatics/biomappings UMLS:C0553695 ncithesaurus:Exocrine_Pancreas exocrine part of pancreas BTO:0000434 A light sensing organ composed of ommatidia. The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures BTO:0001921 FBbt:00004508 HAO:0000217 IDOMAL:0002421 TGMA:0000024 Wikipedia:Compound_eye uberon Facettenauge Komplexauge adult compound eye faceted eye insect eye zusammengesetztes Auge UBERON:0000018 compound eye https://github.com/obophenotype/uberon/issues/457 PMID:21062451 A light sensing organ composed of ommatidia. FB:gg Wikipedia:Compound_eye The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures PMID:21062451 FBbt:00004508 IDOMAL:0002421 https://github.com/biopragmatics/biomappings Facettenauge BTO:0001921 Komplexauge BTO:0001921 zusammengesetztes Auge BTO:0001921 An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. A cavitated compound organ that transduces light waves into neural signals.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this eye AAO:0010340 BIRNLEX:1169 BTO:0004688 EHDAA2:0000484 EHDAA:936 EMAPA:16198 FMA:54448 MA:0000261 NCIT:C12401 SCTID:181143004 TAO:0000107 UMLS:C0015392 UMLS:C1280202 VHOG:0000275 XAO:0000179 ZFA:0000107 regio orbitalis vertebrate eye uberon camera-type eye plus associated structures eyes orbital part of face orbital region UBERON:0000019 camera-type eye definitional An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. GO:0043010 https://orcid.org/0000-0002-6601-2165 A cavitated compound organ that transduces light waves into neural signals.[TAO] 2012-08-14 TAO:0000107 TAO TAO:wd The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000275 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this FMA eye FMA:54448 UMLS:C0015392 BIRNLEX:1169 ncithesaurus:Eye UMLS:C1280202 BIRNLEX:1169 regio orbitalis FMA:54448 FMA:TA eyes TAO:0000107 orbital part of face FMA:54448 orbital region FMA:54448 An organ that is capable of transducing sensory stimulus to the nervous system. AEO:0000094 BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 NCIT:C33224 SCTID:244485009 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensory organ sensory organ system organ sensory system organ sensillum uberon Sinnesorgan sensor UBERON:0000020 sense organ http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png An organ that is capable of transducing sensory stimulus to the nervous system. https://github.com/obophenotype/uberon/issues/549 https://orcid.org/0000-0002-6601-2165 FBbt:00005155 UMLS:C0935626 ncithesaurus:Organ_of_the_Special_Sense organ of sense organ system OBOL:accepted organ of sensory organ system OBOL:accepted organ of sensory system OBOL:accepted sense organ system organ OBOL:automatic sensory organ system organ OBOL:automatic sensory system organ OBOL:accepted sensillum WBbt:0006929 Sinnesorgan BTO:0000202 Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) tubular galen:Tube anatomical tube duct uberon UBERON:0000025 tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. http://orcid.org/0000-0002-6601-2165 Major subdivision of an organism that protrudes from the body[DOS, CARO]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. appendicular this is currently a subtype of organism subdivision - which would exclude feathers AEO:0000193 BILA:0000018 BTO:0001492 CARO:0010003 EFO:0000799 EHDAA2:0003193 EMAPA:37283 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 NCIT:C61460 UMLS:C0598782 VSAO:0000075 Wikipedia:Appendage XAO:0000218 uberon appendages extremitaet extremity limbs/digits/tail UBERON:0000026 appendage Major subdivision of an organism that protrudes from the body[DOS, CARO]. CARO:DOS An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. BILA:0000018 Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. GO:0048736 EMAPA:37283 MA:th FBbt:00007000 UMLS:C0598782 ncithesaurus:Appendage appendages XAO:0000218 extremitaet BTO:0001492 limbs/digits/tail MP:0000001 A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. BTO:0002330 FMA:62517 NCIT:C32918 SCTID:298225002 UMLS:C1179187 Wikipedia:Lamina_propria lamina propria mucosa lamina propria mucosae uberon tunica propria UBERON:0000030 lamina propria https://upload.wikimedia.org/wikipedia/commons/f/fb/GI_Organization.svg A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. Wikipedia:Lamina_propria UMLS:C1179187 ncithesaurus:Lamina_Propria tunica propria BTO:0002330 A lamina propria that is part of a respiratory airway. EMAPA:35877 FMA:265157 MA:0001858 NCIT:C49305 UMLS:C1710457 lamina propria mucosa of trachea lamina propria mucosa of windpipe lamina propria mucosae of trachea lamina propria mucosae of windpipe lamina propria of windpipe trachea lamina propria trachea lamina propria mucosa trachea lamina propria mucosae tracheal lamina propria windpipe lamina propria windpipe lamina propria mucosa windpipe lamina propria mucosae uberon UBERON:0000031 lamina propria of trachea true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a respiratory airway. OBOL:automatic UMLS:C1710457 ncithesaurus:Trachea_Lamina_Propria lamina propria mucosa of trachea OBOL:automatic lamina propria mucosa of windpipe OBOL:automatic lamina propria mucosae of trachea OBOL:automatic lamina propria mucosae of windpipe OBOL:automatic lamina propria of windpipe OBOL:automatic trachea lamina propria mucosa OBOL:automatic trachea lamina propria mucosae OBOL:automatic windpipe lamina propria OBOL:automatic windpipe lamina propria mucosa OBOL:automatic windpipe lamina propria mucosae OBOL:automatic The head is the anterior-most division of the body [GO]. Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] AAO:0010335 AEO:0000106 BILA:0000115 BIRNLEX:1230 BTO:0000282 CALOHA:TS-0436 EFO:0000964 EHDAA2:0003106 EMAPA:31858 FMA:7154 GAID:61 HAO:0000397 MA:0000023 MAT:0000294 MESH:D006257 MIAA:0000294 NCIT:C12419 SCTID:302548004 SPD:0000016 TAO:0001114 TGMA:0000002 UMLS:C0018670 VHOG:0001644 WBbt:0005739 Wikipedia:Head XAO:0003024 ZFA:0001114 galen:Head head (volume) adult head uberon cephalic area UBERON:0000033 head The head is the anterior-most division of the body [GO]. GO:0060322 Wikipedia:Head Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] 2012-06-20 AAO:0010335 AAO AAO:BJB Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] 2012-08-14 TAO:0001114 TAO ZFIN:curator Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] 2012-09-17 VHOG:0001644 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 http://bgee.unil.ch/ UMLS:C0018670 BIRNLEX:1230 ncithesaurus:Head head (volume) FMA:7154 cephalic area SPD:0000016 Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA:9581 GAID:19 MESH:D012704 NCIT:C13169 SCTID:362878009 TAO:0005425 UMLS:C0036760 Wikipedia:Serous_membrane ZFA:0005425 tunica serosa wall of serous sac uberon serosa UBERON:0000042 serous membrane http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. Wikipedia:Serous_membrane https://github.com/obophenotype/uberon/issues/86 A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] 2012-08-14 TAO:0005425 TAO Wikipedia:Serous_membrane a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] Wikipedia:Serous_membrane in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA UMLS:C0036760 ncithesaurus:Serosa tunica serosa FMA:9581 wall of serous sac FMA:9581 serosa Wikipedia:Serous_membrane Dense regular connective tissue that connects muscle to bone[VSAO]. Dense regular connective tissue that connects muscle to bone.[VSAO] Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis AEO:0000091 BTO:0001356 CALOHA:TS-1021 EHDAA2:0003091 EMAPA:35854 EV:0100149 FMA:9721 GAID:276 MA:0000115 MESH:D013710 NCIT:C13045 SCTID:256667004 UMLS:C0039508 VHOG:0001286 VSAO:0000073 Wikipedia:Tendon XAO:0000173 ZFA:0005647 galen:Tendon uberon sinew tendo UBERON:0000043 tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg VSAO OG AEO Dense regular connective tissue that connects muscle to bone[VSAO]. GO_REF:0000034 VSAO:0000073 Wikipedia:Tendon http://dx.plos.org/10.1371/journal.pone.0051070 Dense regular connective tissue that connects muscle to bone.[VSAO] 2012-08-14 VSAO:0000073 VSAO PSPUB:0000170 Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] 2012-09-17 VHOG:0001286 VHOG DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) http://bgee.unil.ch/ in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis FMA UMLS:C0039508 ncithesaurus:Tendon sinew Wikipedia:Tendon tendo Wikipedia:Tendon A biological tissue mass, most commonly a mass of nerve cell bodies. TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] ganglionic AAO:0010426 AEO:0000135 BAMS:G BTO:0000497 CALOHA:TS-0397 EFO:0000899 EHDAA2:0003135 EHDAA:2897 EHDAA:4662 EHDAA:5621 EHDAA:918 EMAPA:32846 EV:0100372 FMA:5884 MA:0002406 MAT:0000207 MAT:0000343 MESH:D005724 MIAA:0000207 MIAA:0000343 NCIT:C12719 NLXANAT:100302 TAO:0000190 TGMA:0001016 UMLS:C0017067 VHOG:0000156 WBbt:0005189 Wikipedia:Ganglion XAO:0000209 ZFA:0000190 uberon ganglia neural ganglion UBERON:0000045 ganglion https://github.com/obophenotype/uberon/issues/2495#issuecomment-1187364719 EHDAA2 Bgee:AN A biological tissue mass, most commonly a mass of nerve cell bodies. Wikipedia:Ganglion https://github.com/obophenotype/uberon/issues/300 A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures PMID:21062451 Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] 2012-06-20 AAO:0010426 AAO AAO:EJS Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000190 TAO ZFIN:curator Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. NLXANAT:100302 Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000156 VHOG DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005) http://bgee.unil.ch/ UMLS:C0017067 ncithesaurus:Ganglion neural ganglion BTO:0000497 An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. TGMA:0000729 Wikipedia:Eye#Simple_eyes uberon UBERON:0000047 simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. Wikipedia:Eye#Simple_eyes A tubular structure that contains, conveys body fluid, such as blood or lymph. uberon UBERON:0000055 vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. https://orcid.org/0000-0002-6601-2165 A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 FBbt:00100314 FMA:30320 NCIT:C12948 SCTID:91726008 TAO:0005171 UMLS:C0687028 Wikipedia:Duct_(anatomy) XAO:0004000 ZFA:0005171 galen:Duct anatomical duct exocrine duct exocrine gland duct uberon ducts UBERON:0000058 duct A tubular structure that transports secreted or excreted substances. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm#ducts A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. ZFA:0005171 FBbt:00100314 UMLS:C0687028 ncithesaurus:Duct ducts XAO:0004000 A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 MA:0000333 MESH:D007420 MIAA:0000046 NCIT:C12379 SCTID:181254001 UMLS:C0021851 VHOG:0000054 Wikipedia:Large_intestine_(anatomy) XAO:0000131 galen:LargeIntestine uberon intestinum crassum UBERON:0000059 large intestine https://ccf-ontology.hubmapconsortium.org/objects/v1.0/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb cjm A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. ISBN:0073040584 Wikipedia:Large_intestine_(anatomy) Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000054 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 http://bgee.unil.ch/ UMLS:C0021851 ncithesaurus:Large_Intestine intestinum crassum BTO:0000706 Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. in FMA, serosa is a wall UBERON:0009915 wall EMAPA:25036 FMA:82482 galen:Wall wall of organ uberon organ wall UBERON:0000060 anatomical wall Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 in FMA, serosa is a wall FMA wall of organ FMA:82482 organ wall FMA:82482 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 FBbt:00007001 connected biological structure CARO:0000003 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 SCTID:272625005 UMLS:C0178784 WBbt:0003760 Wikipedia:Organ_(anatomy) uberon anatomical unit body organ element UBERON:0000062 organ PMID:28192867 Anatomical structure that performs a specific function or group of functions [WP]. Wikipedia:Organ_(anatomy) Wikipedia Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GO:0048513 UMLS:C0178784 ncithesaurus:Organ element http://orcid.org/0000-0002-6601-2165 A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary organ segment segment of organ UBERON:0000063 organ subunit A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. FMA:86140 3 Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 1 organ region with fixed fiat boundary FMA:86140 organ segment FMA:86140 segment of organ FMA:86140 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 SCTID:113343008 SCTID:91717005 cardinal organ part uberon regional part of organ UBERON:0000064 organ part A multicellular structure that is a part of an organ. http://orcid.org/0000-0002-6601-2165 cardinal organ part FMA:82472 regional part of organ BIRNLEX:16 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts. EHDAA2:0001606 EHDAA:1568 EHDAA:2219 EMAPA:16737 FMA:265130 SCTID:361110005 VHOG:0000393 uberon UBERON:0000065 respiratory tract NCBIBook:NBK10107 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts. https://orcid.org/0000-0002-6601-2165 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. adult stage BTO:0001043 BilaDO:0000004 EFO:0001272 FBdv:00005369 WBls:0000041 XtroDO:0000084 fully formed animal stage juvenile-adult stage uberon UBERON:0000066 fully formed stage https://github.com/obophenotype/uberon/issues/566 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. https://orcid.org/0000-0002-6601-2165 A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 SCTID:296280003 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage uberon embryogenesis UBERON:0000068 embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. http://orcid.org/0000-0002-6601-2165 A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. Uberon includes clade-specific subclasses, e.g. nematod larva It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form BTO:0000915 BTO:0000954 EFO:0001303 FBdv:00005336 MIAA:0000400 OGES:000008 Wikipedia:Larva ZFS:0000048 larva stage ammocoete ammocoete stage bipinnaria bipinnaria stage caterpillar caterpillar stage glochidium glochidium stage grub grub stage leptocephalus leptocephalus stage maggot maggot stage metacestode naiad, nymph naiad, nymph stage nauplius nauplius stage nymph nymph stage planula planula stage tornaria trochophore trochophore stage veliger veliger stage wriggler wriggler stage zoea zoea stage uberon larva UBERON:0000069 larval stage A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. Wikipedia:Larva It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form WP ammocoete Wikipedia:Larva ammocoete stage Wikipedia:Larva bipinnaria Wikipedia:Larva bipinnaria stage Wikipedia:Larva caterpillar Wikipedia:Larva caterpillar stage Wikipedia:Larva glochidium Wikipedia:Larva glochidium stage Wikipedia:Larva grub Wikipedia:Larva grub stage Wikipedia:Larva leptocephalus Wikipedia:Larva leptocephalus stage Wikipedia:Larva maggot Wikipedia:Larva maggot stage Wikipedia:Larva metacestode BTO:0000859 naiad, nymph Wikipedia:Larva naiad, nymph stage Wikipedia:Larva nauplius Wikipedia:Larva nauplius stage Wikipedia:Larva nymph Wikipedia:Larva nymph stage Wikipedia:Larva planula Wikipedia:Larva planula stage Wikipedia:Larva tornaria NCBITaxon:10219 trochophore Wikipedia:Larva trochophore stage Wikipedia:Larva veliger Wikipedia:Larva veliger stage Wikipedia:Larva wriggler Wikipedia:Larva wriggler stage Wikipedia:Larva zoea Wikipedia:Larva zoea stage Wikipedia:Larva End of the life of an organism. ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon death UBERON:0000071 death stage End of the life of an organism. XAO:0000437 ncit:Death is an outcome ncit An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole EMAPA:16737 FMA:45660 MA:0000434 uberon respiratory tract subdivision of respiratory tract UBERON:0000072 proximo-distal subdivision of respiratory tract An section of a respiratory tract. http://orcid.org/0000-0002-6601-2165 MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole MA respiratory tract MA:0000434 Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. 2009-06-18T09:00:04Z BIRNLEX:1157 NCIT:C13040 SCTID:25087005 UMLS:C1518256 part of nervous system uberon UBERON:0000073 regional part of nervous system Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. BIRNLEX:1157 UMLS:C1518256 ncithesaurus:Nervous_System_Part part of nervous system BIRNLEX:1157 Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision uberon skeletal system part UBERON:0000075 subdivision of skeletal system cjm Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 UMLS:C1519343 ncithesaurus:Skeletal_System_Part skeletal system subdivision FMA:85544 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis BTO:0006242 EHDAA2:0001968 EHDAA:1494 EHDAA:350 EHDAA:4784 EHDAA:4790 EHDAA:4796 EHDAA:7860 EMAPA:16096 FMA:87656 NCIT:C34309 UMLS:C1515087 Wikipedia:External_ectoderm surface (external) ectoderm surface ectoderm uberon UBERON:0000076 external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png EHDAA2 EHDAA2 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. MGI:anna MP:0012532 BTO:0006242 https://github.com/biopragmatics/biomappings UMLS:C1515087 ncithesaurus:Surface_Ectoderm surface ectoderm MP:0012532 An anatomical structure that develops from the endoderm and the mesoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000077 mixed endoderm/mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. https://orcid.org/0000-0002-6601-2165 An anatomical structure that develops from the ectoderm, mesoderm and endoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000078 mixed ectoderm/mesoderm/endoderm-derived structure An anatomical structure that develops from the ectoderm, mesoderm and endoderm. https://orcid.org/0000-0002-6601-2165 A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum. EHDAA2 has embryo starting later BTO:0001508 EHDAA2:0000005 FMA:292334 GAID:1295 MESH:D009028 NCIT:C34212 SCTID:361474003 UMLS:C0026573 Wikipedia:Morula uberon morula (2-16 cells) UBERON:0000085 morula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png EHDAA2 A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum. MP:0012130 EHDAA2 has embryo starting later EHDAA2 UMLS:C0026573 ncithesaurus:Morula morula (2-16 cells) EHDAA2:0000005 A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes. Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG] zona pellucida - vitelline membrane BTO:0003135 EHDAA2:0002220 EHDAA:31 EHDAA:62 EMAPA:16035 FMA:18674 GAID:410 MA:0001715 MESH:D015044 NCIT:C33896 TAO:0001111 UMLS:C0043519 VHOG:0000720 Wikipedia:Zona_pellucida ZFA:0001111 uberon oolemma pellucid zone striated membrane vitelline envelope vitelline membrane zona radiata zona striata UBERON:0000086 zona pellucida http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes. Wikipedia:Zona_pellucida Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG] 2012-09-17 VHOG:0000720 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159 http://bgee.unil.ch/ zona pellucida - vitelline membrane VHOG:0000720 UMLS:C0043519 ncithesaurus:Zona_Pellucida oolemma BTO:0003135 pellucid zone BTO:0003135 striated membrane BTO:0003135 zona radiata BTO:0003135 zona striata BTO:0003135 A mass of cells that develop into the body of the embryo and some extraembryonic tissues. A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass] EFO:0000547 EHDAA2:0000830 EHDAA:40 EMAPA:16041 FMA:86557 NCIT:C13740 SCTID:361456007 UMLS:C1283994 VHOG:0000742 Wikipedia:Inner_cell_mass uberon ICM early embryoblast embryoblast embryoblastus; massa cellularis interna; pluriblastus senior pluriblast UBERON:0000087 inner cell mass https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg Wikipedia Wikipedia A mass of cells that develop into the body of the embryo and some extraembryonic tissues. ISBN:0-683-40008-8 MGI:pvb A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] 2012-09-17 VHOG:0000742 VHOG http://bgee.unil.ch/ A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] 2012-09-17 VHOG:0000742 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144 http://bgee.unil.ch/ UMLS:C1283994 ncithesaurus:Inner_Cell_Mass ICM VHOG:0000742 early embryoblast FMA:86557 embryoblastus; massa cellularis interna; pluriblastus senior Wikipedia:Inner_cell_mass The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta. the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP] trophoblastic The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta BTO:0001079 CALOHA:TS-1070 EV:0100120 FMA:83029 GAID:1152 MESH:D014327 NCIT:C93292 SCTID:362839005 UMLS:C0041178 Wikipedia:Trophoblast trophoblast layer uberon massa cellularis externa trophoblastus trophoderm UBERON:0000088 Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast] trophoblast https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg MP-def PMID:19829370 The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta. ISBN:0-683-40008-8 MP:0005031 the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP] 2012-08-23 MP:0005031 trophoblast layer MP ISBN:0-683-40008-8 The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta PMID:19829370 UMLS:C0041178 ncithesaurus:Trophoblast trophoblast layer MP:0005031 massa cellularis externa Wikipedia:Trophoblast trophoblastus Wikipedia:Trophoblast trophoderm BTO:0001079 A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. embryonic disc embryonic shield germinal disc germinal disk FMA:293863 NCIT:C34112 UMLS:C1283997 Wikipedia:Bilaminar_disc bilaminary embryonic disc bilaminary germ disc uberon bilaminar disk UBERON:0000091 bilaminar disc http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png Wikipedia A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. MP:0003886 embryonic disc MP:0003886 embryonic shield MP:0003886 germinal disc MP:0003886 germinal disk MP:0003886 UMLS:C1283997 ncithesaurus:Bilaminar_Embryonic_Disc bilaminary germ disc ISBN:9780878932504 bilaminar disk Wikipedia:Bilaminar_disc Stage succeeding embryo, including mature structure. In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 OGES:000024 WBls:0000022 WBls:0000093 WBls:0000103 postembryonic stage post-hatching stage uberon postembryonic UBERON:0000092 post-embryonic stage https://github.com/obophenotype/uberon/issues/344 Stage succeeding embryo, including mature structure. https://orcid.org/0000-0002-6601-2165 Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]. 2009-07-30T05:19:13Z membrane FMA:7145 membrane of organ uberon UBERON:0000094 membrane organ FMA-def Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]. FMA:7145 Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]. A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. ZFA treats this as a subtype of NC. 2009-07-30T07:57:38Z TAO:0002173 Wikipedia:Cardiac_neural_crest XAO:0004190 ZFA:0001648 uberon cardiac neural crest complex complexus cristae neuralis cardiacus UBERON:0000095 cardiac neural crest Wikipedia Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]. Wikipedia:Cardiac_neural_crest A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. DOI:10.1242/dev.091751 ZFA treats this as a subtype of NC. ZFA cardiac neural crest complex Wikipedia:Cardiac_neural_crest complexus cristae neuralis cardiacus Wikipedia:Cardiac_neural_crest A lung lobe is one of the rounded projections that compose the lung[GO]. EMAPA:36281 FMA:7311 MA:0003098 NCIT:C34021 SCTID:245524004 UMLS:C0225752 galen:LobeOfLung lung lobe pulminory lobe pulmonary lobe uberon UBERON:0000101 lobe of lung FMA A lung lobe is one of the rounded projections that compose the lung[GO]. GOC:GO UMLS:C0225752 ncithesaurus:Lung_Lobe pulmonary lobe FMA:7311 The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. FMA:73750 lung vascular network pulmonary vasculature vascular network of lung vasculature of lung uberon UBERON:0000102 lung vasculature The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. GOC:GO lung vascular network OBOL:automatic pulmonary vasculature FMA:73750 vascular network of lung OBOL:automatic vasculature of lung OBOL:automatic An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism. FBdv:00000000 HsapDv:0000001 MmusDv:0000001 OGES:000011 ncithesaurus:Life entire life cycle entire lifespan life lifespan uberon UBERON:0000104 life cycle https://github.com/obophenotype/uberon/issues/532 An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism. https://orcid.org/0000-0002-6601-2165 A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MESH:D008018 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage uberon UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. https://orcid.org/0000-0002-6601-2165 A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 Wikipedia:Zygote XAO:1000001 ZFS:0000001 1-cell stage fertilized egg stage one cell stage uberon fertilized egg stage one-cell stage zygote zygotum UBERON:0000106 zygote stage A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] 2012-09-17 VHOG:0000745 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 http://bgee.unil.ch/ IDOMAL:0000302 https://github.com/biopragmatics/biomappings fertilized egg stage BTO:0000854 one-cell stage VHOG:0000745 zygote VHOG:0000745 zygotum Wikipedia:Zygote The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. BILS:0000107 BilaDO:0000006 EFO:0001290 FBdv:00000054 MESH:D002970 MmusDv:0000004 OGES:000015 OGES:000020 PdumDv:0000200 Wikipedia:Cleavage_(embryo) XAO:1000004 ZFS:0000046 uberon UBERON:0000107 cleavage stage The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. GO:0040016 Wikipedia:Cleavage_(embryo) An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. consider adding a preceding stage 'morula stage' as part of cleavage BILS:0000108 BilaDO:0000007 EFO:0001282 HsapDv:0000006 MmusDv:0000007 OGES:000003 OGES:000016 OGES:000021 WBls:0000005 Wikipedia:Blastula XAO:1000003 ZFS:0000045 uberon UBERON:0000108 blastula stage http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. Wikipedia:Blastula A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. BILS:0000109 BilaDO:0000008 EFO:0001296 FBdv:00005317 HsapDv:0000010 MmusDv:0000013 OGES:000004 OGES:000019 WBls:0000010 XAO:1000005 ZFS:0000047 uberon blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage UBERON:0000109 gastrula stage BILS A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. GO:0007369 blastocystis trilaminaris stage https://orcid.org/0000-0002-6601-2165 trilaminar blastocyst stage https://orcid.org/0000-0002-6601-2165 trilaminar blastoderm stage https://orcid.org/0000-0002-6601-2165 trilaminar disk stage https://orcid.org/0000-0002-6601-2165 trilaminar germ stage https://orcid.org/0000-0002-6601-2165 trilaminar stage https://orcid.org/0000-0002-6601-2165 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 XAO:1000006 uberon UBERON:0000110 neurula stage https://github.com/obophenotype/developmental-stage-ontologies/issues/84 https://github.com/obophenotype/uberon/issues/343 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GO:0001841 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. BILS:0000111 BilaDO:0000010 HsapDv:0000015 MmusDv:0000018 OGES:000005 OGES:000032 Wikipedia:Organogenesis uberon segmentation stage UBERON:0000111 organogenesis stage https://github.com/obophenotype/developmental-stage-ontologies/issues/84 https://github.com/obophenotype/uberon/issues/533 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. Wikipedia:Organogenesis The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin. it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces EMAPA:35521 FMA:27533 MA:0001782 SCTID:201609008 connective tissue of lung pulmonary interstitium uberon lung interstitial tissue lung interstitium pulmonary connective tissue pulmonary interstitial tissue UBERON:0000114 lung connective tissue The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin. ISBN:0-683-40008-8 MGI:anna MP:0002276 PMID:14635660 connective tissue of lung OBOL:automatic pulmonary interstitium FMA:27533 lung interstitial tissue MA:0001782 pulmonary connective tissue EMAPA:35521 The epithelial layer of the lung. A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469] BTO:0001653 EMAPA:32860 MA:0001783 epithelial tissue of lung epithelium of lung lung epithelial tissue uberon pulmonary epithelium UBERON:0000115 lung epithelium The epithelial layer of the lung. MP:0006382 epithelial tissue of lung OBOL:automatic epithelium of lung OBOL:automatic lung epithelial tissue OBOL:automatic pulmonary epithelium BTO:0001653 A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) EMAPA:37946 FMA:12224 segment of tracheobronchial tree respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment uberon airway UBERON:0000117 respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. GO:0030323 http://orcid.org/0000-0002-6601-2165 in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) GO EMAPA:37946 MA:th segment of tracheobronchial tree FMA:12224 respiratory conducting tube MP:0004391 segment of tracheobronchial tree FMA:12224 tracheobronchial tree segment FMA:12224 Structure derived from foregut that becomes a lung[GO]. clarify successors - include bronchi? BTO:0001643 EHDAA2:0004089 NCIT:C34260 NCIT:C34282 SCTID:361427007 UMLS:C1514420 UMLS:C1514897 Wikipedia:Respiratory_bud uberon gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum UBERON:0000118 lung bud http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png GO:0060441 EHDAA2 Structure derived from foregut that becomes a lung[GO]. GO:0060431 Wikipedia:Respiratory_bud UMLS:C1514420 ncithesaurus:Primary_Bronchial_Bud UMLS:C1514897 ncithesaurus:Respiratory_Diverticulum gemma pulmonalis Wikipedia:Lung_buds gemma respiratoria Wikipedia:Lung_buds lung bud primary lung bud GO:0060572 respiratory diverticulum Wikipedia:Lung_buds A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. UBERON:0005163 CARO:0001001 FBbt:00005099 NLX:147821 funiculus nerve fiber bundle neural fiber bundle uberon UBERON:0000122 neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBC:DOS FBbt:00005099 FBbt:00005099 nerve fiber bundle FBbt:00005099 A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO). Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. nucleus AEO:0000136 FMA:83686 NCIT:C13197 NLX:28443 Wikipedia:Nucleus_(neuroanatomy) nervous system nucleus neuraxis nucleus neuronal nucleus nucleus of CNS uberon nucleus of neuraxis UBERON:0000125 neural nucleus we limit this structure by definition to chordate and vertebrate nervous systems A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO). NLX:28443 Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. GO_REF:0000021 neuraxis nucleus FMA:83686 neuronal nucleus AEO:0000136 nucleus of CNS NLX:28443 Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves. EMAPA:37066 FMA:54501 NLX:28532 SCTID:280160003 Wikipedia:Cranial_nerve_nucleus cranial neural nucleus nucleus of cranial nerve uberon nucleus nervi cranialis UBERON:0000126 cranial nerve nucleus http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves. NLX:28532 EMAPA:37066 MA:th cranial neural nucleus FMA:54501 nucleus nervi cranialis Wikipedia:Cranial_nerve_nucleus uberon UBERON:0000153 anterior region of body lexical uberon UBERON:0000154 posterior region of body lexical A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. membrane FMA:30322 FMA:82500 MESH:D008566 NCIT:C12749 membranous organ component uberon UBERON:0000158 membranous layer A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. ncithesaurus:Membrane membranous organ component FMA:82500 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. requires alignment with EHDAA2 and complete developmental relationships BTO:0001978 CALOHA:TS-2160 EMAPA:18256 FMA:15703 MA:0000330 MESH:D001003 NCIT:C12375 SCTID:245438008 UMLS:C0227411 Wikipedia:Anal_canal galen:AnalCanal anal canal anal canal viewed anatomically anatomical anal canal uberon anal pad anus canalis analis cloaca cloacal chamber mesenteron pars analis recti UBERON:0000159 anal canal https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png Wikipathways:WP2062 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. Wikipedia:Anal_canal MESH:D001003 https://github.com/biopragmatics/biomappings UMLS:C0227411 ncithesaurus:Anal_Canal canalis analis BTO:0001978 Wikipedia:Anal_canal pars analis recti BTO:0001978 Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. This class is probably too inclusive Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] intestinal In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EV:0100071 FMA:7199 GAID:295 MA:0000328 MA:0001524 MESH:D007422 MIAA:0000043 NCIT:C12736 SCTID:256876008 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 Wikipedia:Intestine XAO:0000129 ZFA:0001338 galen:Intestine bowel uberon intestinal tract UBERON:0000160 intestine cjm Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. GOC:GO Wikipedia:Intestine Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] 2012-06-20 AAO:0000246 AAO AAO:EJS The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000056 VHOG http://bgee.unil.ch/ UMLS:C0021853 ncithesaurus:Intestine Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. in FMA, this is an anatomical conduit *space*, rather than anatomical conduit anatomical ostium ostium FMA:3724 SCTID:91837002 anatomical orifice hilum uberon UBERON:0000161 orifice Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 in FMA, this is an anatomical conduit *space*, rather than anatomical conduit FMA anatomical ostium FMA:3724 anatomical orifice FMA:3724 Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] cloacal Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs hindgut endoderm and proctodeal ectoderm. AAO:0000095 GAID:1206 MESH:D002988 NCIT:C34127 SCTID:362857006 SCTID:370631000 UMLS:C0008987 VHOG:0001186 Wikipedia:Cloaca XAO:0000244 ZFA:0005781 uberon cloacal chamber vent UBERON:0000162 cloaca ZFA AAO Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. ISBN:0073040584 Wikipedia:Cloaca most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults. A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] 2012-09-17 VHOG:0001186 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/cloaca Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] 2012-06-20 AAO:0000095 AAO AAO:BJB A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001186 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572 http://bgee.unil.ch/ hindgut endoderm and proctodeal ectoderm. WP UMLS:C0008987 ncithesaurus:Cloaca cloacal chamber AAO:0000095 vent XAO:0000244 Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. EHDAA2:0000256 EHDAA:4895 EMAPA:27573 Wikipedia:Cloaca_(embryology) uberon cloaca UBERON:0000163 embryonic cloaca EHDAA2 EHDAA2 Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. MP:0010115 Wikipedia:Cloaca_(embryology) cloaca The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] oral some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 SCTID:21082005 TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 VHOG:0000280 VHOG:0000812 Wikipedia:Mouth XAO:0003029 ZFA:0000547 ZFA:0000590 galen:Mouth http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg regio oralis adult mouth uberon cavital oralis cavitas oris cavum oris mouth cavity oral region oral vestibule rima oris stoma stomatodaeum trophic apparatus vestibule of mouth vestibulum oris UBERON:0000165 mouth https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] 2012-06-20 AAO:0010355 AAO AAO:BJB Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] 2012-09-17 VHOG:0000812 VHOG DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) http://bgee.unil.ch/ in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips FMA FBbt:00003126 regio oralis BTO:0004698 FMA:49184 FMA:TA cavital oralis Wikipedia:Mouth cavitas oris BTO:0001090 cavum oris BTO:0001090 mouth cavity BTO:0001090 oral region EHDAA2:0001326 oral vestibule BTO:0001090 rima oris BTO:0001090 stomatodaeum VHOG:0000812 trophic apparatus http://orcid.org/0000-0002-6601-2165 vestibule of mouth BTO:0001090 vestibulum oris BTO:0001090 The orifice that connects the mouth to the exterior of the body. (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] FMA:59806 oral fissure oral orifice uberon mouth oral part of face UBERON:0000166 oral opening FMA The orifice that connects the mouth to the exterior of the body. https://github.com/obophenotype/uberon/wiki/The-digestive-tract (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] 2012-09-17 VHOG:0000280 VHOG DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007) http://bgee.unil.ch/ oral fissure FMA:59806 oral orifice FMA:59806 mouth Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present). Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] AAO:0000053 AAO:0000960 BSA:0000107 CALOHA:TS-1315 EFO:0001975 EHDAA2:0001324 EHDAA:6970 EMAPA:17411 EMAPA:18399 EV:0100057 FMA:20292 HAO:0000669 MESH:D009055 NCIT:C12421 SCTID:181220002 TAO:0001027 TGMA:0000102 UMLS:C0226896 VHOG:0000188 WBbt:0005255 XAO:0000126 ZFA:0001027 buccal cavity cavity of mouth uberon bucca UBERON:0000167 oral cavity Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present). ISBN:0073040584 https://github.com/obophenotype/uberon/wiki/The-digestive-tract https://orcid.org/0000-0002-6601-2165 Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000960 AAO AAO:EJS The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] 2012-09-17 VHOG:0000188 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/oral+cavity Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] 2012-09-17 VHOG:0000188 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32 http://bgee.unil.ch/ MESH:D009055 https://github.com/biopragmatics/biomappings UMLS:C0226896 ncithesaurus:Oral_Cavity buccal cavity FMA:20292 ISBN:0073040584 A section dividing a colon along a proximal-distal axis. FMA:222905 uberon segment of colon UBERON:0000168 proximal-distal subdivision of colon 4 cjm A section dividing a colon along a proximal-distal axis. http://orcid.org/0000-0002-6601-2165 segment of colon FMA:222905 1 1 The pair of anatomical structures comprised of a left lung and right lung. FMA:68877 lungs lungs pair pulmones set of lungs uberon UBERON:0000170 pair of lungs FMA-abduced The pair of anatomical structures comprised of a left lung and right lung. http://orcid.org/0000-0002-6601-2165 pulmones FMA:68877 FMA:TA Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. EMAPA:17607 SCTID:272626006 SPD:0000428 TGMA:0001247 apparatus respiratorius organ breathing organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ uberon gas exchange organ UBERON:0000171 respiration organ Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. GO:0007585 apparatus respiratorius organ OBOL:automatic organ of apparatus respiratorius OBOL:automatic organ of respiratory system OBOL:automatic respiratory system organ OBOL:automatic A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. UBERON:0000324 UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance uberon excretion UBERON:0000174 excreta A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. GO:0007588 http://orcid.org/0000-0002-6601-2165 portion of excreted substance FMA:9674 waste substance AEO:0000184 excretion BTO:0000491 A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 TAO:0000007 UMLS:C0005767 VHOG:0000224 Wikipedia:Blood XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood uberon whole blood UBERON:0000178 blood CL:tm https://github.com/obophenotype/uberon/issues/1330 Bgee:AN A fluid that is composed of blood plasma and erythrocytes. FMA:9670 Wikipedia:Blood http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000007 TAO ZFIN:curator Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] 2012-06-20 AAO:0000046 AAO AAO:LAP relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000046 AAO Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] 2012-09-17 VHOG:0000224 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) http://bgee.unil.ch/ UMLS:C0005767 ncithesaurus:Blood whole blood BTO:0000089 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. 2009-04-08T04:38:19Z CARO:0000081 uberon blood or blood analog circulating fluid UBERON:0000179 haemolymphatic fluid Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. http://orcid.org/0000-0002-6601-2165 The bone forming the forehead and roof of the eye orbit. fused in humans, paired in other animals In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993). AAO:0000206 EMAPA:19016 FMA:52734 GAID:226 MA:0001466 MESH:D005624 NCIT:C32635 SCTID:181793006 UMLS:C0016732 VHOG:0001324 VSAO:0000208 Wikipedia:Frontal_bone frontal frontal bone os frontal uberon os frontale UBERON:0000209 tetrapod frontal bone http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png FMA cjm The bone forming the forehead and roof of the eye orbit. ISBN:0-683-40008-8 MP:0000107 PMID:7914451 Wikipedia:Frontal_bone UMLS:C0016732 ncithesaurus:Frontal_Bone frontal AAO:0000206 frontal bone FMA:52734 MA:0001466 os frontal Wikipedia:Frontal_bone os frontale Wikipedia:Frontal_bone FMA:24293 SCTID:281228008 Wikipedia:Atlas_(anatomy)#Vertebral_foramen vertebral foramen of cervical vertebra 1 uberon UBERON:0000219 vertebral foramen of atlas The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital. FMA:24939 MESH:D001269 NCIT:C32158 SCTID:361831006 UMLS:C0004169 Wikipedia:Atlanto-occipital_joint ncithesaurus:Atlanto-occipital_Joint-Atlanto articulatio atlanto-occipitalis atlanto occipital joint atlantooccipital joint craniovertebral joint occipito atlantal joint occipito-atlantal joint uberon articulatio atlantooccipitalis UBERON:0000220 atlanto-occipital joint http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png FMA-abduced-lr The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital. Wikipedia:Atlanto-occipital_joint MESH:D001269 https://github.com/biopragmatics/biomappings UMLS:C0004169 ncithesaurus:Atlanto-occipital_Joint articulatio atlanto-occipitalis FMA:24939 craniovertebral joint FMA:24939 articulatio atlantooccipitalis Wikipedia:Atlanto-occipital_joint A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath. TODO - add layer relations. 'tendon sheath' GAT in FMA. BTO:0000051 FMA:45087 FMA:76715 NCIT:C96299 SCTID:361885006 UMLS:C0224856 Wikipedia:Tendon_sheath synovial tendon sheath uberon vagina tendinis UBERON:0000304 tendon sheath A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath. Wikipedia:Tendon_sheath UMLS:C0224856 ncithesaurus:Tendon_Sheath synovial tendon sheath FMA:45087 vagina tendinis Wikipedia:Tendon_sheath Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 MESH:D036703 OGEM:000006 Wikipedia:Blastula blastula embryo uberon blastosphere UBERON:0000307 blastula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. Wikipedia:Blastula blastula embryo BILA:0000059 blastosphere Wikipedia:Blastula Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. UBERON:0003347 UBERON:0004981 BTO:0000271 CALOHA:TS-0164 EFO:0003038 EMAPA:27375 FMA:14984 FMA:85388 MA:0003194 SCTID:362157008 colon mucosa colon mucous membrane colonic mucosa colonic mucous membrane large bowel mucosa mucosa of colon mucosa of large bowel uberon UBERON:0000317 colonic mucosa Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. http://orcid.org/0000-0002-6601-2165 colon mucosa FMA:14984 colon mucous membrane OBOL:automatic colonic mucous membrane FMA:14984 large bowel mucosa OBOL:automatic mucosa of colon FMA:14984 mucosa of large bowel OBOL:automatic A mucosa that is part of a duodenum [Automatically generated definition]. UBERON:0003348 BTO:0000367 CALOHA:TS-0213 EMAPA:27235 FMA:14942 MA:0003207 SCTID:362146003 doudenal mucosa duodenal mucous membrane mucosa of duodenum mucous membrane of duodenum uberon duodenum mucosa UBERON:0000320 duodenal mucosa A mucosa that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal mucosa FMA:14942 duodenal mucous membrane FMA:14942 mucosa of duodenum OBOL:automatic mucous membrane of duodenum OBOL:automatic duodenum mucosa BTO:0000367 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. BTO:0000503 EMAPA:27181 FMA:14919 uberon UBERON:0000325 gastric gland cjm ISBN:0073040584 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. MGI:anna Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach. BTO:0000504 CALOHA:TS-2235 FMA:62973 GAID:1166 MESH:D010189 uberon pancreatic fluid pancreatic secretion succus pancreaticus UBERON:0000326 pancreatic juice Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach. GO:0030157 succus pancreaticus BTO:0000504 The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). We model the digestive tract as consisting of two parts: the wall and the lumen. BTO:0000547 FMA:45653 digestive tract wall wall of digestive tract wall of gut uberon wall of alimentary tract UBERON:0000328 gut wall The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). http://orcid.org/0000-0002-6601-2165 wall of gut FMA:45653 Bone marrow in which the fat cells predominate in the meshes of the reticular network. BTO:0000635 FMA:74596 SCTID:328639002 SCTID:5023006 medulla ossium flava yellow marrow uberon fat marrow UBERON:0000332 yellow bone marrow Bone marrow in which the fat cells predominate in the meshes of the reticular network. http://medical-dictionary.thefreedictionary.com/Yellow+Marrow medulla ossium flava BTO:0000635 yellow marrow BTO:0000635 fat marrow BTO:0000635 A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. Note that some sources treat 'intestinal gland' as synonymous with crypts BTO:0000640 FMA:15052 SCTID:266297002 bowel mucosa gland bowel mucosa of organ gland bowel mucous membrane gland bowel organ mucosa gland gland of bowel mucosa gland of bowel mucosa of organ gland of bowel mucous membrane gland of bowel organ mucosa gland of intestinal mucosa gland of intestine mucosa gland of intestine mucosa of organ gland of intestine mucous membrane gland of intestine organ mucosa gland of mucosa of bowel gland of mucosa of intestine gland of mucosa of organ of bowel gland of mucosa of organ of intestine gland of mucous membrane of bowel gland of mucous membrane of intestine gland of organ mucosa of bowel gland of organ mucosa of intestine glandula intestinalis intestinal mucosa gland intestine mucosa gland intestine mucosa of organ gland intestine mucous membrane gland intestine organ mucosa gland mucosa of bowel gland mucosa of intestine gland mucosa of organ of bowel gland mucosa of organ of intestine gland mucous membrane of bowel gland mucous membrane of intestine gland organ mucosa of bowel gland organ mucosa of intestine gland uberon glandulae intestinales UBERON:0000333 intestinal gland A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. https://orcid.org/0000-0002-6601-2165 bowel mucosa gland OBOL:automatic bowel mucosa of organ gland OBOL:automatic bowel mucous membrane gland OBOL:automatic bowel organ mucosa gland OBOL:automatic gland of bowel mucosa OBOL:automatic gland of bowel mucosa of organ OBOL:automatic gland of bowel mucous membrane OBOL:automatic gland of bowel organ mucosa OBOL:automatic gland of intestinal mucosa OBOL:automatic gland of intestine mucosa OBOL:automatic gland of intestine mucosa of organ OBOL:automatic gland of intestine mucous membrane OBOL:automatic gland of intestine organ mucosa OBOL:automatic gland of mucosa of bowel OBOL:automatic gland of mucosa of intestine OBOL:automatic gland of mucosa of organ of bowel OBOL:automatic gland of mucosa of organ of intestine OBOL:automatic gland of mucous membrane of bowel OBOL:automatic gland of mucous membrane of intestine OBOL:automatic gland of organ mucosa of bowel OBOL:automatic gland of organ mucosa of intestine OBOL:automatic glandula intestinalis FMA:15052 intestinal mucosa gland OBOL:automatic intestine mucosa gland OBOL:automatic intestine mucosa of organ gland OBOL:automatic intestine mucous membrane gland OBOL:automatic intestine organ mucosa gland OBOL:automatic mucosa of bowel gland OBOL:automatic mucosa of intestine gland OBOL:automatic mucosa of organ of bowel gland OBOL:automatic mucosa of organ of intestine gland OBOL:automatic mucous membrane of bowel gland OBOL:automatic mucous membrane of intestine gland OBOL:automatic organ mucosa of bowel gland OBOL:automatic organ mucosa of intestine gland OBOL:automatic A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]. mucosal FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 FMA:85355 FMA:85358 GAID:297 MESH:D009092 NCIT:C13166 SCTID:361693009 UMLS:C0026724 Wikipedia:Mucous_membrane galen:Mucosa mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa uberon region of mucosa tunica mucosa UBERON:0000344 mucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]. Wikipedia:Mucous_membrane FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately FMA UMLS:C0026724 ncithesaurus:Mucosa mucosa of organ FMA:85355 mucosa of organ part FMA:85358 mucosal region FMA:85358 mucous membrane FMA:85355 organ mucosa FMA:85355 region of mucosa FMA:85358 tunica mucosa BTO:0000886 Wikipedia:Mucous_membrane Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. parenchymal Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated BTO:0000999 BTO:0001539 EHDAA:3015 EHDAA:3905 EHDAA:3999 EHDAA:4005 EHDAA:6899 EHDAA:6903 EHDAA:6994 EHDAA:8086 EHDAA:9182 EHDAA:9190 EHDAA:9196 EHDAA:9202 FMA:45732 NCIT:C74601 UMLS:C0933845 Wikipedia:Parenchyma uberon UBERON:0000353 parenchyma Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. Wikipedia:Parenchyma Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin WP the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated FMA BTO:0000999 https://github.com/biopragmatics/biomappings BTO:0001539 https://github.com/biopragmatics/biomappings UMLS:C0933845 ncithesaurus:Parenchyma A mucosa that is part of a pharynx [Automatically generated definition]. UBERON:0003344 BTO:0001047 EMAPA:26957 FMA:55031 MA:0003143 SCTID:362121003 mucosa of organ of pharynx mucosa of pharynx mucous membrane of pharynx organ mucosa of pharynx pharynx mucosa pharynx mucosa of organ pharynx mucous membrane pharynx organ mucosa tunica mucosa pharyngea tunica mucosa pharyngis uberon mucous membrane of the pharynx UBERON:0000355 pharyngeal mucosa A mucosa that is part of a pharynx [Automatically generated definition]. OBOL:automatic mucosa of organ of pharynx OBOL:automatic mucosa of pharynx OBOL:automatic mucous membrane of pharynx FMA:55031 OBOL:automatic organ mucosa of pharynx OBOL:automatic pharynx mucosa OBOL:automatic pharynx mucosa of organ OBOL:automatic pharynx mucous membrane OBOL:automatic pharynx organ mucosa OBOL:automatic tunica mucosa pharyngea FMA:55031 FMA:TA mucous membrane of the pharynx BTO:0001047 The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm) BTO:0001099 CALOHA:TS-0076 EFO:0000295 EMAPA:36035 EV:0100394 FMA:83041 GAID:1153 MESH:D001755 NCIT:C13739 SCTID:308837009 UMLS:C1281743 Wikipedia:Blastocyst uberon blastocystis blastula UBERON:0000358 blastocyst https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. GO:0001824 Wikipedia:Blastocyst UMLS:C1281743 ncithesaurus:Blastocyst blastocystis Wikipedia:Blastocyst blastula FMA:83041 The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream. BTO:0001160 FMA:74595 SCTID:328538003 SCTID:75330005 medulla ossium rubra parenchymal red marrow red marrow uberon parenchyma of none marrow marrow UBERON:0000361 red bone marrow The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream. http://medical-dictionary.thefreedictionary.com/red+marrow medulla ossium rubra BTO:0001160 parenchymal red marrow http://orcid.org/0000-0002-6601-2165 red marrow BTO:0001160 parenchyma of none marrow marrow http://orcid.org/0000-0002-6601-2165 Extraembryonic cells of trophoblastic shell surrounding embryo, outside the cytotrophoblast layer, involved with implantation of the blastocyst by eroding extracellular matrix surrounding maternal endometrial cells at site of implantation, also contribute to villi. (dark staining, multinucleated). BTO:0001335 EHDAA:129 EHDAA:91 EMAPA:16068 FMA:83040 NCIT:C33918 SCTID:256965005 UMLS:C1135936 Wikipedia:Syncytiotrophoblast syncytial trophoblast syntrophoblast layer uberon syncitiotrophoblast syncitiotrophoblastus syntrophoblast UBERON:0000371 syncytiotrophoblast http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png FMA EMAPA Extraembryonic cells of trophoblastic shell surrounding embryo, outside the cytotrophoblast layer, involved with implantation of the blastocyst by eroding extracellular matrix surrounding maternal endometrial cells at site of implantation, also contribute to villi. (dark staining, multinucleated). Wikipedia:Syncytiotrophoblast http://embryology.med.unsw.edu.au/Notes/placenta5.htm UMLS:C1135936 ncithesaurus:Syncytiotrophoblast syncytial trophoblast FMA:83040 syntrophoblast layer ISBN:0073040584 syncitiotrophoblastus Wikipedia:Syncytiotrophoblast The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. Medial ramus (sensory) of the trigeminal nerve.[AAO] relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] AAO:0010670 BTO:0001378 EHDAA2:0002087 EMAPA:17799 FMA:52724 GAID:836 MA:0001103 MESH:D008442 SCTID:280211001 VHOG:0001346 Wikipedia:Maxillary_nerve maxillary division [V2] maxillary division [Vb] maxillary division of fifth cranial nerve maxillary division of trigeminal nerve (Vb; V2) maxillary nerve [V2] maxillary nerve [Vb] nervus maxillaris (Vb; V2) nervus maxillaris [v2] nervus maxillaris [vb] ramus maxillaris (ramus V2) second division of fifth cranial nerve second division of trigeminal nerve trigeminal V nerve maxillary division uberon n. maxillaris nervus maxillaris trigeminal nerve maxillary division UBERON:0000377 maxillary nerve http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. MP:0009799 Wikipedia:Maxillary_nerve Medial ramus (sensory) of the trigeminal nerve.[AAO] 2012-06-20 AAO:0010670 AAO AAO:EJS relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] 2012-06-20 AAO:0010670 AAO maxillary division [V2] FMA:52724 maxillary division [Vb] FMA:52724 maxillary division of fifth cranial nerve FMA:52724 maxillary division of trigeminal nerve (Vb; V2) FMA:52724 maxillary nerve [V2] FMA:52724 maxillary nerve [Vb] FMA:52724 nervus maxillaris (Vb; V2) FMA:52724 nervus maxillaris [v2] FMA:52724 FMA:TA nervus maxillaris [vb] FMA:52724 FMA:TA ramus maxillaris (ramus V2) AAO:0010670 second division of fifth cranial nerve FMA:52724 second division of trigeminal nerve FMA:52724 trigeminal V nerve maxillary division MA:0001103 n. maxillaris Wikipedia:Maxillary_nerve nervus maxillaris BTO:0001378 trigeminal nerve maxillary division EMAPA:17799 A mucosa that is part of a respiratory airway. BTO:0001390 FMA:7471 SCTID:660006 mucosa of organ of trachea mucosa of organ of windpipe mucosa of trachea mucosa of windpipe mucous membrane of trachea mucous membrane of windpipe organ mucosa of trachea organ mucosa of windpipe trachea mucosa trachea mucosa of organ trachea mucous membrane trachea organ mucosa tracheal mucous membrane tunica mucosa (tracheae) tunica mucosa tracheae windpipe mucosa windpipe mucosa of organ windpipe mucous membrane windpipe organ mucosa uberon UBERON:0000379 tracheal mucosa A mucosa that is part of a respiratory airway. OBOL:automatic mucosa of organ of trachea OBOL:automatic mucosa of organ of windpipe OBOL:automatic mucosa of trachea OBOL:automatic mucosa of windpipe OBOL:automatic mucous membrane of trachea FMA:7471 OBOL:automatic mucous membrane of windpipe OBOL:automatic organ mucosa of trachea OBOL:automatic organ mucosa of windpipe OBOL:automatic trachea mucosa OBOL:automatic trachea mucosa of organ OBOL:automatic trachea mucous membrane OBOL:automatic trachea organ mucosa OBOL:automatic tracheal mucous membrane FMA:7471 tunica mucosa (tracheae) FMA:7471 tunica mucosa tracheae FMA:7471 FMA:TA windpipe mucosa OBOL:automatic windpipe mucosa of organ OBOL:automatic windpipe mucous membrane OBOL:automatic windpipe organ mucosa OBOL:automatic The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 Anatomical system that consists of the muscles of the body.[VSAO] we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 MIAA:0000025 VSAO:0000033 XAO:0004042 muscle system muscle system of body muscular system musculature system set of all muscles set of muscles of body vertebrate muscular system uberon muskelsystem UBERON:0000383 musculature of body The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 Anatomical system that consists of the muscles of the body.[VSAO] 2012-08-14 VSAO:0000033 VSAO VSAO:curator we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA MA muscular system FMA:72954 musculature system BILA:0000088 set of all muscles FMA:72954 set of muscles of body FMA:72954 vertebrate muscular system BTO:0001369 muskelsystem BTO:0001485 Tissue that surrounds the lens nucleus. BTO:0001632 CALOHA:TS-0542 FMA:58970 MESH:D007904 SCTID:280626006 cortex of lens uberon UBERON:0000389 lens cortex Tissue that surrounds the lens nucleus. http://www.thefreedictionary.com/lens+cortex cortex of lens FMA:58970 The core of the crystalline lens, surrounded by the cortex. BTO:0001633 FMA:58971 MESH:D007907 SCTID:280628007 nucleus of lens uberon UBERON:0000390 lens nucleus The core of the crystalline lens, surrounded by the cortex. BTO:0001633 nucleus of lens FMA:58971 An epithelium that is part of a colon [Automatically generated definition]. Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] BTO:0001709 CALOHA:TS-0163 EMAPA:18941 FMA:17302 MA:0003195 SCTID:42978003 TAO:0005128 ZFA:0005128 colon epithelial tissue colon epithelium epithelial tissue of colon epithelial tissue of large bowel epithelium of colon epithelium of large bowel large bowel epithelial tissue large bowel epithelium posterior intestine epithelium uberon UBERON:0000397 colonic epithelium An epithelium that is part of a colon [Automatically generated definition]. OBOL:automatic Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] 2012-08-14 TAO:0005128 TAO ZFIN:curator colon epithelial tissue OBOL:automatic colon epithelium FMA:17302 OBOL:automatic epithelial tissue of colon OBOL:automatic epithelial tissue of large bowel OBOL:automatic epithelium of colon OBOL:automatic epithelium of large bowel OBOL:automatic large bowel epithelial tissue OBOL:automatic large bowel epithelium OBOL:automatic posterior intestine epithelium ZFA:0005128 A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. BTO:0001837 EMAPA:37950 FMA:62889 Wikipedia:Serous_gland uberon UBERON:0000409 serous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png A gland in which the principal secretory cells are serous secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. MP:0008052 EMAPA:37950 MA:th A gland in which the principal secretory cells are mucus secreting cells. In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] AAO:0010601 BTO:0001979 EMAPA:37913 FMA:62888 Wikipedia:Mucous_gland glandula mucosa uberon muciparous gland mucous secreting gland mucus gland mucus-secreting gland UBERON:0000414 mucous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png A gland in which the principal secretory cells are mucus secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] NCBITaxon:8292 ISBN:0073040584 EMAPA:37913 MA:th glandula mucosa Wikipedia:Mucous_gland muciparous gland BTO:0001979 An anatomical wall that is part of an artery [Automatically generated definition]. BTO:0002009 FMA:14155 galen:ArterialWall arterial wall wall of artery uberon UBERON:0000415 artery wall An anatomical wall that is part of an artery [Automatically generated definition]. OBOL:automatic arterial wall FMA:14155 wall of artery FMA:14155 A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]. trabecular BTO:0002501 FMA:85273 Wikipedia:Trabecula trabeculae uberon UBERON:0000440 trabecula A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]. GO:0060343 Wikipedia:Trabecula trabeculae A portion of organism substance that is produced by exocrine glands. BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions UBERON:0006540 secretion AEO:0001005 BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 NCIT:C34062 UMLS:C1516992 galen:Secretion bodily secretion exocrine gland fluid/secretion secreted substance uberon exocrine gland fluid exocrine gland fluid or secretion exocrine gland secretion external secretion UBERON:0000456 secretion of exocrine gland A portion of organism substance that is produced by exocrine glands. http://orcid.org/0000-0002-6601-2165 BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions BTO secretion FMA:9675 UMLS:C1516992 ncithesaurus:Exocrine_Gland_Fluid_or_Secretion bodily secretion MESH:D012634 exocrine gland fluid/secretion MA:0002504 external secretion BTO:0002977 Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance uberon UBERON:0000463 organism substance this relationship may be too strong and may be weakened in future Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 FBbt:00007019 body fluid or substance MA:0002450 body substance FMA:9669 organism substance CARO:0000004 portion of body substance FMA:9669 portion of organism substance ZFA:0001487 Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. lumen space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 TAO:0001668 TGMA:0001825 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 lumen space uberon anatomical spaces UBERON:0000464 anatomical space Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 FBbt:00007017 UMLS:C0524461 ncithesaurus:Lumen_Space anatomical spaces ZFA:0001643 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 FBbt:00007016 Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 VHOG:0001727 immaterial physical anatomical entity uberon UBERON:0000466 immaterial anatomical entity Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 FBbt:00007015 immaterial physical anatomical entity FMA:67112 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system AAO:0000007 AEO:0000011 BILA:0000011 BIRNLEX:14 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 Wikipedia:Organ_system XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. CARO:0000011 system GO:0048731 FBbt:00004856 IDOMAL:0002460 https://github.com/biopragmatics/biomappings UMLS:C0460002 ncithesaurus:Organ_System body system BIRNLEX:14 connected anatomical system CARO:0000011 anatomical systems ZFA:0001439 Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal organism AAO:0010026 AEO:0000191 BILA:0000012 BIRNLEX:18 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 SCTID:243928005 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 Wikipedia:Multi-cellular_organism XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism uberon Koerper body whole body whole organism UBERON:0000468 multicellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. CARO:0000012 Wikipedia:Multi-cellular_organism http://orcid.org/0000-0001-9114-8737 organism FBbt:00000001 VHOG:0000671 WBbt:0007833 FBbt:00000001 multi-cellular organism CARO:0000012 Koerper BTO:0001489 body AEO:0000103 BIRNLEX:18 FMA:256135 NCIT:C13041 whole body BTO:0001489 whole organism FBbt:00000001 Multi-tissue structure that is part of a compound organ. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010017 AEO:0000019 BILA:0000019 CARO:0000019 EHDAA2:0003019 HAO:0000019 TAO:0001489 TGMA:0001835 XAO:0003039 ZFA:0001489 uberon compound organ components UBERON:0000471 compound organ component Multi-tissue structure that is part of a compound organ. CARO:0000019 http://orcid.org/0000-0001-9114-8737 compound organ components ZFA:0001489 The organs and associated structures associated with bearing offspring in a female animal. By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] BTO:0000083 CALOHA:TS-1303 EFO:0000969 EHDAA2:0000506 EHDAA:8116 EMAPA:17959 EV:0100110 FBbt:00004864 FMA:45663 GAID:364 HAO:0000324 MA:0000381 MESH:D005836 MIAA:0000028 NCIT:C12402 SCTID:361386004 TGMA:0000635 UMLS:C0700038 VHOG:0000726 Wikipedia:Female_genitalia WikipediaCategory:Female_reproductive_system XAO:0000156 female organism genitalia female organism reproductive system genitalia of female organism reproductive system of female organism uberon female genital system female genital tract female genitalia female genitals female reproductive tract gynaecological tissue systema genitale femininum UBERON:0000474 female reproductive system http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg The organs and associated structures associated with bearing offspring in a female animal. MP:0001119 Wikipedia:Female_genitalia http://orcid.org/0000-0002-6601-2165 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000726 VHOG ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 http://bgee.unil.ch/ FBbt:00004864 UMLS:C0700038 ncithesaurus:Female_Reproductive_System female organism genitalia OBOL:automatic female organism reproductive system OBOL:automatic genitalia of female organism OBOL:automatic reproductive system of female organism OBOL:automatic female genitals XAO:0000156 female reproductive tract MA:0000381 gynaecological tissue BTO:0000083 systema genitale femininum BTO:0000083 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency AAO:0010053 AEO:0000032 BILA:0000032 BIRNLEX:7 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 Wikipedia:Body_part XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region uberon body part body region cardinal body part UBERON:0000475 organism subdivision CARO Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. CARO:0000032 CARO:DOS http://orcid.org/0000-0001-9114-8737 FBbt:00007009 UMLS:C0229962 ncithesaurus:Body_Part anatomic region MA:0002433 body region FMA:7153 cardinal body part FMA:7153 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 uberon acellular anatomical structures UBERON:0000476 acellular anatomical structure CARO Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 FBbt:00007013 acellular anatomical structures ZFA:0000382 Anatomical group that has its parts adjacent to one another. Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 anatomical cluster Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 FBbt:00007277 A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. AAO:0010020 AEO:0000042 BILA:0000042 CALOHA:TS-2119 CARO:0000042 EHDAA2:0003042 EHDAA:46 FBbt:00005835 FMA:85537 HAO:0000042 NCIT:C34055 SCTID:314908006 TAO:0000020 TGMA:0001843 UMLS:C1282438 VHOG:0000292 XAO:0004005 ZFA:0000020 extra-embryonic structure uberon extraembryonic structures extraembryonic tissue UBERON:0000478 see also conceptus extraembryonic component in EHDAA2. extraembryonic structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. CARO:DOS http://orcid.org/0000-0001-9114-8737 https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279 FBbt:00005835 UMLS:C1282438 ncithesaurus:Extraembryonic_Structure extraembryonic structures ZFA:0000020 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 BIRNLEX:19 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 tissue CARO Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 FBbt:00007003 UMLS:C0040300 ncithesaurus:Tissue portion of tissue CARO:0000043 simple tissue AEO:0000043 Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. AAO:0010048 AEO:0000055 BILA:0000055 CARO:0000055 EHDAA2:0003055 FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 VHOG:0001762 XAO:0003037 ZFA:0001488 uberon multi-tissue structures UBERON:0000481 multi-tissue structure CARO Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. CARO:0000055 http://orcid.org/0000-0001-9114-8737 FBbt:00007010 multi-tissue structures ZFA:0001488 Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] epithelial AAO:0000144 AAO:0010055 AEO:0000066 BILA:0000066 BTO:0000416 CALOHA:TS-0288 CARO:0000066 EHDAA2:0003066 EMAPA:32738 FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 MA:0003060 MESH:D004848 NCIT:C12710 SCTID:31610004 TAO:0001486 UMLS:C0014609 VHOG:0000387 Wikipedia:Epithelium XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium uberon UBERON:0000483 Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it? epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg http://palaeos.com/metazoa/porifera/homoscleromorpha.html Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] 2012-09-17 VHOG:0000387 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 http://bgee.unil.ch/ FBbt:00007005 UMLS:C0014609 ncithesaurus:Epithelium portion of epithelium FMA:9639 Unilaminar epithelium that consists of a single layer of cuboidal cells. needs to be synchronized with CL - there is no distinct cuboidal cell in CL AAO:0010064 AEO:0000067 BILA:0000067 CARO:0000067 EHDAA2:0003067 FMA:45566 HAO:0000067 NCIT:C33553 TAO:0001497 UMLS:C0836134 Wikipedia:Simple_cuboidal_epithelium XAO:0004009 ZFA:0001497 epithelium simplex cuboideum uberon simple cuboidal epithelia UBERON:0000484 simple cuboidal epithelium http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png Unilaminar epithelium that consists of a single layer of cuboidal cells. Wikipedia:Simple_cuboidal_epithelium http://orcid.org/0000-0001-9114-8737 UMLS:C0836134 ncithesaurus:Simple_Cuboidal_Epithelium simple cuboidal epithelia ZFA:0001497 Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]. columnar epithelium columnar epithlium AAO:0010063 AEO:0000068 BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 FBbt:00007027 FMA:45567 HAO:0000068 NCIT:C33552 SCTID:32210007 TAO:0001496 UMLS:C0836135 Wikipedia:Simple_columnar_epithelium XAO:0004008 ZFA:0001496 epithelium simplex columnare simple columnar epithelium uberon simple columnar epithelia UBERON:0000485 simple columnar epithelium http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]. FMA:FMA Wikipedia:Simple_columnar_epithelium http://orcid.org/0000-0001-9114-8737 columnar epithelium EHDAA2:0003068 columnar epithlium AEO:0000068 FBbt:00007027 UMLS:C0836135 ncithesaurus:Simple_Columnar_Epithelium simple columnar epithelia ZFA:0001496 Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]. Epithelium that consists of more than one layer of epithelial cells.[CARO] AAO:0010059 AEO:0000069 BILA:0000069 BTO:0002074 CARO:0000069 EHDAA2:0003069 FMA:45562 HAO:0000069 NCIT:C33622 SCTID:309044005 TAO:0001494 UMLS:C0682575 Wikipedia:Stratified_epithelium XAO:0004006 ZFA:0001494 stratified epithelium uberon laminated epithelium UBERON:0000486 multilaminar epithelium Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]. FMA:FMA Wikipedia:Stratified_epithelium http://orcid.org/0000-0001-9114-8737 Epithelium that consists of more than one layer of epithelial cells.[CARO] 2012-06-20 CARO:0000069 CARO FMA:45562 http://orcid.org/0000-0001-9114-8737 UMLS:C0682575 ncithesaurus:Stratified_Epithelium laminated epithelium BTO:0002074 Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 BTO:0002073 CARO:0000070 EHDAA2:0003070 FMA:45565 HAO:0000070 NCIT:C13178 TAO:0001498 UMLS:C0836133 Wikipedia:Simple_squamous_epithelium XAO:0004010 ZFA:0001498 epithelium simplex squamosum uberon simple squamous epithelia UBERON:0000487 simple squamous epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. FMA:45565 Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] 2012-06-20 CARO:0000070 CARO FMA:45565 http://orcid.org/0000-0001-9114-8737 UMLS:C0836133 ncithesaurus:Simple_Squamous_Epithelium simple squamous epithelia ZFA:0001498 Epithelium that consists of epithelial cells not arranged in one ore more layers. AAO:0010057 AEO:0000071 BILA:0000071 CARO:0000071 EHDAA2:0003071 FMA:61741 HAO:0000071 TAO:0001493 XAO:0004004 ZFA:0001493 heterogenous epithelium uberon atypical epithelia UBERON:0000488 atypical epithelium Epithelium that consists of epithelial cells not arranged in one ore more layers. http://orcid.org/0000-0001-9114-8737 atypical epithelia ZFA:0001493 Compound organ that contains one or more macroscopic anatomical spaces. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated organ uberon cavitated compound organs UBERON:0000489 cavitated compound organ Compound organ that contains one or more macroscopic anatomical spaces. http://orcid.org/0000-0001-9114-8737 cavitated organ FMA:55671 cavitated compound organs ZFA:0001490 Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 BTO:0002073 CARO:0000073 EHDAA2:0003073 FMA:45561 HAO:0000073 NCIT:C33554 SCTID:309043004 TAO:0001495 UMLS:C0682574 XAO:0004007 ZFA:0001495 simple epithelium uberon unilaminar epithelia UBERON:0000490 unilaminar epithelium Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. FMA:45561 http://orcid.org/0000-0001-9114-8737 Epithelium that consists of a single layer of epithelial cells.[CARO] 2012-06-20 CARO:0000073 CARO FMA:45561 http://orcid.org/0000-0001-9114-8737 UMLS:C0682574 ncithesaurus:Simple_Epithelium simple epithelium FMA:45561 unilaminar epithelia ZFA:0001495 Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. mucoid mucous CALOHA:TS-2144 ENVO:02000040 FMA:66938 GAID:1164 MESH:D009093 NCIT:C13259 UMLS:C0026727 Wikipedia:Mucus galen:Mucus uberon UBERON:0000912 mucus Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. Wikipedia:Mucus UMLS:C0026727 ncithesaurus:Mucus Subdivision of trunk that lies between the head and the abdomen. note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest EMAPA:35862 FMA:259209 MA:0000022 SCTID:302551006 Wikipedia:Thorax thorax uberon anterior subdivision of trunk upper body upper trunk UBERON:0000915 thoracic segment of trunk FMA Subdivision of trunk that lies between the head and the abdomen. http://orcid.org/0000-0002-6601-2165 thorax MA:0000022 upper trunk FMA:259209 The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class abdominal celiac BTO:0000020 CALOHA:TS-0001 EFO:0000968 EMAPA:35102 EV:0100011 FMA:9577 GAID:16 MA:0000029 MAT:0000298 MESH:D000005 MIAA:0000298 SCTID:302553009 Wikipedia:Abdomen galen:Abdomen abdominopelvic region abdominopelvis uberon adult abdomen belly celiac region UBERON:0000916 abdomen MA The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. http://orcid.org/0000-0002-6601-2165 abdominopelvic region FMA:9577 abdominopelvis FMA:9577 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryonic Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 SCTID:57991002 UMLS:C0013935 VHOG:0001766 Wikipedia:Embryo XAO:0000113 ZFA:0000103 http://neurolex.org/wiki/Category:Embryonic_organism embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo https://github.com/obophenotype/uberon/issues/503 https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. BTO:0000379 FB:FBrf0039741 FB:FBrf0041814 GO:0009790 Wikipedia:Embryo Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo ZFA FBbt:00000052 IDOMAL:0000646 https://github.com/biopragmatics/biomappings UMLS:C0013935 ncithesaurus:Embryo embryonic organism BILA:0000056 developing organism BILA:0000056 A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 NCIT:C12950 NCIT:C54105 TAO:0001122 UMLS:C0920502 UMLS:C1708239 VHOG:0001223 Wikipedia:Germ_layer XAO:0003011 ZFA:0001122 germinal layer primary germ layer uberon embryonic germ layer embryonic germ layers UBERON:0000923 Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] germ layer A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0001223 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ embryonic tissue FMA:69069 FBbt:00000110 UMLS:C0920502 ncithesaurus:Embryonic_Tissue UMLS:C1708239 ncithesaurus:Germinal_Layer germinal layer ncithesaurus:Germinal_Layer primary germ layer GO:0001704 ZFA:0001122 Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] ectodermal AAO:0000137 BILA:0000036 BTO:0000315 CALOHA:TS-0216 EFO:0000414 EHDAA2:0000428 EMAPA:16069 EV:0100003 FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 MAT:0000173 MESH:D004475 MIAA:0000173 NCIT:C12703 SCTID:362851007 TAO:0000016 UMLS:C0013574 VHOG:0000153 Wikipedia:Ectoderm XAO:0000001 ZFA:0000016 embryonic ectoderm uberon UBERON:0000924 ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png Bgee:AN Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] 2012-06-20 AAO:0000137 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000153 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ FBbt:00000111 UMLS:C0013574 ncithesaurus:Ectoderm embryonic ectoderm VHOG:0000153 Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal AAO:0000139 BILA:0000038 BTO:0000800 CALOHA:TS-0273 EFO:0002545 EHDAA2:0000436 EMAPA:16062 EV:0100005 FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 MESH:D004707 MIAA:0000175 NCIT:C12706 SCTID:362855003 TAO:0000017 UMLS:C0014144 VHOG:0000154 Wikipedia:Endoderm XAO:0000090 ZFA:0000017 uberon entoderm UBERON:0000925 endoderm http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png Bgee:AN Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000154 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ FBbt:00000125 UMLS:C0014144 ncithesaurus:Endoderm entoderm DOI:10.5962/bhl.title.1013 The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] mesodermal sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 CALOHA:TS-0623 EFO:0001981 EHDAA2:0001128 EHDAA:124 EHDAA:160 EHDAA:183 EMAPA:16083 EV:0100006 FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 MESH:D008648 MIAA:0000174 NCIT:C12750 SCTID:362854004 TAO:0000041 UMLS:C0025485 VHOG:0000152 Wikipedia:Mesoderm XAO:0000050 ZFA:0000041 uberon embryonic mesoderm entire mesoderm mesodermal mantle UBERON:0000926 mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png sometimes not considered primary Bgee:AN The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm Primary germ layer that is the middle of the embryonic germ layers.[AAO] 2012-06-20 AAO:0000304 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000152 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates https://github.com/obophenotype/uberon/wiki/The-neural-crest FBbt:00000126 UMLS:C0025485 ncithesaurus:Mesoderm embryonic mesoderm VHOG:0000152 entire mesoderm SCTID:362854004 https://orcid.org/0000-0002-6601-2165 Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx stomodeal This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 TGMA:0000135 UMLS:C1514977 Wikipedia:Stomodeum XAO:0000269 ZFA:0001290 mouth primordium primitive oral cavity stomatodeum stomodaeum uberon mouth pit oral ectoderm oral pit UBERON:0000930 stomodeum http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. Wikipedia:Stomodeum http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] 2012-08-14 TAO:0001290 TAO ZFIN:curator the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx MP:0012522 NCBITaxon:40674 stomodeal-hypophyseal primordium XAO:0000269 FBbt:00000439 UMLS:C1514977 ncithesaurus:Stomodeum mouth primordium XAO:0000269 primitive oral cavity https://orcid.org/0000-0002-6601-2165 stomatodeum Wikipedia:Stomodeum mouth pit EMAPA:16263 oral ectoderm ZFA:0001290 ZFIN:ZDB-PUB-100726-23 oral pit EMAPA:16263 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] proctodeal AAO:0011087 EHDAA2:0000121 EMAPA:25038 FBbt:00000123 NCIT:C34278 TAO:0000066 UMLS:C0231054 VHOG:0000139 Wikipedia:Proctodeum XAO:0001019 ZFA:0000066 embryonic proctodaeum proctodaeum amnioproctodeal invagination uberon anal pit anus porus UBERON:0000931 proctodeum https://github.com/obophenotype/uberon/issues/685 EHDAA2 EHDAA2 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. ZFA:0000066 https://github.com/obophenotype/uberon/issues/685 https://sourceforge.net/p/fbbtdv/tickets/52 An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] 2012-08-14 TAO:0000066 TAO ZFIN:curator Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] 2012-06-20 AAO:0011087 AAO ZFA:0000066 FBbt:00000123 UMLS:C0231054 ncithesaurus:Proctodeum amnioproctodeal invagination FBbt:00000123 anal pit VHOG:0000139 anus porus XAO:0001019 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa AAO:0000579 ANISEED:1235297 BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 MA:0000353 MAT:0000051 MESH:D013270 MIAA:0000051 NCIT:C12391 SCTID:181246003 TAO:0002121 UMLS:C0038351 VHOG:0000408 Wikipedia:Stomach XAO:0000128 galen:Stomach stomach chamber uberon anterior intestine gaster mesenteron ventriculus UBERON:0000945 stomach https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg cjm cjm absent in lampreys and hagfishes ISBN:0073040584 ISBN:0486692132 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. ISBN:0073040584 Wikipedia:Stomach https://orcid.org/0000-0002-6601-2165 Wikipedia Wikipedia ZFA Wikipedia Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] 2012-06-20 AAO:0000579 AAO AAO:EJS It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] 2012-09-17 VHOG:0000408 VHOG DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000) http://bgee.unil.ch/ We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa WP:Stomach#In_other_animals UMLS:C0038351 ncithesaurus:Stomach gaster BTO:0001307 ventriculus Wikipedia:Stomach The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] aortic All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches AAO:0010213 BTO:0000135 CALOHA:TS-0046 EFO:0000265 EMAPA:18601 EV:0100027 FMA:3734 GAID:469 MA:0000062 MAT:0000035 MESH:D001011 MIAA:0000035 NCIT:C12669 SCTID:181298001 UMLS:C0003483 VHOG:0001523 Wikipedia:Aorta XAO:0003010 galen:Aorta trunk of aortic tree trunk of systemic arterial tree dorsal aorta uberon arteria maxima UBERON:0000947 aorta https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg MA EHDAA2 The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. ISBN:0-683-40008-8 MESH:A07.231.114.056 MP:0000272 Wikipedia:Aorta http://orcid.org/0000-0002-6601-2165 This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. WP The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] 2012-06-20 AAO:0010213 AAO AAO:BJB When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0001523 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0003483 ncithesaurus:Aorta dorsal aorta Wikipedia:Aorta#In_other_animals ZFA:0000014 arteria maxima Wikipedia:Aorta A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] cardiac AAO:0010210 BILA:0000020 BTO:0000562 CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 NCIT:C12727 SCTID:302509004 TAO:0000114 UMLS:C0018787 VHOG:0000276 Wikipedia:Heart XAO:0000064 ZFA:0000114 galen:Heart chambered heart vertebrate heart branchial heart uberon cardium UBERON:0000948 Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb MA A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] 2012-08-14 TAO:0000114 TAO ZFIN:curator Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] 2012-06-20 AAO:0010210 AAO AAO:BJB relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0010210 AAO As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] 2012-09-17 VHOG:0000276 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ UMLS:C0018787 ncithesaurus:Heart chambered heart https://orcid.org/0000-0002-6601-2165 branchial heart cardium EMAPA:16105 Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] endocrine AAO:0010279 CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 FBbt:00005068 FMA:9668 GAID:439 MA:0000012 MESH:D004703 NCIT:C12705 SCTID:278876000 TAO:0001158 UMLS:C0014136 VHOG:0000098 Wikipedia:Endocrine_system XAO:0000158 ZFA:0001158 endocrine glandular system endocrine system systema endocrinum uberon UBERON:0000949 endocrine system Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. NLM:endocrine+system Wikipedia:Endocrine_system Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] 2012-06-20 AAO:0010279 AAO AAO:BJB Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] 2012-09-17 VHOG:0000098 VHOG DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009) http://bgee.unil.ch/ FBbt:00005068 UMLS:C0014136 ncithesaurus:Endocrine_System endocrine glandular system EHDAA2:0002224 The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BIRNLEX:796 BTO:0000142 CALOHA:TS-0095 DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MBA:8 MBA:997 MESH:D001921 MIAA:0000098 NCIT:C12439 PBA:3999 SCTID:258335003 TAO:0000008 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 Wikipedia:Brain XAO:0000010 ZFA:0000008 galen:Brain neuronames:21 uberon encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain UBERON:0000955 brain https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb GO FMA Bgee:AN The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. Wikipedia:Brain https://github.com/obophenotype/uberon/issues/300 Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] 2012-08-14 TAO:0000008 TAO ZFIN:curator Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] 2012-06-20 AAO:0010478 AAO AAO:BJB The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) http://neurolex.org/wiki/Cumbo_terms (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000157 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 http://bgee.unil.ch/ FBbt:00005095 UMLS:C0006104 BIRNLEX:796 ncithesaurus:Brain UMLS:C1269537 BIRNLEX:796 neuronames:21 BIRNLEX:796 encephalon BTO:0000142 suprasegmental levels of nervous system NeuroNames:21 suprasegmental structures NeuroNames:21 the brain NeuroNames:21 Any thin layer or plate. TODO - merge with cell layer? laminar Wikipedia:Lamina_of_the_vertebral_arch laminar tissue uberon UBERON:0000957 lamina http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png Any thin layer or plate. Wikipedia:Lamina_of_the_vertebral_arch The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. BAMS:cern FMA:5859 NCIT:C32299 NLXANAT:20090207 SCTID:360497008 UMLS:C0228815 Wikipedia:Cervical_nerves neuronames:2351 cervical nerve cervical nerve tree cervical spinal nerve nervus cervicalis uberon UBERON:0000962 Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP] nerve of cervical vertebra http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. Wikipedia:Cervical_nerves UMLS:C0228815 ncithesaurus:Cervical_Nerve cervical nerve FMA:5859 nervus cervicalis FMA:5859 FMA:TA this term should be ceded to the arthropod anatomy ontology FBbt:00004114 MAT:0000204 MIAA:0000204 uberon UBERON:0000963 head sensillum FBbt:00004114 The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure. corneal Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water AAO:0010344 BTO:0000286 CALOHA:TS-0171 EFO:0000377 EHDAA2:0000316 EHDAA:10199 EMAPA:17161 EV:0100341 FMA:58238 GAID:892 MA:0000266 MESH:D003315 NCIT:C12342 SCTID:181162001 TAO:0000640 UMLS:C0010031 VHOG:0000164 Wikipedia:Cornea XAO:0000180 ZFA:0000640 cornea of camera-type eye uberon corneas tunica cornea UBERON:0000964 cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg MA MA FMA-isa definitional The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure. ISBN:0-683-40008-8 MESH:A09.371.060.217 MP:0001312 UMLS:C0010031 ncithesaurus:Cornea cornea of camera-type eye GO:0061303 corneas ZFA:0000640 A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] This class excludes compound eye corneal lenses. AAO:0010348 BTO:0000723 CALOHA:TS-0545 EHDAA:9057 EMAPA:17838 EV:0100343 FMA:58241 MA:0000275 MAT:0000141 MESH:D007908 MIAA:0000141 NCIT:C12743 RETIRED_EHDAA2:0000975 SCTID:181169005 TAO:0000035 UMLS:C0023317 VHOG:0000169 Wikipedia:Lens_(anatomy) XAO:0000008 ZFA:0000035 camera-type eye lens eye lens lens lens crystallina uberon crystalline lens lenses ocular lens UBERON:0000965 The lens is avascular and nourished by diffusion from the aqueous and vitreous humors. lens of camera-type eye A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina. Wikipedia:Lens_(anatomy) http://orcid.org/0000-0002-6601-2165 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000169 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0023317 ncithesaurus:Crystalline_Lens camera-type eye lens GO:0002088 eye lens lens lens crystallina Wikipedia:Lens_(anatomy) crystalline lens BTO:0000723 PMID:36055924 lenses ZFA:0000035 ocular lens BTO:0000723 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] retinal AAO:0010352 BAMS:R BIRNLEX:1153 BTO:0001175 CALOHA:TS-0865 EFO:0000832 EHDAA2:0001627 EHDAA:4757 EMAPA:17168 EV:0100348 FMA:58301 GAID:755 MA:0000276 MAT:0000142 MBA:304325711 MESH:D012160 MIAA:0000142 NCIT:C12343 NIFSTD_RETIRED:birnlex_1156 SCTID:181171005 TAO:0000152 UMLS:C0035298 UMLS:C1278894 VHOG:0000229 Wikipedia:Retina XAO:0000009 ZFA:0000152 neuronames:1862 inner layer of eyeball retina of camera-type eye tunica interna of eyeball uberon Netzhaut retinas UBERON:0000966 Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png FMA FMA FMA EHDAA2 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. Wikipedia:Retina ZFIN:curator The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000152 TAO ZFIN:curator The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000229 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0035298 BIRNLEX:1153 ncithesaurus:Retina UMLS:C1278894 BIRNLEX:1153 retina of camera-type eye GO:0060041 Netzhaut BTO:0001175 retinas ZFA:0000152 An organ that detects light. This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) ocular optic Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 MIAA:0000140 Wikipedia:Eye uberon light-detecting organ visual apparatus UBERON:0000970 eye PMID:21062451 PMID:21062451 An organ that detects light. https://orcid.org/0000-0002-6601-2165 FBbt:00005162 visual apparatus EV:0100336 The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells. ommatidial BTO:0001922 FBbt:00004510 HAO:0000666 MAT:0000143 MIAA:0000143 Wikipedia:Ommatidium omatidium uberon omatidia UBERON:0000971 ommatidium PMID:21062451 The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells. PMID:21062451 FBbt:00004510 omatidia An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck. cervical AEO:0000108 BTO:0000420 CALOHA:TS-2045 EFO:0000967 EHDAA2:0003108 EMAPA:35587 FMA:7155 GAID:86 MA:0000024 MAT:0000297 MESH:D009333 MIAA:0000297 NCIT:C13063 SCTID:302550007 UMLS:C0027530 Wikipedia:Neck galen:Neck uberon collum neck (volume) UBERON:0000974 neck https://upload.wikimedia.org/wikipedia/commons/9/99/Female_neck.jpg An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. http://orcid.org/0000-0002-6601-2165 ISBN:9780674021839 UMLS:C0027530 ncithesaurus:Neck collum Wikipedia:Neck neck (volume) FMA:7155 The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] pleural In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86 BTO:0001791 CALOHA:TS-2081 EFO:0001980 EMAPA:16775 EV:0100044 FMA:9583 GAID:360 MA:0000433 MESH:D010994 NCIT:C12469 SCTID:181609007 UMLS:C0032225 VHOG:0000394 Wikipedia:Pleura wall of pleural sac uberon pleura pleural tissue UBERON:0000977 pleura http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png https://github.com/obophenotype/uberon/issues/86 The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). ISBN:0-683-40008-8 MP:0010820 UBERON:cjm Wikipedia:Pulmonary_pleurae https://github.com/obophenotype/uberon/issues/1231 ISBN:978-0030223693 https://orcid.org/0000-0003-3308-6245 The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] 2012-09-17 VHOG:0000394 VHOG ISBN:0124020607 http://bgee.unil.ch/ UMLS:C0032225 ncithesaurus:Pleural_Tissue pleural tissue BTO:0001791 NCIT:C12469 Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 NCIT:C13044 RETIRED_EHDAA2:0003182 SCTID:302536002 TAO:0000367 UMLS:C0022417 VHOG:0001276 VSAO:0000101 Wikipedia:Joint XAO:0000171 ZFA:0001596 galen:Joint uberon articular joint joints UBERON:0000982 skeletal joint Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. GO_REF:0000034 VSAO:0000101 Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] 2012-08-14 VSAO:0000101 VSAO PSPUB:0000170 Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] 2012-08-14 TAO:0000367 TAO TAO:pem articulation VSAO:0000101 joint FMA:7490 VSAO:0000101 UMLS:C0022417 ncithesaurus:Joint articular joint BTO:0001686 joints ZFA:0001596 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] BAMS:PONS BAMS:Pons BIRNLEX:733 BM:Pons BTO:0001101 CALOHA:TS-0813 DHBA:10661 EFO:0001394 EHDAA2:0004394 EMAPA:17563 EV:0100253 FMA:67943 GAID:578 HBA:9131 MA:0000204 MAT:0000115 MBA:771 MESH:D011149 MIAA:0000115 NCIT:C12511 SCTID:279103004 UMLS:C0032639 UMLS:C1280999 VHOG:0001176 Wikipedia:Pons neuronames:547 pons Varolii pons of Varolius uberon pons cerebri UBERON:0000988 pons http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png neuronames The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. VHOG:0001176 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] 2012-09-17 VHOG:0001176 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pons During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] 2012-09-17 VHOG:0001176 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474 http://bgee.unil.ch/ UMLS:C0032639 BIRNLEX:733 ncithesaurus:Pons_Varolii UMLS:C1280999 BIRNLEX:733 neuronames:547 BIRNLEX:733 pons Varolii ncithesaurus:Pons_Varolii pons cerebri NeuroNames:547 Anatomical system that has as its parts the organs concerned with reproduction. consider splitting genitalia from reproductive system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] 2022-06-10T18:22:34Z AAO:0010258 BILA:0000103 BTO:0000081 CALOHA:TS-1318 EFO:0000809 EHDAA2:0001603 EHDAA:5923 EMAPA:17381 EV:0100100 FBbt:00004857 FMA:7160 GAID:363 HAO:0000374 HAO:0000895 MA:0000326 MESH:D005835 MIAA:0000305 NCIT:C12841 SCTID:278875001 TAO:0000632 UMLS:C1261210 VHOG:0000182 WBbt:0005747 Wikipedia:Reproductive_system XAO:0000142 ZFA:0000632 genital system genitalia uberon Geschlechtsorgan animal reproductive system genital tract organa genitalia reproductive tissue reproductive tract systemata genitalia UBERON:0000990 reproductive system http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg Anatomical system that has as its parts the organs concerned with reproduction. Wikipedia:Reproductive_system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] 2012-06-20 AAO:0010258 AAO AAO:BJB Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] 2012-09-17 VHOG:0000182 VHOG PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007) http://bgee.unil.ch/ FBbt:00004857 MESH:D005835 https://github.com/biopragmatics/biomappings UMLS:C1261210 ncithesaurus:Reproductive_System genitalia Geschlechtsorgan BTO:0000081 animal reproductive system BTO:0000081 organa genitalia BTO:0000081 reproductive tissue BTO:0000081 systemata genitalia Wikipedia:Reproductive_system Reproductive organ that produces and releases eggs (ovary) or sperm (testis). Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] gonadal FMA xref is a 'general anatomical term' AAO:0000213 BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:17383 FBbt:00004858 FMA:18250 GAID:368 HAO:0000379 MA:0002420 MESH:D006066 NCIT:C12725 SCTID:304623008 TAO:0000413 UMLS:C0018067 VHOG:0000397 WBbt:0005175 Wikipedia:Gonad XAO:0003146 ZFA:0000413 gonada uberon gonads UBERON:0000991 gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). ISBN:0140512888 Wikipedia:Gonad ZFA:0000413 ZFIN:curator Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] 2012-06-20 AAO:0000213 AAO AAO:BJB The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] 2012-08-14 TAO:0000413 TAO ZFIN:curator Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] 2012-09-17 VHOG:0000397 VHOG DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) http://bgee.unil.ch/ FMA xref is a 'general anatomical term' FMA FBbt:00004858 UMLS:C0018067 ncithesaurus:Gonad gonads ZFA:0000413 The gonad of a female organism which contains germ cells. Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] Female reproductive organ.[TAO] (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] ovarian Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo AAO:0000371 BILA:0000125 BSA:0000080 BTO:0000975 CALOHA:TS-0730 EFO:0000973 EHDAA2:0001360 EHDAA:8124 EMAPA:17962 EV:0100111 FBbt:00004865 FMA:7209 GAID:367 MA:0000384 MESH:D010053 MIAA:0000125 NCIT:C12404 SCTID:181464007 TAO:0000403 UMLS:C0029939 VHOG:0000251 Wikipedia:Ovary XAO:0000258 ZFA:0000403 animal ovary female gonad female organism genitalia gonad female organism genitalia gonada female organism reproductive system gonad female organism reproductive system gonada female reproductive system gonad female reproductive system gonada genitalia of female organism gonad genitalia of female organism gonada gonad of female organism genitalia gonad of female organism reproductive system gonad of female reproductive system gonad of genitalia of female organism gonad of reproductive system of female organism gonada of female organism genitalia gonada of female organism reproductive system gonada of female reproductive system gonada of genitalia of female organism gonada of reproductive system of female organism ovum-producing ovary reproductive system of female organism gonad reproductive system of female organism gonada uberon ovaries ovarium UBERON:0000992 ovary http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png The gonad of a female organism which contains germ cells. ISBN:0-683-40008-8 MP:0001126 Wikipedia:Ovary Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] 2012-06-20 AAO:0000371 AAO AAO:BJB Female reproductive organ.[TAO] 2012-08-14 TAO:0000403 TAO ZFIN:curator (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0000251 VHOG DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) http://bgee.unil.ch/ Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo WP FBbt:00004865 UMLS:C0029939 ncithesaurus:Ovary animal ovary EFO:0000973 female organism genitalia gonad OBOL:automatic female organism genitalia gonada OBOL:automatic female organism reproductive system gonad OBOL:automatic female organism reproductive system gonada OBOL:automatic female reproductive system gonad OBOL:automatic female reproductive system gonada OBOL:automatic genitalia of female organism gonad OBOL:automatic genitalia of female organism gonada OBOL:automatic gonad of female organism genitalia OBOL:automatic gonad of female organism reproductive system OBOL:automatic gonad of female reproductive system OBOL:automatic gonad of genitalia of female organism OBOL:automatic gonad of reproductive system of female organism OBOL:automatic gonada of female organism genitalia OBOL:automatic gonada of female organism reproductive system OBOL:automatic gonada of female reproductive system OBOL:automatic gonada of genitalia of female organism OBOL:automatic gonada of reproductive system of female organism OBOL:automatic ovum-producing ovary GO:0061039 reproductive system of female organism gonad OBOL:automatic reproductive system of female organism gonada OBOL:automatic ovaries ovarium Wikipedia:Ovary The outer epithelial layer of the skin that is superficial to the dermis. A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] relationship loss: subclass external integument structures (AAO:0000961)[AAO] (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] epidermal Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). epidermis skin AAO:0000143 BTO:0000404 CALOHA:TS-0283 EFO:0000954 EMAPA:17528 EV:0100153 FMA:70596 GAID:932 MA:0000153 MAT:0000154 MESH:D004817 MIAA:0000154 NCIT:C12708 SCTID:361694003 TAO:0000105 UMLS:C0014520 VHOG:0000077 Wikipedia:Epidermis_(skin) XAO:0000028 ZFA:0000105 vertebrate epidermis uberon UBERON:0001003 skin epidermis The outer epithelial layer of the skin that is superficial to the dermis. ISBN:0073040584 http://orcid.org/0000-0002-6601-2165 A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000105 TAO ZFIN:curator The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] 2012-06-20 AAO:0000143 AAO AAO:BJB relationship loss: subclass external integument structures (AAO:0000961)[AAO] 2012-06-20 AAO:0000143 AAO (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] 2012-09-17 VHOG:0000077 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72 http://bgee.unil.ch/ UMLS:C0014520 ncithesaurus:Epidermis Functional system which consists of structures involved in respiration. The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] AAO:0000541 BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 NCIT:C12779 SCTID:278197002 TAO:0000272 UMLS:C0035237 VHOG:0000202 Wikipedia:Respiratory_system XAO:0000117 ZFA:0000272 apparatus respiratorius respiratory system uberon Atmungssystem apparatus respiratorius systema respiratorium UBERON:0001004 respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb Functional system which consists of structures involved in respiration. Wikipedia:Respiratory_system http://orcid.org/0000-0002-6601-2165 Wikipedia:Acoelomorpha The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] 2012-06-20 AAO:0000541 AAO AAO:BJB There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] 2012-09-17 VHOG:0000202 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23 http://bgee.unil.ch/ UMLS:C0035237 ncithesaurus:Respiratory_System Atmungssystem BTO:0000203 apparatus respiratorius BTO:0000203 systema respiratorium Wikipedia:Respiratory_system An airway through which respiratory air passes in organisms. This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends airway airways FMA:265130 SCTID:361380005 Wikipedia:Trachea uberon UBERON:0001005 respiratory airway An airway through which respiratory air passes in organisms. Wikipedia:Trachea airway http://orcid.org/0000-0002-6601-2165 airways http://orcid.org/0000-0002-6601-2165 Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] digestive many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MA:0002431 MAT:0000018 MESH:D004064 MIAA:0000018 SCTID:278859004 TADS:0000170 TAO:0000339 WBbt:0005748 Wikipedia:Digestive_system XAO:0000125 ZFA:0000339 galen:DigestiveSystem ncithesaurus:Digestive_System uberon alimentary system alimentary tract gastrointestinal system gut UBERON:0001007 digestive system Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. FB:gg NLM:alimentary+system Wikipedia:Digestive_system An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] 2012-06-20 AAO:0000129 AAO AAO:BJB many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class MA FBbt:00005055 The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans excretory system AAO:0010257 BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 FBbt:00005056 FMA:7159 GAID:391 MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 NCIT:C12413 SCTID:362204003 TADS:0000162 TAO:0000163 UMLS:C1508753 VHOG:0000723 WBbt:0005736 Wikipedia:Excretory_system XAO:0000143 ZFA:0000163 galen:UrinaryTract systema urinaria systema urinarium urinary system urinary tract uberon renal or urinary system renal/urinary system UBERON:0001008 EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here renal system The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. DOI:10.1371/journal.pone.0099864 GO:0072001 Wikipedia Wikipedia:Acoelomorpha An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] 2012-06-20 AAO:0010257 AAO AAO:BJB Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] 2012-09-17 VHOG:0000723 VHOG ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406 http://bgee.unil.ch/ In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels GO This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans DOI:10.1371/journal.pone.0099864 FBbt:00005056 UMLS:C1508753 ncithesaurus:Urinary_System systema urinaria FMA:7159 systema urinarium BTO:0003092 renal or urinary system EHDAA:5901 Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. the cardiovascular system and the lymphatic system are parts of the circulatory system Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon systema cardiovasculare UBERON:0001009 circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. Wikipedia:Circulatory_system Wikipedia:Acoelomorpha WBbt coelomocyte currently classified as circulating cell Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] 2012-06-20 AAO:0000959 AAO AAO:BJB We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] 2012-09-17 VHOG:0001248 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 http://bgee.unil.ch/ MESH:D002319 https://github.com/biopragmatics/biomappings systema cardiovasculare Wikipedia:Circulatory_system Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. Connective tissue in which fat is stored.[TAO] Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] adipose In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen. in FMA this is dense irregular connective tissue AAO:0000001 AEO:000020 BTO:0001487 CALOHA:TS-0013 EFO:0000790 EHDAA2:0003120 EMAPA:35112 EV:0100381 FMA:20110 GAID:920 MA:0000009 MAT:0000015 MESH:D000273 MIAA:0000015 NCIT:C12472 SCTID:55603005 TAO:0002134 UMLS:C0001527 VHOG:0001284 Wikipedia:Adipose_tissue XAO:0003049 ZFA:0005345 galen:FattyTissue fat fat tissue fatty tissue uberon adipose bodyfat fatty depot UBERON:0001013 adipose tissue FMA Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. MESH:A10.165.114 MGI:cwg MP:0000003 Wikipedia:Adipose_tissue http://orcid.org/0000-0002-6601-2165 Connective tissue in which fat is stored.[TAO] 2012-08-14 TAO:0002134 TAO ZFIN:curator Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] 2012-06-20 AAO:0000001 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000001 AAO Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] 2012-09-17 VHOG:0001284 VHOG DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007) http://bgee.unil.ch/ in FMA this is dense irregular connective tissue FMA UMLS:C0001527 ncithesaurus:Adipose_Tissue fat MA:0000009 adipose BTO:0001487 bodyfat BTO:0001487 A subdivision of the muscular system corresponding to a subdisivision of an organism. In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. AAO:0011066 BTO:0000887 EFO:0001949 EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 NCIT:C13056 TAO:0000548 UMLS:C0026845 VSAO:0005038 WBbt:0005737 Wikipedia:Muscular_system ZFA:0000548 muscle group muscles set musculature musculi set of muscles set of skeletal muscles uberon muscle system muscles musculature system UBERON:0001015 musculature http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png A subdivision of the muscular system corresponding to a subdisivision of an organism. Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. FMA UMLS:C0026845 ncithesaurus:Muscle musculi FMA:32558 FMA:TA set of muscles FMA:32558 set of skeletal muscles MA:0000165 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] nervous neural AAO:0000324 BILA:0000079 BIRNLEX:844 BTO:0001484 CALOHA:TS-1313 EFO:0000802 EHDAA2:0001246 EHDAA:826 EMAPA:16469 EV:0100162 FBbt:00005093 FMA:7157 GAID:466 MA:0000016 MAT:0000026 MESH:D009420 MIAA:0000026 NCIT:C12755 SCTID:278196006 TAO:0000396 UMLS:C0027763 VHOG:0000402 WBbt:0005735 Wikipedia:Nervous_system XAO:0000177 ZFA:0000396 neuronames:3236 neurological system nerve net uberon systema nervosum UBERON:0001016 nervous system http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png Bgee:AN The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. BIRNLEX:844 ISBN:0-14-051288-8 ISBN:3110148986 NLM:nervous+system WB:rynl Wikipedia:Nervous_system ZFIN:curator A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000396 TAO ZFIN:curator Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] 2012-06-20 AAO:0000324 AAO AAO:BJB Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] 2012-09-17 VHOG:0000402 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 http://bgee.unil.ch/ FBbt:00005093 UMLS:C0027763 ncithesaurus:Nervous_System neurological system GO:0050877 nerve net Wikipedia:Nerve_net systema nervosum Wikipedia:Nervous_system The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] The brain and spinal cord. Kimmel et al, 1995.[TAO] The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 BIRNLEX:1099 BTO:0000227 CALOHA:TS-0150 EFO:0000908 EHDAA2:0000225 EHDAA:828 EMAPA:16470 EMAPA:16754 EV:0100163 FBbt:00005094 FMA:55675 GAID:570 MA:0000167 MAT:0000457 MESH:D002490 NCIT:C12438 SCTID:278199004 TAO:0000012 UMLS:C0927232 VHOG:0000293 Wikipedia:Central_nervous_system XAO:0000215 ZFA:0000012 neuronames:854 CNS systema nervosum centrale cerebrospinal axis uberon neuraxis UBERON:0001017 central nervous system FBbt cjm Bgee:AN The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. GO:0021551 http://www.frontiersinzoology.com/content/7/1/29 https://sourceforge.net/p/geneontology/ontology-requests/11422/ Wikipedia:Acoelomorpha Part of the nervous system which includes the brain and spinal cord.[AAO] 2012-06-20 AAO:0000090 AAO AAO:BJB The brain and spinal cord. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000012 TAO ZFIN:curator The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). BIRNLEX:1099 (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] 2012-09-17 VHOG:0000293 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) http://bgee.unil.ch/ FBbt:00005094 UMLS:C0927232 BIRNLEX:1099 ncithesaurus:Central_Nervous_System CNS systema nervosum centrale FMA:55675 FMA:TA cerebrospinal axis FMA:55675 neuraxis FMA:55675 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. A portion of tissue which is a fasiculated group of axons.[TAO] nervous AAO:0011070 AEO:0000137 BAMS:n BIRNLEX:1615 BSA:0000098 BTO:0000925 BTO:0001027 CALOHA:TS-0772 EHDAA2:0003137 EHDAA:2851 EHDAA:3776 EHDAA:4657 EMAPA:32808 EMAPA:32815 EV:0100371 FBbt:00005105 FMA:65132 FMA:65239 GAID:747 GAID:758 MA:0000217 MA:0000228 MESH:D010525 NCIT:C12466 NCIT:C12768 NLX:147826 SCTID:244457007 SCTID:256864008 TAO:0007009 UMLS:C0027740 UMLS:C0031119 VHOG:0000901 Wikipedia:Nervous_system XAO:0000204 XAO:0003047 ZFA:0007009 galen:Nerve nerves peripheral nerve uberon neural subtree UBERON:0001021 nerve FBbt An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. FBbt:00005105 http://orcid.org/0000-0002-6601-2165 A portion of tissue which is a fasiculated group of axons.[TAO] 2012-08-14 TAO:0007009 TAO ZFIN:curator FBbt:00005105 UMLS:C0027740 ncithesaurus:Nerve UMLS:C0031119 ncithesaurus:Peripheral_Nerve nerves TAO:0007009 peripheral nerve http://orcid.org/0000-0002-6601-2165 neural subtree FMA:65132 A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. AEO:0000201 EHDAA2:0003200 FBbt:00005136 FMA:5868 Wikipedia:Sensory_nerve nervus sensorius uberon afferent nerve UBERON:0001027 sensory nerve AEO A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. UBERON:cjm Wikipedia:Sensory_nerve FBbt:00005136 nervus sensorius Wikipedia:Sensory_nerve Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 MIAA:0000031 NLXANAT:090816 TAO:0000282 VHOG:0001674 Wikipedia:Sensory_system XAO:0003194 ZFA:0000282 organa sensuum sense organ subsystem sense organs sense organs set sensory subsystem sensory systems uberon organa sensuum sensory organ system set of sense organs UBERON:0001032 sensory system http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. Wikipedia:Sensory_system An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] 2012-09-17 VHOG:0001674 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ FBbt:00007692 organa sensuum FMA:75259 FMA:TA sense organs FMA:75259 sense organs set FMA:75259 sensory systems TAO:0000282 organa sensuum Wikipedia:Sensory_system set of sense organs FMA:75259 A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. consider splitting class One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)] BTO:0001471 CALOHA:TS-1130 EFO:0003078 EHDAA2:0002212 EHDAA:164 EMAPA:16085 FMA:87180 GAID:1301 MESH:D015017 NCIT:C14128 SCTID:362845002 UMLS:C0043425 VHOG:0000830 Wikipedia:Yolk_sac uberon saccus vitellinus vesicula umbilicalis UBERON:0001040 yolk sac http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png https://github.com/obophenotype/uberon/issues/635 EHDAA2 ISBN:0073040584 ISBN:0073040584 A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. Wikipedia:Yolk_sac One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] 2012-09-17 VHOG:0000830 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/yolk+sac the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells MP:0001718 Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] 2012-09-17 VHOG:0000830 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 http://bgee.unil.ch/ UMLS:C0043425 ncithesaurus:Yolk_Sac saccus vitellinus Wikipedia:Yolk_sac vesicula umbilicalis Wikipedia:Yolk_sac Anterior subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] AAO:0011042 BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 FBbt:00005379 FMA:45616 MA:0001526 NCIT:C34180 SCTID:361409009 TGMA:0001014 UMLS:C0231051 VHOG:0000285 Wikipedia:Foregut XAO:0000232 uberon praeenteron proenteron UBERON:0001041 foregut http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png Anterior subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. MP:0000474 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000285 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ FBbt:00005379 UMLS:C0231051 ncithesaurus:Foregut praeenteron Wikipedia:Foregut proenteron Wikipedia:Foregut A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme pharynx AAO:0000967 BTO:0001049 CALOHA:TS-0785 EFO:0000836 EHDAA2:0001458 EHDAA:2947 EMAPA:16706 EV:0100065 FMA:46688 GAID:155 MA:0000432 MESH:D010614 NCIT:C12425 SCTID:181211006 TAO:0000056 UMLS:C0031354 VHOG:0000462 Wikipedia:Pharynx XAO:0003227 ZFA:0000056 galen:Pharynx uberon UBERON:0001042 Consider generalizing to deuterostome pharynx chordate pharynx EHDAA2 A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. http://www.feedexp.org A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. MESH:A03.867 Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000967 AAO AAO:EJS Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000056 TAO ZFIN:curator Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000462 VHOG http://bgee.unil.ch/ relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] 2012-09-17 VHOG:0000462 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503 http://bgee.unil.ch/ MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme MA pharynx FMA:46688 UMLS:C0031354 ncithesaurus:Pharynx Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] esophageal esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) AAO:0000145 ANISEED:1235301 BTO:0000959 CALOHA:TS-0700 EFO:0000835 EHDAA2:0001285 EHDAA:2937 EMAPA:16833 EV:0100069 FMA:7131 GAID:291 MA:0000352 MAT:0000048 MESH:D004947 MIAA:0000048 NCIT:C12389 SCTID:181245004 TAO:0000204 UMLS:C0014876 VHOG:0000450 Wikipedia:Esophagus XAO:0000127 ZFA:0000204 galen:Esophagus gullet oesophagus uberon UBERON:0001043 esophagus http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Wikipedia:Esophagus http://www.rivm.nl/interspeciesinfo/inter/oesophagus/ Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] 2012-06-20 AAO:0000145 AAO AAO:EJS The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] 2012-09-17 VHOG:0000450 VHOG DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996) http://bgee.unil.ch/ esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) MA UMLS:C0014876 ncithesaurus:Esophagus Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon in FMA this represents an embryonic region. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 SCTID:361410004 TGMA:0001036 UMLS:C0231052 VHOG:0000290 Wikipedia:Midgut XAO:0000103 uberon mesenteron UBERON:0001045 midgut http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. GO:0007494 Wikipedia:Midgut The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000290 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon WP in FMA this represents an embryonic region. FMA FBbt:00005383 UMLS:C0231052 ncithesaurus:Midgut mesenteron Wikipedia:Midgut The caudalmost subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class the caudal portion of the primitive digestive tube of the embryo The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] in FMA this class has no children. In MA it has a single child hindgut epithelium AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 SCTID:362856002 TGMA:0001020 UMLS:C0231053 VHOG:0000459 Wikipedia:Hindgut XAO:0000104 uberon metenteron UBERON:0001046 hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png Wikipedia The caudalmost subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 the caudal portion of the primitive digestive tube of the embryo MP:0008786 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000459 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ in FMA this class has no children. In MA it has a single child hindgut epithelium FMA FBbt:00005384 UMLS:C0231053 ncithesaurus:Hindgut metenteron Wikipedia:Hindgut Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. AEO:0000171 BTO:0001886 EFO:0001652 EHDAA2:0003171 FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 UMLS:C0678727 Wikipedia:Primordium XAO:0003043 uberon bud future organ placode primordia rudiment UBERON:0001048 primordium EHDAA2 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. BTO:0001886 FB:DJS FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html FBbt:00005495 UMLS:C0678727 ncithesaurus:Primordium placode FBbt:00005495 primordia XAO:0003043 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 DHBA:10154 EHDAA2:0001254 EHDAA:2869 EHDAA:908 EMAPA:16164 EMAPA:16757 FMA:293882 MAT:0000069 MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 TAO:0001135 UMLS:C0231024 VHOG:0000307 Wikipedia:Neural_tube XAO:0003204 ZFA:0001135 neuronames:1365 uberon neural primordium presumptive central nervous system tubus neuralis UBERON:0001049 neural tube http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] 2012-06-20 AAO:0010617 AAO AAO:JOR The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000307 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/neural+tube (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000307 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium GO:0021915 MESH:D054259 https://github.com/biopragmatics/biomappings UMLS:C0231024 ncithesaurus:Neural_Tube tubus neuralis Wikipedia:Neural_tube The terminal portion of the intestinal tube, terminating with the anus. The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] rectal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 MA:0000336 MAT:0000050 MESH:D012007 MIAA:0000050 NCIT:C12390 SCTID:181261002 UMLS:C0034896 VHOG:0001751 Wikipedia:Rectum XAO:0000238 galen:Rectum terminal portion of intestine uberon intestinum rectum rectal sac terminal portion of large intestine UBERON:0001052 rectum http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb 4 cjm MA EHDAA2 ISBN:0073040584 The terminal portion of the intestinal tube, terminating with the anus. ISBN:0-683-40008-8 MP:0000492 http://orcid.org/0000-0002-6601-2165 The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0001751 VHOG http://bgee.unil.ch/ UMLS:C0034896 ncithesaurus:Rectum intestinum rectum BTO:0001158 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 spatial uberon CARO:0000000 UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. CARO:MAH Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 http://orcid.org/0000-0001-9114-8737 FBbt:10000000 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct. UBERON:0005627 pancreatic duct BTO:0002362 EHDAA2:0001396 EHDAA:6905 EMAPA:17510 FMA:16003 GAID:337 MA:0000126 MESH:D010183 NCIT:C12272 RETIRED_EHDAA2:0002177 SCTID:245385001 UMLS:C0030288 VHOG:0000256 Wikipedia:Pancreatic_duct chief pancreatic duct duct of Wirsung main pancreatic duct uberon canal of Wirsung ductus pancreatis ventralis hepaticopancreatic duct UBERON:0001064 EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue ventral pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png FMA EHDAA2 A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. Wikipedia:Pancreatic_duct These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] 2012-09-17 VHOG:0000256 VHOG DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005) http://bgee.unil.ch/ Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct. WP pancreatic duct MESH:A03.734.667 UMLS:C0030288 ncithesaurus:Pancreatic_Duct chief pancreatic duct FMA:16003 duct of Wirsung Wikipedia:Pancreatic_duct main pancreatic duct MA:0000126 canal of Wirsung BTO:0002362 hepaticopancreatic duct BTO:0002362 A zone of skin that is part of a back [Automatically generated definition]. EMAPA:36392 FMA:10462 FMA:22985 MA:0000498 SCTID:181492002 back skin back zone of skin skin, dorsal region zone of skin of back uberon UBERON:0001068 EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of back MA MA A zone of skin that is part of a back [Automatically generated definition]. OBOL:automatic back zone of skin OBOL:automatic skin, dorsal region https://orcid.org/0000-0002-6601-2165 zone of skin of back OBOL:automatic A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]. not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO AAO:0010218 AAO:0010416 BTO:0004696 EFO:0001953 EHDAA2:0000461 EMAPA:18611 FMA:10635 GAID:480 MA:0001929 MESH:D002342 NCIT:C32551 SCTID:362044002 UMLS:C0007275 VHOG:0000265 Wikipedia:External_carotid_artery XAO:0000345 external carotid uberon arteria carotis externa UBERON:0001070 external carotid artery https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif MA FMA EHDAA2 FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]. MGI:anna UMLS:C0007275 ncithesaurus:External_Carotid_Artery external carotid AAO:0010218 arteria carotis externa Wikipedia:External_carotid_artery It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. EMAPA:37117 FMA:10665 MA:0002052 NCIT:C53005 SCTID:161746006 UMLS:C0226271 Wikipedia:Superficial_part_of_transverse_cervical_artery superficial branch of transverse cervical artery uberon UBERON:0001071 The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] superficial cervical artery It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. Wikipedia:Superficial_part_of_transverse_cervical_artery EMAPA:37117 MA:th UMLS:C0226271 ncithesaurus:Superficial_Cervical_Artery superficial branch of transverse cervical artery Wikipedia:Superficial_part_of_transverse_cervical_artery A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] AAO:0011083 BTO:0002682 EHDAA2:0000611 EMAPA:18416 FMA:10951 GAID:548 MA:0000480 MESH:D014682 NCIT:C12815 SCTID:181369003 UMLS:C0042458 VHOG:0001194 Wikipedia:Inferior_vena_cava XAO:0000388 galen:InferiorVenaCava inferior caval vein inferior vena cava posterior vena cava uberon caudal vena cava postcava vena cava inferior UBERON:0001072 posterior vena cava http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png lexical A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. Wikipedia:Inferior_vena_cava http://orcid.org/0000-0002-6601-2165 Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. FMA:10951 Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] 2012-09-17 VHOG:0001194 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 http://bgee.unil.ch/ UMLS:C0042458 ncithesaurus:Inferior_Vena_Cava inferior caval vein http://orcid.org/0000-0002-6601-2165 inferior vena cava Wikipedia:Venae_cavae posterior vena cava Wikipedia:Venae_cavae caudal vena cava VHOG:0001194 vena cava inferior BTO:0002682 Wikipedia:Inferior_vena_cava A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice. EMAPA:37601 FMA:11338 MA:0000332 SCTID:264021000 ileocaecal junction uberon UBERON:0001073 ileocecal junction A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice. http://www.medilexicon.com/medicaldictionary.php?t=46539 EMAPA:37601 MA:th A potential space between the visceral and parietal layers of the pericardium. Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal) BSA:0000091 EHDAA2:0001434 EMAPA:16131 EMAPA:16132 FMA:11350 MA:0000053 NCIT:C38662 SCTID:362027001 TAO:0002220 UMLS:C0225972 VHOG:0000556 Wikipedia:Pericardial_cavity ZFA:0001655 galen:PericardialSpace cavity of pericardial sac pericardial space uberon cavitas pericardiaca UBERON:0001074 pericardial cavity MA FMA Wikipedia A potential space between the visceral and parietal layers of the pericardium. Wikipedia:Pericardium Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] 2012-08-14 TAO:0002220 TAO ZFIN:curator In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000556 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal) ZFA UMLS:C0225972 ncithesaurus:Pericardial_Cavity pericardial space Wikipedia:Pericardial_cavity cavitas pericardiaca Wikipedia:Pericardial_cavity Endocardium that is part of the cardiac ventricle. EMAPA:32747 FMA:12148 MA:0000079 SCTID:192172004 TAO:0002247 VHOG:0000607 ZFA:0001615 cardiac ventricle endocardium endocardium of cardiac ventricle endocardium of heart ventricle endocardium of lower chamber of heart endocardium of ventricle of heart heart ventricle endocardium lower chamber of heart endocardium ventricle endocardium ventricle of heart endocardium ventricular endocardium uberon ventricle endocardial tissue UBERON:0001081 endocardium of ventricle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Endocardium that is part of the cardiac ventricle. ZFIN:curator cardiac ventricle endocardium OBOL:automatic endocardium of cardiac ventricle OBOL:automatic endocardium of heart ventricle OBOL:automatic endocardium of lower chamber of heart OBOL:automatic endocardium of ventricle of heart OBOL:automatic heart ventricle endocardium OBOL:automatic lower chamber of heart endocardium OBOL:automatic ventricle of heart endocardium OBOL:automatic ventricle endocardial tissue VHOG:0000607 An epicardial layer that lines a cardiac ventricle. The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO] FMA:12150 TAO:0005058 ZFA:0005058 cardiac ventricle epicardium ventricular epicardium uberon UBERON:0001082 epicardium of ventricle An epicardial layer that lines a cardiac ventricle. http://orcid.org/0000-0002-6601-2165 The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO] 2012-08-14 TAO:0005058 TAO ZFIN:curator cardiac ventricle epicardium OBOL:automatic Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003088 EMAPA:32748 FMA:12151 MA:0000082 SCTID:192084000 TAO:0005061 VHOG:0000604 ZFA:0005061 ventricle myocardium ventricular myocardium uberon ventricle cardiac muscle UBERON:0001083 myocardium of ventricle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. ZFIN:curator Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] 2012-08-14 TAO:0005061 TAO ZFIN:curator As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000604 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ ventricle cardiac muscle VHOG:0000604 A zone of skin that is part of a head [Automatically generated definition]. FMA:12166 FMA:24756 MA:0000582 NCIT:C52757 SCTID:181484006 UMLS:C0205029 adult head zone of skin head skin head zone of skin zone of skin of adult head zone of skin of head uberon UBERON:0001084 EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of head A zone of skin that is part of a head [Automatically generated definition]. OBOL:automatic UMLS:C0205029 ncithesaurus:Head_Skin adult head zone of skin OBOL:automatic head zone of skin OBOL:automatic zone of skin of adult head OBOL:automatic zone of skin of head OBOL:automatic A zone of skin that is part of a trunk [Automatically generated definition]. EMAPA:37278 FMA:12167 FMA:23093 MA:0000517 NCIT:C12295 SCTID:181489001 UMLS:C0205031 torso zone of skin trunk skin trunk zone of skin zone of skin of torso zone of skin of trunk uberon UBERON:0001085 EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of trunk A zone of skin that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37278 MA:th UMLS:C0205031 ncithesaurus:Skin_of_the_Trunk torso zone of skin OBOL:automatic trunk zone of skin OBOL:automatic zone of skin of torso OBOL:automatic zone of skin of trunk OBOL:automatic Transudate contained in the pleural cavity. BTO:0003080 FMA:12273 MA:0002532 MAT:0000500 Wikipedia:Pleural_fluid ncithesaurus:Pleural_Fluid uberon UBERON:0001087 pleural fluid Transudate contained in the pleural cavity. FMA:12273 Joint fluid is a transudate of plasma that is actively secreted by synovial cells. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] It provides nutrients and lubrication for articular cartilage The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 NCIT:C33718 TAO:0005154 UMLS:C0039097 Wikipedia:Synovial_fluid ZFA:0005154 galen:SynovialFluid joint fluid uberon UBERON:0001090 synovial fluid FMA Joint fluid is a transudate of plasma that is actively secreted by synovial cells. https://www.ncbi.nlm.nih.gov/books/NBK274/ Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] 2012-08-14 TAO:0005154 TAO ZFIN:curator UMLS:C0039097 ncithesaurus:Synovial_Fluid joint fluid https://www.ncbi.nlm.nih.gov/books/NBK274/ The first vertebral bone in the vertebral column. First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO] Vertebra that is posteriorly adjacent to the neurocranium.[TAO] 1 C1 AAO:0000709 EHDAA:10606 EMAPA:19431 FMA:12519 GAID:236 MA:0001421 MESH:D001270 NCIT:C32239 SCTID:181818007 TAO:0001167 UMLS:C0004170 Wikipedia:Atlas_(anatomy) ZFA:0001167 C1 vertebra atlas atlas (CI) atlas [C I] atlas vertebra cervical atlas cervical vertebra 1 first cervical vertebra vertebra 1 uberon UBERON:0001092 vertebral bone 1 The first vertebral bone in the vertebral column. http://orcid.org/0000-0002-6601-2165 First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO] 2012-06-20 AAO:0000709 AAO AAO:Duellman_and_Trueb_1994 Vertebra that is posteriorly adjacent to the neurocranium.[TAO] 2012-08-14 TAO:0001167 TAO TAO:wd UMLS:C0004170 ncithesaurus:C1_Vertebra atlas [C I] FMA:12519 FMA:TA cervical atlas MP:0011576 cervical vertebra 1 MA:0001421 vertebra 1 TAO:0001167 The second vertebral bone in the vertebral column. Vertebra that is posteriorly adjacent to vertebra 1.[TAO] not the same as ZFA term 'axis' 2 EHDAA:10608 EMAPA:19432 FMA:12520 GAID:237 MA:0001422 MESH:D001368 NCIT:C32240 SCTID:181819004 TAO:0001168 UMLS:C0004457 Wikipedia:Axis_(anatomy) ZFA:0001168 axis (CII) axis [C II] axis vertebra cervical axis vertebra 2 C2 vertebra cervical vertebra 2 second cervical vertebra uberon C2 axis UBERON:0001093 vertebral bone 2 FMA The second vertebral bone in the vertebral column. http://orcid.org/0000-0002-6601-2165 Vertebra that is posteriorly adjacent to vertebra 1.[TAO] 2012-08-14 TAO:0001168 TAO TAO:wd UMLS:C0004457 ncithesaurus:C2_Vertebra axis [C II] FMA:12520 FMA:TA cervical axis MP:0004608 vertebra 2 ZFA:0001168 cervical vertebra 2 MA:0001422 axis MA:0001422 Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] we deliberately merge the MA classes as we believe them equivalent UBERON:0006070 caudal vertebra EMAPA:18374 FMA:12527 MA:0000310 MA:0001420 NCIT:C32334 SCTID:361774004 TAO:0000326 UMLS:C0223616 Wikipedia:Caudal_vertebra XAO:0003079 ZFA:0000326 galen:CoccygealVertebra caudal vertebrae caudal vertebral bone caudal vertebral bone element coccygeal segment coccygeal vertebra fused tail vertebra uberon coccygea tail vertebra UBERON:0001095 Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae caudal vertebra Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). http://orcid.org/0000-0002-6601-2165 Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] 2012-08-14 TAO:0000326 TAO ZFIN:curator we deliberately merge the MA classes as we believe them equivalent MA caudal vertebra FMA:12527 UMLS:C0223616 ncithesaurus:Coccygeal_Vertebra caudal vertebrae coccygeal vertebra FMA:12527 fused tail vertebra https://orcid.org/0000-0002-6601-2165 coccygea MA:0001420 tail vertebra MA:0000310 An anatomical wall that is part of a esophagus [Automatically generated definition]. EMAPA:35326 FMA:12611 MA:0002691 anatomical wall of esophagus anatomical wall of gullet anatomical wall of oesophagus esophageal wall esophagus anatomical wall esophagus wall gullet anatomical wall gullet wall oesophagus anatomical wall oesophagus wall wall of gullet wall of oesophagus uberon UBERON:0001096 wall of esophagus An anatomical wall that is part of a esophagus [Automatically generated definition]. OBOL:automatic anatomical wall of esophagus OBOL:automatic anatomical wall of gullet OBOL:automatic anatomical wall of oesophagus OBOL:automatic esophagus anatomical wall OBOL:automatic gullet anatomical wall OBOL:automatic gullet wall OBOL:automatic oesophagus anatomical wall OBOL:automatic oesophagus wall OBOL:automatic wall of gullet OBOL:automatic wall of oesophagus OBOL:automatic A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] phrenic The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3] The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution) barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus breathing control originate from the cervical somites, likely C3-C5[PMID:23586979] BTO:0000341 CALOHA:TS-0198 EFO:0000937 EHDAA2:0003495 EMAPA:17701 EV:0100376 FMA:13295 GAID:158 MA:0001904 MAT:0000502 MESH:D003964 NCIT:C12702 SCTID:181614006 UMLS:C0011980 VHOG:0000713 Wikipedia:Thoracid_diaphragm diaphragm muscle diaphragm of thorax thoracic diaphragm uberon midriff phren UBERON:0001103 diaphragm PMID:23586979 definitional A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. MP:0002279 Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. GO:0060539 The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] 2012-09-17 VHOG:0000713 VHOG ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278 http://bgee.unil.ch/ UMLS:C0011980 ncithesaurus:Diaphragm diaphragm muscle BTO:0000341 midriff BTO:0000341 phren BTO:0000341 Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe. some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts EMAPA:18306 FMA:13361 MA:0000360 NCIT:C49579 SCTID:245378000 UMLS:C0447541 Wikipedia:Liver#Lobes hepatic lobe liver lobe lobus hepatis uberon UBERON:0001113 lobe of liver FMA Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe. Wikipedia:Liver#Lobes UMLS:C0447541 ncithesaurus:Liver_Lobe The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]. Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO] EHDAA2:0001008 EHDAA:4001 EMAPA:18311 FMA:13362 MA:0000363 NCIT:C33481 SCTID:362182008 TAO:0005173 UMLS:C0227481 VHOG:0001424 Wikipedia:Right_lobe_of_liver ZFA:0005173 liver right lobe lobus hepaticus dexter right liver lobe uberon 2nd lobe gall bladder lobe lobus hepatis dexter right hepatic lobe second lobe UBERON:0001114 right lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]. Wikipedia:Right_lobe_of_liver Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO] 2012-08-14 TAO:0005173 TAO ZFIN:curator UMLS:C0227481 ncithesaurus:Right_Lobe_of_the_Liver lobus hepaticus dexter right liver lobe ZFA:0005173 2nd lobe TAO:0005173 gall bladder lobe ZFA:0005173 lobus hepatis dexter Wikipedia:Right_lobe_of_liver right hepatic lobe EMAPA:18311 second lobe TAO:0005173 The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]. Portion of the liver which develops on the fish's left side.[TAO] EHDAA2:0001000 EHDAA:3995 EMAPA:18307 FMA:13363 MA:0000361 NCIT:C32965 SCTID:362183003 TAO:0005172 UMLS:C0227486 VHOG:0001423 Wikipedia:Left_lobe_of_liver ZFA:0005172 left liver lobe liver left lobe lobus hepaticus sinister uberon left hepatic lobe lobus hepatis sinister UBERON:0001115 left lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]. Wikipedia:Left_lobe_of_liver Portion of the liver which develops on the fish's left side.[TAO] 2012-08-14 TAO:0005172 TAO ZFIN:curator UMLS:C0227486 ncithesaurus:Left_Lobe_of_the_Liver lobus hepaticus sinister left hepatic lobe EMAPA:18307 lobus hepatis sinister Wikipedia:Left_lobe_of_liver Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton Anatomical cluster that consists of all the vertebra in the body.[VSAO] The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG] Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG] spine AAO:0000699 AAO:0000734 BTO:0000818 EFO:0001369 EHDA:10119 EMAPA:35919 FMA:13478 GAID:106 MA:0002416 MESH:D013131 NCIT:C12998 NCIT:C33588 NIF_Subcellular:sao1145756102 SCTID:44300000 TAO:0001559 UMLS:C0037949 UMLS:C1519455 VHOG:0001142 VSAO:0000185 Wikipedia:Vertebral_column XAO:0003074 ZFA:0001559 galen:SpinalColumn backbone vertebral column skeleton uberon columna vertebralis dorsal spine spinal column vertebral region UBERON:0001130 vertebral column cjm Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. VSAO:0000185 https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/tracker/?func=detail&aid=3530322&group_id=76834&atid=2257941 Anatomical cluster that consists of all the vertebra in the body.[VSAO] 2012-08-14 VSAO:0000185 VSAO VSAO:curator The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0001142 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/vertebral+column Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG] 2012-09-17 VHOG:0001142 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53 http://bgee.unil.ch/ spine FMA:13478 UMLS:C0037949 ncithesaurus:Vertebral_Column UMLS:C1519455 ncithesaurus:Spinal_Cord_Column backbone FMA:13478 vertebral column skeleton AAO:0000699 columna vertebralis BTO:0000818 dorsal spine BTO:0000818 spinal column MESH:A02.835.232.834 A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch. Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO] AAO:0000729 EMAPA:37803 FMA:13479 MA:0001454 SCTID:280734009 Wikipedia:Vertebral_foramen vertebra neural canal uberon foramen vertebrale UBERON:0001131 vertebral foramen http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch. Wikipedia:Vertebral_foramen http://orcid.org/0000-0002-6601-2165 Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO] 2012-06-20 AAO:0000729 AAO AAO:LAP EMAPA:37803 MA:th foramen vertebrale Wikipedia:Vertebral_foramen Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit UBERON:0007096 AAO:0010245 AEO:0000142 BILA:0000134 BTO:0000199 CALOHA:TS-0440 EHDAA2:0003142 EMAPA:32688 FMA:14068 TAO:0005280 Wikipedia:Cardiac_muscle ZFA:0005280 galen:CardiacMuscle galen:CardiacMuscleTissue ncithesaurus:Heart_Muscle cardiac muscle cardiac muscle muscle tissue cardiac muscle textus muscularis heart muscle muscle tissue heart muscle textus muscularis heart myocardium muscle tissue heart myocardium textus muscularis muscle of heart muscle tissue muscle of heart textus muscularis muscle tissue of cardiac muscle muscle tissue of heart muscle muscle tissue of heart myocardium muscle tissue of muscle of heart muscle tissue of myocardium myocardium muscle tissue myocardium textus muscularis textus muscularis of cardiac muscle textus muscularis of heart muscle textus muscularis of heart myocardium textus muscularis of muscle of heart textus muscularis of myocardium uberon cardiac musculature UBERON:0001133 cardiac muscle tissue Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. ZFA:0005280 cardiac muscle muscle tissue OBOL:automatic cardiac muscle textus muscularis OBOL:automatic heart muscle muscle tissue OBOL:automatic heart muscle textus muscularis OBOL:automatic heart myocardium muscle tissue OBOL:automatic heart myocardium textus muscularis OBOL:automatic muscle of heart muscle tissue OBOL:automatic muscle of heart textus muscularis OBOL:automatic muscle tissue of cardiac muscle OBOL:automatic muscle tissue of heart muscle OBOL:automatic muscle tissue of heart myocardium OBOL:automatic muscle tissue of muscle of heart OBOL:automatic muscle tissue of myocardium OBOL:automatic myocardium muscle tissue OBOL:automatic myocardium textus muscularis OBOL:automatic textus muscularis of cardiac muscle OBOL:automatic textus muscularis of heart muscle OBOL:automatic textus muscularis of heart myocardium OBOL:automatic textus muscularis of muscle of heart OBOL:automatic textus muscularis of myocardium OBOL:automatic cardiac musculature BILA:0000134 Muscle tissue that consists primarily of skeletal muscle fibers. TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] skeletal muscle EMAPA:32716 FMA:14069 MA:0002439 NCIT:C13050 SCTID:426215008 UMLS:C0242692 Wikipedia:Skeletal_striated_muscle uberon skeletal muscle system somatic muscle UBERON:0001134 skeletal muscle tissue https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg Muscle tissue that consists primarily of skeletal muscle fibers. https://github.com/obophenotype/uberon/issues/324 Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] 2012-08-14 TAO:0005277 TAO ZFIN:curator Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] FMA:14069 FMA This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] 2012-09-17 VHOG:0000319 VHOG PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999) http://bgee.unil.ch/ UMLS:C0242692 ncithesaurus:Skeletal_Muscle_Tissue skeletal muscle system BTO:0001103 somatic muscle BTO:0001103 Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. AAO:0010244 AEO:0000141 BTO:0001260 CALOHA:TS-0943 EFO:0000889 EHDAA2:0003141 EMAPA:32717 EV:0100378 FMA:14070 GAID:167 MA:0000166 MAT:0000303 MESH:D009130 MIAA:0000303 NCIT:C12437 TAO:0005274 UMLS:C1267092 VHOG:0001246 WBbt:0005781 Wikipedia:Smooth_muscle_tissue XAO:0000175 ZFA:0005274 galen:SmoothMuscle galen:SmoothMuscleTissue involuntary muscle non-striated muscle smooth muscle textus muscularis nonstriatus visceral muscle visceral muscle tissue uberon textus muscularis levis; textus muscularis nonstriatus UBERON:0001135 smooth muscle tissue https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. GO:0006939 Wikipedia:Smooth_muscle_tissue A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] 2012-08-14 TAO:0005274 TAO ZFIN:curator Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] 2012-06-20 AAO:0010244 AAO AAO:CAM (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] 2012-09-17 VHOG:0001246 VHOG DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) http://bgee.unil.ch/ UMLS:C1267092 ncithesaurus:Smooth_Muscle_Tissue textus muscularis nonstriatus FMA:14070 FMA:TA visceral muscle visceral muscle tissue textus muscularis levis; textus muscularis nonstriatus Wikipedia:Smooth_muscle_tissue Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 CALOHA:TS-1183 EHDAA2_RETIRED:0003111 EHDAA:2331 EHDAA:2349 EHDAA:295 EHDAA:6073 EHDAA:640 EHDAA:646 EMAPA:32856 FMA:14074 MA:0000565 NCIT:C33105 SCTID:361918002 UMLS:C0086610 Wikipedia:Mesothelium uberon UBERON:0001136 mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg FMA Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). FMA:14074 Wikipedia:Mesothelium UMLS:C0086610 ncithesaurus:Mesothelium A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. dorsal In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body BTO:0001713 CALOHA:TS-2223 EFO:0001405 FMA:14181 GAID:30 MESH:D001415 NCIT:C13062 SCTID:123961009 UMLS:C0004600 Wikipedia:Dorsum_(anatomy) galen:Back back back of body proper dorsal part of organism uberon UBERON:0001137 dorsum http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. BSPO:0000063 UBERONREF:0000006 Wikipedia:Dorsum_(anatomy) UMLS:C0004600 ncithesaurus:Back back FMA:14181 back of body proper FMA:14181 In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002783 EHDAA2:0001951 EHDAA:5414 EMAPA:18643 FMA:14332 MA:0002179 NCIT:C33687 SCTID:278031001 UMLS:C0226742 VHOG:0000552 Wikipedia:Superior_mesenteric_vein uberon upper mesenteric vein vena mesenterica superior UBERON:0001138 superior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png Wikipedia:Vitelline_vein In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. Wikipedia:Superior_mesenteric_vein UMLS:C0226742 ncithesaurus:Superior_Mesenteric_Vein upper mesenteric vein BTO:0002783 vena mesenterica superior Wikipedia:Superior_mesenteric_vein Vein that carries blood away from the liver[ZFA]. todo - add developmental relationships for other taxa AAO:0010216 EMAPA:19221 FMA:14337 GAID:534 MA:0003015 MESH:D006503 NCIT:C32736 SCTID:278191001 TAO:0000670 UMLS:C0019155 Wikipedia:Hepatic_vein XAO:0000387 ZFA:0000670 galen:HepaticVein liver vein vein of liver vena hepatica uberon hepatic veins venae hepaticae UBERON:0001143 hepatic vein http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png FMA-abduced-lr Vein that carries blood away from the liver[ZFA]. Wikipedia:Hepatic_vein ZFA:0000670 https://sourceforge.net/tracker/?func=detail&aid=3565355&group_id=76834&atid=1205376 UMLS:C0019155 ncithesaurus:Hepatic_Vein liver vein OBOL:automatic vein of liver OBOL:automatic vena hepatica hepatic veins venae hepaticae Wikipedia:Hepatic_vein A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. EMAPA:18644 FMA:14346 MA:0002186 NCIT:C53058 SCTID:278193003 UMLS:C0226720 Wikipedia:Ovarian_vein female reproductive system gonad vein female reproductive system gonada vein gonad of female reproductive system vein gonada of female reproductive system vein ovary vein vein of female reproductive system gonad vein of female reproductive system gonada vein of gonad of female reproductive system vein of gonada of female reproductive system vein of ovary uberon vena ovarica dextra vena ovarica sinistra UBERON:0001145 ovarian vein http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. Wikipedia:Ovarian_vein UMLS:C0226720 ncithesaurus:Ovarian_Vein female reproductive system gonad vein OBOL:automatic female reproductive system gonada vein OBOL:automatic gonad of female reproductive system vein OBOL:automatic gonada of female reproductive system vein OBOL:automatic ovary vein OBOL:automatic vein of female reproductive system gonad OBOL:automatic vein of female reproductive system gonada OBOL:automatic vein of gonad of female reproductive system OBOL:automatic vein of gonada of female reproductive system OBOL:automatic vein of ovary OBOL:automatic vena ovarica dextra Wikipedia:Ovarian_vein vena ovarica sinistra Wikipedia:Ovarian_vein The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct. Duct that connects the gall bladder and the common bile duct.[TAO] The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] EHDAA2:0000333 EHDAA:3045 EMAPA:16841 FMA:14539 GAID:290 MA:0000355 MESH:D003549 NCIT:C32421 SCTID:245398005 TAO:0005166 UMLS:C0010672 VHOG:0000213 Wikipedia:Cystic_duct ZFA:0005166 galen:CysticDuct uberon ductus cysticus UBERON:0001152 cystic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png FMA EHDAA2 The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct. ISBN:0-683-40008-8 MP:0009493 Duct that connects the gall bladder and the common bile duct.[TAO] 2012-08-14 TAO:0005166 TAO ZFIN:Curator The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000213 VHOG http://bgee.unil.ch/ UMLS:C0010672 ncithesaurus:Cystic_Duct ductus cysticus Wikipedia:Cystic_duct A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. Some references do not consider the caecum to be part of the colon. TODO - abstract this such that it legitimately covers all vertebrates The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] colonic In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] it extracts water and salt from solid wastes before they are eliminated from the body[WP] AAO:0010400 BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 MA:0000335 MAP:0000001 MAT:0000526 MESH:D003106 NCIT:C12382 SCTID:302508007 TAO:0000706 UMLS:C0009368 VHOG:0000648 Wikipedia:Colon_(anatomy) XAO:0000243 ZFA:0000706 galen:Colon large bowel posterior intestine uberon hindgut UBERON:0001155 colon 3 cjm FMA A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. Wikipedia:Colon_(anatomy) ZFIN:curator http://orcid.org/0000-0002-2825-0621 http://orcid.org/0000-0002-6601-2165 Some references do not consider the caecum to be part of the colon. http://orcid.org/0000-0002-1572-1316 The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] 2012-06-20 AAO:0010400 AAO UBERON:0001155 The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0000706 TAO ZFIN:curator Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000648 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0009368 ncithesaurus:Colon The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. BTO:0000645 CALOHA:TS-2044 EFO:0000846 EMAPA:36391 FMA:14548 MAT:0000314 MESH:D012809 MIAA:0000314 NCIT:C12384 NCIT:C33550 SCTID:362166007 UMLS:C0227391 UMLS:C0682612 Wikipedia:Sigmoid_colon galen:SigmoidColon uberon colon sigmoideum pelvic colon sigmoid colon sigmoid flexure UBERON:0001159 sigmoid colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb FMA Wikipedia The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. Wikipedia:Sigmoid_colon UMLS:C0227391 ncithesaurus:Sigmoid_Colon UMLS:C0682612 ncithesaurus:Sigmoid_Flexure colon sigmoideum Wikipedia:Sigmoid_colon The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. we include this as zone of stomach even though it is not distinguished by gland type BTO:0000505 EMAPA:35810 FMA:14560 MA:0002559 NCIT:C12258 SCTID:362140009 UMLS:C0227230 Wikipedia:Body_of_stomach galen:GastricCorpus corpus gastricum (ventriculare) gastric body stomach body uberon corpus gastricum corpus ventriculare corpus ventriculi gastric corpus UBERON:0001161 body of stomach http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg FMA The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. GO:0014845 Wikipedia:Body_of_stomach UMLS:C0227230 ncithesaurus:Body_of_Stomach corpus gastricum BTO:0000505 Wikipedia:Body_of_stomach corpus ventriculare BTO:0000505 corpus ventriculi BTO:0000505 The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells. antrum BTO:0001732 EFO:0002555 EMAPA:17891 FMA:14579 GAID:332 MA:0001624 MESH:D011706 NCIT:C12259 SCTID:362142001 UMLS:C0034193 Wikipedia:Pyloric_antrum galen:PyloricAntrum antrum of stomach stomach pyloric antrum uberon antrum of Willis antrum pylori antrum pyloricum gastric antrum stomach antrum UBERON:0001165 pyloric antrum http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg FMA Wikipedia The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells. ISBN:0-683-40008-8 MP:0010790 UMLS:C0034193 ncithesaurus:Antrum_Pylori antrum of Willis BTO:0001732 antrum pylori BTO:0001732 antrum pyloricum BTO:0001732 Wikipedia:Pyloric_antrum gastric antrum BTO:0001732 The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum. We follow Kardong in defining stomach regions by glands The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] pyloric BTO:0001146 EHDAA2:0001580 EHDAA:4860 EMAPA:17631 FMA:14581 GAID:333 MA:0002560 MESH:D011708 NCIT:C12260 SCTID:362143006 UMLS:C0034196 VHOG:0000420 Wikipedia:Pylorus galen:Pylorus pars pylorica pars pylorica gastricae pyloric part of stomach pyloric region stomach pyloric region uberon valvula pylori UBERON:0001166 pylorus http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum. MGI:csmith MP:0010785 The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000420 VHOG http://bgee.unil.ch/ Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000420 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0034196 ncithesaurus:Pylorus pars pylorica pars pylorica gastricae FMA:14581 FMA:TA stomach pyloric region EHDAA2:0001580 valvula pylori Wikipedia:Pylorus The layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between. EMAPA:35826 FMA:14582 MA:0002692 SCTID:279995000 galen:WallOfStomach anatomical wall of stomach anatomical wall of ventriculus gastric wall stomach anatomical wall stomach wall ventriculus anatomical wall ventriculus wall wall of ventriculus uberon UBERON:0001167 wall of stomach The layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between. MGI:csmith MP:0010783 anatomical wall of stomach OBOL:automatic anatomical wall of ventriculus OBOL:automatic stomach anatomical wall OBOL:automatic ventriculus anatomical wall OBOL:automatic ventriculus wall OBOL:automatic wall of ventriculus OBOL:automatic An anatomical wall that is part of a small intestine [Automatically generated definition]. EMAPA:35785 FMA:14615 MA:0002696 NCIT:C33573 UMLS:C1519375 anatomical wall of small bowel anatomical wall of small intestine small bowel anatomical wall small bowel wall small intestinal wall small intestine anatomical wall small intestine wall wall of small bowel uberon UBERON:0001168 wall of small intestine An anatomical wall that is part of a small intestine [Automatically generated definition]. OBOL:automatic UMLS:C1519375 ncithesaurus:Small_Intestinal_Wall_Tissue anatomical wall of small bowel OBOL:automatic anatomical wall of small intestine OBOL:automatic small bowel anatomical wall OBOL:automatic small bowel wall OBOL:automatic small intestine anatomical wall OBOL:automatic wall of small bowel OBOL:automatic An anatomical wall that is part of a large intestine [Automatically generated definition]. EMAPA:35470 FMA:14619 MA:0002695 anatomical wall of large intestine large intestinal wall large intestine anatomical wall large intestine wall uberon UBERON:0001169 wall of large intestine An anatomical wall that is part of a large intestine [Automatically generated definition]. OBOL:automatic anatomical wall of large intestine OBOL:automatic large intestine anatomical wall OBOL:automatic The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP]. EMAPA:37745 FMA:14643 MA:0001555 SCTID:245456008 Wikipedia:Mesentery#Mesentery_.28proper.29 mesentery (proper) mesentery proper small intestinal mesentery small intestine mesentery uberon UBERON:0001170 mesentery of small intestine FMA The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP]. Wikipedia:Mesentery#Mesentery_.28proper.29 EMAPA:37745 MA:th mesentery (proper) Wikipedia:Mesentery mesentery proper FMA:14643 small intestinal mesentery FMA:14643 small intestine mesentery OBOL:automatic The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. FMA:14653 MA:0002498 NCIT:C33341 UMLS:C0682620 uberon UBERON:0001171 portal lobule FMA MA MP The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. MP:0008992 UMLS:C0682620 ncithesaurus:Portal_Lobule The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. EMAPA:35497 FMA:14654 MA:0002496 NCIT:C32992 SCTID:272214009 UMLS:C0227519 liver acinus portal acinus uberon UBERON:0001172 hepatic acinus cjm The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. http://orcid.org/0000-0002-6601-2165 http://www.vivo.colostate.edu/hbooks/pathphys/digestion/liver/histo_acinus.html UMLS:C0227519 ncithesaurus:Liver_Acinus A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] AAO:0011020 EMAPA:35172 FMA:14665 MESH:D001659 SCTID:181267003 UMLS:C0005423 Wikipedia:Biliary_tract XAO:0000455 uberon biliary tract UBERON:0001173 The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP] biliary tree A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. DOI:10.1002/ar.20664 Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] 2012-06-20 AAO:0011020 AAO UBERON:0001173 MESH:D001659 https://github.com/biopragmatics/biomappings UMLS:C0005423 ncithesaurus:Biliary_Tract biliary tract MA:0001273 The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct. Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO] The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] EHDAA2:0000303 EHDAA:3981 EMAPA:17201 FMA:14667 GAID:282 MA:0001631 MESH:D003135 NCIT:C12698 SCTID:362199009 TAO:0005165 UMLS:C0009437 VHOG:0000214 Wikipedia:Common_bile_duct ZFA:0005165 galen:CommonBileDuct ductus choledochus (biliaris) uberon ductus choledochus UBERON:0001174 common bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct. MGI:csmith MP:0009495 Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO] 2012-08-14 TAO:0005165 TAO ZFIN:Curator The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000214 VHOG http://bgee.unil.ch/ UMLS:C0009437 ncithesaurus:Common_Bile_Duct ductus choledochus Wikipedia:Common_bile_duct Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]. TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] EMAPA:19101 FMA:14668 GAID:286 MA:0002660 MESH:D006500 NCIT:C32356 SCTID:245403006 UMLS:C0019149 VHOG:0000220 Wikipedia:Common_hepatic_duct uberon ductus hepaticus communis hepatic duct UBERON:0001175 common hepatic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg FMA MA Wikipedia Wikipedia definitional Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]. Wikipedia:Common_hepatic_duct ZFIN:curator The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000220 VHOG http://bgee.unil.ch/ UMLS:C0019149 ncithesaurus:Common_Hepatic_Duct ductus hepaticus communis Wikipedia:Common_hepatic_duct The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct. The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] EHDAA2:0001727 EHDAA:3992 EMAPA:32797 FMA:14669 MA:0001639 NCIT:C33476 SCTID:245401008 UMLS:C0227557 VHOG:0000217 uberon ductus hepaticus dexter UBERON:0001176 right hepatic duct The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct. http://www.medterms.com/script/main/art.asp?articlekey=26034 The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] 2012-09-17 VHOG:0000217 VHOG http://bgee.unil.ch/ UMLS:C0227557 ncithesaurus:Right_Hepatic_Duct ductus hepaticus dexter The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct. The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] EHDAA2:0000941 EHDAA:3990 EMAPA:32795 FMA:14670 MA:0001638 NCIT:C32960 SCTID:245400009 UMLS:C0227560 VHOG:0000218 uberon ductus hepaticus sinister UBERON:0001177 left hepatic duct The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct. http://www.medterms.com/script/main/art.asp?articlekey=26035 The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] 2012-09-17 VHOG:0000218 VHOG http://bgee.unil.ch/ UMLS:C0227560 ncithesaurus:Left_Hepatic_Duct ductus hepaticus sinister The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. EMAPA:16592 FMA:14703 SCTID:362702003 TAO:0005132 VHOG:0001528 Wikipedia:Visceral_peritoneum ZFA:0005132 visceral serous membrane of peritoneum uberon UBERON:0001178 visceral peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. Wikipedia:Peritoneum#Types http://orcid.org/0000-0002-6601-2165 visceral serous membrane of peritoneum UBERON:cjm Anatomical cavity bounded by visceral and parietal peritoneum. The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] BTO:0001782 EHDAA2:0001446 EMAPA:16138 FMA:14704 GAID:24 MA:0000054 MESH:D010529 NCIT:C12769 SCTID:181616008 UMLS:C1704247 VHOG:0000852 Wikipedia:Peritoneal_cavity uberon cavitas peritonealis saccus serosus peritonei UBERON:0001179 peritoneal cavity Wikipedia Anatomical cavity bounded by visceral and parietal peritoneum. Wikipedia:Peritoneal_cavity http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/86 The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] 2012-09-17 VHOG:0000852 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/peritoneal+cavity In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000852 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ UMLS:C1704247 ncithesaurus:Peritoneal_Cavity cavitas peritonealis BTO:0001782 Wikipedia:Peritoneal_cavity saccus serosus peritonei Wikipedia:Peritoneal_cavity An artery that supplies an ovary. In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. EMAPA:18620 FMA:14761 MA:0002012 NCIT:C33242 SCTID:244280002 UMLS:C0226411 Wikipedia:Ovarian_artery ovarian arterial tree uberon arteria ovarica UBERON:0001190 ovarian artery http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png An artery that supplies an ovary. OBOL:automatic In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. Wikipedia:Ovarian_artery UMLS:C0226411 ncithesaurus:Ovarian_Artery arteria ovarica Wikipedia:Ovarian_artery An artery that supplies the liver. currently defined in a generic fashion. Artery that supplies blood to the liver.[TAO] BTO:0004307 EMAPA:17859 FMA:14769 GAID:496 MA:0001963 MESH:D006499 NCIT:C32729 SCTID:76015000 TAO:0005161 UMLS:C0019145 ZFA:0005161 galen:HepaticArtery arteria hepatica propria uberon arteria hepatica UBERON:0001193 hepatic artery http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png An artery that supplies the liver. Wikipedia:Hepatic_artery_proper https://orcid.org/0000-0002-6601-2165 Artery that supplies blood to the liver.[TAO] 2012-08-14 TAO:0005161 TAO ZFIN:curator UMLS:C0019145 ncithesaurus:Hepatic_Artery arteria hepatica propria arteria hepatica BTO:0004307 An artery that supplies the spleen. EMAPA:19216 FMA:14773 GAID:510 MA:0001991 MA:0003177 MESH:D013157 NCIT:C33597 SCTID:244266009 UMLS:C0037996 Wikipedia:Splenic_artery galen:SplenicArtery arteria splenica lienal artery uberon arteria lienalis UBERON:0001194 splenic artery https://github.com/obophenotype/uberon/issues/268 http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb An artery that supplies the spleen. http://orcid.org/0000-0002-6601-2165 UMLS:C0037996 ncithesaurus:Splenic_Artery arteria splenica Wikipedia:Splenic_artery lienal artery MA:0001991 arteria lienalis Wikipedia:Splenic_artery The mucosal layer that lines the stomach. The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. BTO:0001308 CALOHA:TS-0404 EMAPA:35817 FMA:14907 GAID:321 MA:0002683 MESH:D005753 NCIT:C32656 SCTID:362131005 UMLS:C0017136 Wikipedia:Gastric_mucosa galen:GastricMucosa gastric mucosa gastric mucous membrane mucosa of organ of stomach mucosa of organ of ventriculus mucosa of ventriculus mucous membrane of stomach mucous membrane of ventriculus organ mucosa of stomach organ mucosa of ventriculus stomach mucosa stomach mucosa of organ stomach mucous membrane stomach organ mucosa tunica mucosa (gaster) tunica mucosa gastricae ventriculus mucosa ventriculus mucosa of organ ventriculus mucous membrane ventriculus organ mucosa uberon Magenschleimhaut tunica mucosa gastris UBERON:0001199 mucosa of stomach https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg The mucosal layer that lines the stomach. http://orcid.org/0000-0002-6601-2165 The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. Wikipedia:Gastric_mucosa UMLS:C0017136 ncithesaurus:Gastric_Mucosa mucosa of organ of stomach OBOL:automatic mucosa of organ of ventriculus OBOL:automatic mucosa of ventriculus OBOL:automatic mucous membrane of ventriculus OBOL:automatic organ mucosa of stomach OBOL:automatic organ mucosa of ventriculus OBOL:automatic stomach mucosa of organ OBOL:automatic stomach mucous membrane OBOL:automatic stomach organ mucosa OBOL:automatic tunica mucosa gastricae FMA:14907 FMA:TA ventriculus mucosa OBOL:automatic ventriculus mucosa of organ OBOL:automatic ventriculus mucous membrane OBOL:automatic ventriculus organ mucosa OBOL:automatic Magenschleimhaut BTO:0001308 tunica mucosa gastris BTO:0001308 Wikipedia:Gastric_mucosa The fibrous connective tissue layer beneath the stomach mucosa. BTO:0002110 EMAPA:35825 FMA:14908 MA:0002685 NCIT:C32663 SCTID:52459002 UMLS:C0227211 gastric submucosa stomach submucosa submucosa of ventriculus tela submucosa (gaster) tela submucosa gastricae ventriculus submucosa uberon submucous layer of stomach tela submucosa ventriculi UBERON:0001200 submucosa of stomach The fibrous connective tissue layer beneath the stomach mucosa. MGI:csmith MP:0010794 UMLS:C0227211 ncithesaurus:Gastric_Submucosa submucosa of ventriculus OBOL:automatic tela submucosa gastricae FMA:14908 FMA:TA ventriculus submucosa OBOL:automatic submucous layer of stomach BTO:0002110 tela submucosa ventriculi BTO:0002110 The outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum. TODO - check serosa/peritoneum EMAPA:35822 FMA:14914 MA:0001626 NCIT:C32662 SCTID:1353004 UMLS:C1517453 anatomical wall of stomach serosa anatomical wall of stomach serous membrane anatomical wall of ventriculus serosa anatomical wall of ventriculus serous membrane gastric wall serosa gastric wall serous membrane serosa of anatomical wall of stomach serosa of anatomical wall of ventriculus serosa of gastric wall serosa of stomach anatomical wall serosa of stomach wall serosa of ventriculus anatomical wall serosa of ventriculus wall serosa of wall of stomach serosa of wall of ventriculus serous coat of stomach serous membrane of anatomical wall of stomach serous membrane of anatomical wall of ventriculus serous membrane of gastric wall serous membrane of stomach anatomical wall serous membrane of stomach wall serous membrane of ventriculus anatomical wall serous membrane of ventriculus wall serous membrane of wall of stomach serous membrane of wall of ventriculus stomach anatomical wall serosa stomach anatomical wall serous membrane stomach serosa stomach wall serosa stomach wall serous membrane tunica serosa (gaster) tunica serosa gastricae ventriculus anatomical wall serosa ventriculus anatomical wall serous membrane ventriculus wall serosa ventriculus wall serous membrane visceral peritoneum of stomach wall of stomach serosa wall of stomach serous membrane wall of ventriculus serosa wall of ventriculus serous membrane uberon gastric serosa UBERON:0001201 serosa of stomach The outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum. MGI:csmith MP:0010793 UMLS:C1517453 ncithesaurus:Gastric_Serosal_Surface anatomical wall of stomach serosa OBOL:automatic anatomical wall of stomach serous membrane OBOL:automatic anatomical wall of ventriculus serosa OBOL:automatic anatomical wall of ventriculus serous membrane OBOL:automatic gastric wall serosa OBOL:automatic gastric wall serous membrane OBOL:automatic serosa of anatomical wall of stomach OBOL:automatic serosa of anatomical wall of ventriculus OBOL:automatic serosa of gastric wall OBOL:automatic serosa of stomach anatomical wall OBOL:automatic serosa of stomach wall OBOL:automatic serosa of ventriculus anatomical wall OBOL:automatic serosa of ventriculus wall OBOL:automatic serosa of wall of stomach OBOL:automatic serosa of wall of ventriculus OBOL:automatic serous membrane of anatomical wall of stomach OBOL:automatic serous membrane of anatomical wall of ventriculus OBOL:automatic serous membrane of gastric wall OBOL:automatic serous membrane of stomach anatomical wall OBOL:automatic serous membrane of stomach wall OBOL:automatic serous membrane of ventriculus anatomical wall OBOL:automatic serous membrane of ventriculus wall OBOL:automatic serous membrane of wall of stomach OBOL:automatic serous membrane of wall of ventriculus OBOL:automatic stomach anatomical wall serosa OBOL:automatic stomach anatomical wall serous membrane OBOL:automatic stomach wall serosa OBOL:automatic stomach wall serous membrane OBOL:automatic tunica serosa gastricae FMA:14914 FMA:TA ventriculus anatomical wall serosa OBOL:automatic ventriculus anatomical wall serous membrane OBOL:automatic ventriculus wall serosa OBOL:automatic ventriculus wall serous membrane OBOL:automatic wall of stomach serosa OBOL:automatic wall of stomach serous membrane OBOL:automatic wall of ventriculus serosa OBOL:automatic wall of ventriculus serous membrane OBOL:automatic A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]. (...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG] AAO:0011093 EMAPA:19251 FMA:14916 MA:0002952 NCIT:C33433 SCTID:268073008 UMLS:C0227238 VHOG:0001466 XAO:0000457 pyloric valve uberon UBERON:0001202 pyloric sphincter A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]. https://orcid.org/0000-0002-6601-2165 (...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG] 2012-09-17 VHOG:0001466 VHOG DOI:10.1046/j.1525-142x.2000.00076.x http://bgee.unil.ch/ UMLS:C0227238 ncithesaurus:Pyloric_Sphincter pyloric valve Wikipedia:Pylorus A mucosa that is part of a small intestine [Automatically generated definition]. BTO:0001259 CALOHA:TS-0941 EMAPA:35780 FMA:14933 MA:0002686 NCIT:C33568 SCTID:362144000 UMLS:C0227261 mucosa of organ of small bowel mucosa of organ of small intestine mucosa of small bowel mucous membrane of small bowel mucous membrane of small intestine organ mucosa of small bowel organ mucosa of small intestine small bowel mucosa small bowel mucosa of organ small bowel mucous membrane small bowel organ mucosa small intestinal mucosa small intestine mucosa small intestine mucosa of organ small intestine mucous membrane small intestine organ mucosa tunica mucosa (intestinum tenue) tunica mucosa intestini tenuis uberon UBERON:0001204 mucosa of small intestine A mucosa that is part of a small intestine [Automatically generated definition]. OBOL:automatic UMLS:C0227261 ncithesaurus:Small_Intestinal_Mucosa mucosa of organ of small bowel OBOL:automatic mucosa of organ of small intestine OBOL:automatic mucosa of small bowel OBOL:automatic mucous membrane of small bowel OBOL:automatic organ mucosa of small bowel OBOL:automatic organ mucosa of small intestine OBOL:automatic small bowel mucosa OBOL:automatic small bowel mucosa of organ OBOL:automatic small bowel mucous membrane OBOL:automatic small bowel organ mucosa OBOL:automatic small intestine mucosa of organ OBOL:automatic small intestine organ mucosa OBOL:automatic tunica mucosa intestini tenuis FMA:14933 FMA:TA Submucosal tissue in the small intestines. BTO:0002112 EMAPA:37564 FMA:14934 MA:0001562 NCIT:C33572 SCTID:691000 UMLS:C0227268 Wikipedia:Small_intestinal_submucosa small bowel submucosa small intestinal submucosa small intestine submucosa submucosa of small bowel tela submucosa (intestinum tenue) tela submucosa intestini tenuis uberon UBERON:0001205 submucosa of small intestine Submucosal tissue in the small intestines. Wikipedia:Small_intestinal_submucosa EMAPA:37564 MA:th UMLS:C0227268 ncithesaurus:Small_Intestinal_Submucosa small bowel submucosa OBOL:automatic submucosa of small bowel OBOL:automatic tela submucosa intestini tenuis BTO:0002112 A serous membrane that is part of a small intestine [Automatically generated definition]. duodenum, 1st part serosa, 2nd - 4th adventitia EMAPA:37561 FMA:14938 MA:0001558 SCTID:8266009 serosa of small bowel serous coat of small intestine serous membrane of small bowel serous membrane of small intestine small bowel serosa small bowel serous membrane small intestinal serosa small intestine serosa small intestine serous membrane tunica serosa (intestinum tenue) tunica serosa intestini tenuis visceral peritoneum of small intestine uberon UBERON:0001206 serosa of small intestine A serous membrane that is part of a small intestine [Automatically generated definition]. OBOL:automatic EMAPA:37561 MA:th serosa of small bowel OBOL:automatic serous membrane of small bowel OBOL:automatic serous membrane of small intestine OBOL:automatic small bowel serosa OBOL:automatic small bowel serous membrane OBOL:automatic small intestine serous membrane OBOL:automatic tunica serosa intestini tenuis FMA:14938 FMA:TA A mucosa that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2106 EMAPA:35467 FMA:14969 MA:0002688 NCIT:C32926 UMLS:C0734203 large intestinal mucosa large intestine mucosa large intestine mucosa of organ large intestine mucous membrane large intestine organ mucosa mucosa of organ of large intestine mucous membrane of large intestine organ mucosa of large intestine tunica mucosa intestini crassi uberon UBERON:0001207 mucosa of large intestine A mucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic UMLS:C0734203 ncithesaurus:Large_Intestinal_Mucosa large intestine mucosa of organ OBOL:automatic large intestine mucous membrane OBOL:automatic large intestine organ mucosa OBOL:automatic mucosa of organ of large intestine OBOL:automatic organ mucosa of large intestine OBOL:automatic tunica mucosa intestini crassi FMA:14969 FMA:TA A submucosa that is part of a large intestine [Automatically generated definition]. BTO:0002111 EMAPA:37560 FMA:14970 MA:0002690 NCIT:C32930 UMLS:C0734204 large intestinal submucosa large intestine submucosa tela submucosa intestini crassi uberon submucous layer of large intestine UBERON:0001208 submucosa of large intestine A submucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37560 MA:th UMLS:C0734204 ncithesaurus:Large_Intestinal_Submucosa tela submucosa intestini crassi FMA:14970 FMA:TA submucous layer of large intestine BTO:0002111 A serous membrane that is part of a large intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37557 FMA:14975 MA:0001546 NCIT:C32929 UMLS:C1517727 large intestinal serosa large intestine serosa large intestine serous membrane serous coat of large intestine serous membrane of large intestine tunica serosa intestini crassi visceral peritoneum of large intestine uberon UBERON:0001209 serosa of large intestine A serous membrane that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37557 MA:th UMLS:C1517727 ncithesaurus:Large_Intestinal_Serosal_Surface large intestine serous membrane OBOL:automatic serous membrane of large intestine OBOL:automatic tunica serosa intestini crassi FMA:14975 FMA:TA A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. currently defined as equivalent to any submucosal gland in the duodenum. Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds BTO:0002376 EMAPA:36522 FMA:15060 GAID:314 MA:0001551 MESH:D002011 NCIT:C13010 SCTID:41298001 UMLS:C0006323 Wikipedia:Brunner's_glands Brunner's gland gland of Brunner submucosal gland of duodenum uberon glandula duodenales glandula duodenales Brunneri UBERON:0001212 duodenal gland compound tubular FMA, modified unclear for Aves ISBN:9780521617147 A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. Wikipedia:Brunner's_glands Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds ISBN:9780521617147 UMLS:C0006323 ncithesaurus:Brunner_s_Gland Brunner's gland FMA:15060 gland of Brunner FMA:15060 glandula duodenales BTO:0002376 glandula duodenales Brunneri BTO:0002376 The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold. in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO] the BTO class refers to a generic villous UBERON:0007607 BTO:0003121 EMAPA:35784 FMA:15072 MA:0001563 NCIT:C33874 SCTID:23230007 TAO:0005125 UMLS:C1519988 Wikipedia:Intestinal_villus ZFA:0005125 enteric villi enteric villous enteric villus intestinal villi villi intestinales villus villus intestinalis (intestinum tenue) uberon intestinal villus layer small intestine villus villi intestinales UBERON:0001213 intestinal villus http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg FMA ZFA The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold. MGI:csmith MGI:rbabiuk MP:0008108 The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO] 2012-08-14 TAO:0005125 TAO ZFIN:curator the BTO class refers to a generic villous BTO UMLS:C1519988 ncithesaurus:Villus enteric villi HP:0011473 enteric villous HP:0011473 enteric villus HP:0011473 intestinal villi ZFA:0005125 villi intestinales villus BTO:0003121 villus intestinalis (intestinum tenue) FMA:15072 small intestine villus MA:0001563 villi intestinales Wikipedia:Intestinal_villus A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002782 EHDAA2:0000819 EHDAA:8712 EMAPA:18642 FMA:15391 MA:0002178 NCIT:C32782 SCTID:281055007 UMLS:C0226754 VHOG:0001118 Wikipedia:Inferior_mesenteric_vein uberon lower mesenteric vein vena mesenterica inferior UBERON:0001215 inferior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA/obol A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. Wikipedia:Inferior_mesenteric_vein UMLS:C0226754 ncithesaurus:Inferior_Mesenteric_Vein lower mesenteric vein BTO:0002782 vena mesenterica inferior Wikipedia:Inferior_mesenteric_vein Lamina propria that is part_of the small intestine. EMAPA:35779 FMA:15651 MA:0001554 NCIT:C49297 SCTID:63588008 UMLS:C1711325 lamina propria mucosa of small bowel lamina propria mucosa of small intestine lamina propria mucosae of small bowel lamina propria mucosae of small intestine lamina propria of mucosa of small intestine lamina propria of small bowel small bowel lamina propria small bowel lamina propria mucosa small bowel lamina propria mucosae small intestine lamina propria small intestine lamina propria mucosa small intestine lamina propria mucosae uberon UBERON:0001238 lamina propria of small intestine Lamina propria that is part_of the small intestine. GOC:Obol UMLS:C1711325 ncithesaurus:Small_Intestinal_Lamina_Propria lamina propria mucosa of small bowel OBOL:automatic lamina propria mucosa of small intestine OBOL:automatic lamina propria mucosae of small bowel OBOL:automatic lamina propria of small bowel OBOL:automatic small bowel lamina propria OBOL:automatic small bowel lamina propria mucosa OBOL:automatic small bowel lamina propria mucosae OBOL:automatic small intestine lamina propria mucosa OBOL:automatic small intestine lamina propria mucosae OBOL:automatic Mucosal layer that lines the intestine. BTO:0000642 EMAPA:35440 FMA:15695 GAID:296 MA:0001537 MESH:D007413 NCIT:C49241 SCTID:362080002 UMLS:C0021839 bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini uberon UBERON:0001242 intestinal mucosa Mucosal layer that lines the intestine. UBERON:cjm UMLS:C0021839 ncithesaurus:Intestinal_Mucosa bowel mucosa OBOL:automatic bowel mucosa of organ OBOL:automatic bowel mucous membrane OBOL:automatic bowel organ mucosa OBOL:automatic intestine mucosa of organ OBOL:automatic intestine mucous membrane OBOL:automatic intestine organ mucosa OBOL:automatic mucosa of bowel OBOL:automatic mucosa of organ of bowel OBOL:automatic mucosa of organ of intestine OBOL:automatic mucous membrane of bowel OBOL:automatic mucous membrane of intestine OBOL:automatic organ mucosa of bowel OBOL:automatic organ mucosa of intestine OBOL:automatic A serous membrane that is part of a wall of intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37619 FMA:15701 MA:0001538 anatomical wall of bowel serosa anatomical wall of bowel serous membrane anatomical wall of intestine serosa anatomical wall of intestine serous membrane bowel anatomical wall serosa bowel anatomical wall serous membrane bowel wall serosa bowel wall serous membrane intestinal serosa intestinal wall serosa intestinal wall serous membrane intestine anatomical wall serosa intestine anatomical wall serous membrane intestine serosa intestine wall serosa intestine wall serous membrane serosa of anatomical wall of bowel serosa of anatomical wall of intestine serosa of bowel anatomical wall serosa of bowel wall serosa of intestinal wall serosa of intestine anatomical wall serosa of intestine wall serosa of wall of bowel serosa of wall of intestine serous membrane of anatomical wall of bowel serous membrane of anatomical wall of intestine serous membrane of bowel anatomical wall serous membrane of bowel wall serous membrane of intestinal wall serous membrane of intestine anatomical wall serous membrane of intestine wall serous membrane of wall of bowel serous membrane of wall of intestine visceral peritoneum of intestine wall of bowel serosa wall of bowel serous membrane wall of intestine serosa wall of intestine serous membrane uberon UBERON:0001243 serosa of intestine A serous membrane that is part of a wall of intestine [Automatically generated definition]. OBOL:automatic EMAPA:37619 MA:th anatomical wall of bowel serosa OBOL:automatic anatomical wall of bowel serous membrane OBOL:automatic anatomical wall of intestine serosa OBOL:automatic anatomical wall of intestine serous membrane OBOL:automatic bowel anatomical wall serosa OBOL:automatic bowel anatomical wall serous membrane OBOL:automatic bowel wall serosa OBOL:automatic bowel wall serous membrane OBOL:automatic intestinal wall serosa OBOL:automatic intestinal wall serous membrane OBOL:automatic intestine anatomical wall serosa OBOL:automatic intestine anatomical wall serous membrane OBOL:automatic intestine wall serosa OBOL:automatic intestine wall serous membrane OBOL:automatic serosa of anatomical wall of bowel OBOL:automatic serosa of anatomical wall of intestine OBOL:automatic serosa of bowel anatomical wall OBOL:automatic serosa of bowel wall OBOL:automatic serosa of intestinal wall OBOL:automatic serosa of intestine anatomical wall OBOL:automatic serosa of intestine wall OBOL:automatic serosa of wall of bowel OBOL:automatic serosa of wall of intestine OBOL:automatic serous membrane of anatomical wall of bowel OBOL:automatic serous membrane of anatomical wall of intestine OBOL:automatic serous membrane of bowel anatomical wall OBOL:automatic serous membrane of bowel wall OBOL:automatic serous membrane of intestinal wall OBOL:automatic serous membrane of intestine anatomical wall OBOL:automatic serous membrane of intestine wall OBOL:automatic serous membrane of wall of bowel OBOL:automatic serous membrane of wall of intestine OBOL:automatic wall of bowel serosa OBOL:automatic wall of bowel serous membrane OBOL:automatic wall of intestine serosa OBOL:automatic wall of intestine serous membrane OBOL:automatic Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. anal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html BTO:0001680 CALOHA:TS-2005 EV:0100082 FBbt:00047153 FMA:15711 GAID:312 MA:0000331 NCIT:C43362 SCTID:181262009 TADS:0000066 TGMA:0001279 UMLS:C0003461 WBbt:0005364 Wikipedia:Anus galen:Anus anal opening anal orifice opening of terminal part of digestive tract uberon proctodeum UBERON:0001245 anus http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. Wikipedia:Anus ZFIN:curator FBbt:00047153 UMLS:C0003461 ncithesaurus:Anus The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. FMA:15767 MA:0002668 NCIT:C32827 SCTID:83488001 UMLS:C0227515 Wikipedia:Interlobular_bile_ducts interlobular ductule uberon UBERON:0001246 interlobular bile duct FMA MA-part-of FMA MA MP The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. MP:0009500 UMLS:C0227515 ncithesaurus:Interlobular_Bile_Duct interlobular ductule MP:0009500 An anatomical wall that is part of a intestine [Automatically generated definition]. we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different BTO:0000647 EMAPA:35444 FMA:15949 MA:0001525 MA:0002693 NCIT:C49478 UMLS:C1708548 anatomical wall of bowel anatomical wall of intestine bowel anatomical wall bowel wall intestinal wall intestine anatomical wall intestine wall wall of bowel uberon bowel wall UBERON:0001262 wall of intestine An anatomical wall that is part of a intestine [Automatically generated definition]. OBOL:automatic UMLS:C1708548 ncithesaurus:Intestinal_Wall_Tissue anatomical wall of bowel OBOL:automatic anatomical wall of intestine OBOL:automatic bowel anatomical wall OBOL:automatic bowel wall OBOL:automatic intestine anatomical wall OBOL:automatic wall of bowel OBOL:automatic bowel wall MA:0001525 The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. BTO:0000028 EMAPA:35651 FMA:16011 MA:0002417 NCIT:C49268 SCTID:247604006 UMLS:C0227578 acinus pancreaticus pancreas acinus uberon pancreatic acinar pancreatic acini UBERON:0001263 pancreatic acinus FMA The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. MP:0009145 BTO:0000028 https://github.com/biopragmatics/biomappings UMLS:C0227578 ncithesaurus:Pancreatic_Acinus acinus pancreaticus FMA:16011 pancreatic acini An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] pancreatic As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans AAO:0010112 BTO:0000988 CALOHA:TS-0736 EFO:0000855 EHDAA2:0001367 EHDAA:6893 EMAPA:17503 EV:0100092 FMA:7198 GAID:334 MA:0000120 MAT:0000075 MESH:D010179 MIAA:0000075 NCIT:C12393 SCTID:181277001 TAO:0000140 UMLS:C0030274 VHOG:0000050 Wikipedia:Pancreas XAO:0000136 ZFA:0000140 galen:Pancreas uberon UBERON:0001264 pancreas https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pancreas.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png PMID:16417468 Wikipedia Wikipedia An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. GO:0031016 Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] 2012-06-20 AAO:0010112 AAO AAO:BJB In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000050 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) http://bgee.unil.ch/ As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) PMID:20959416 The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans PMID:16417468 UMLS:C0030274 ncithesaurus:Pancreas A trabecula that is part of a spleen. EMAPA:35808 FMA:16027 MA:0000758 NCIT:C33607 SCTID:61987002 UMLS:C0229688 Wikipedia:Trabeculae_of_spleen spleen trabeculum splenic trabecula trabeculae of spleen uberon UBERON:0001265 trabecula of spleen FMA A trabecula that is part of a spleen. OBOL:automatic UMLS:C0229688 ncithesaurus:Splenic_Trabecula trabeculae of spleen Transudate contained in the peritoneal cavity. BTO:0001031 EMAPA:35683 FMA:16515 MA:0002531 MESH:D001202 Wikipedia:Peritoneal_fluid ncithesaurus:Peritoneal_Fluid uberon UBERON:0001268 peritoneal fluid FMA Transudate contained in the peritoneal cavity. FMA:16515 MESH:D001202 https://github.com/biopragmatics/biomappings The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions. this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] EMAPA:37862 FMA:16581 NCIT:C33291 SCTID:360010001 UMLS:C0684083 VSAO:0000304 uberon girdle - pelvic pelvic girdle UBERON:0001271 pelvic girdle region The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions. DOI:10.1002/dvdy.22617 FMA:16581 FMA:23217 UBERONREF:0000003 https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion https://orcid.org/0000-0002-6601-2165 Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] 2012-08-14 VSAO:0000304 VSAO https://orcid.org/0000-0002-6601-2165 EMAPA:37862 MA:th UMLS:C0684083 ncithesaurus:Pelvic_Girdle pelvic girdle The epithelial layer of the stomach . in FMA this is classified as simple columnar, MA divides this into squamous and glandular BTO:0000500 CALOHA:TS-2068 EHDAA2:0001918 EMAPA:17023 FMA:17091 MA:0001610 SCTID:64977002 VHOG:0001433 epithelial tissue of stomach epithelial tissue of ventriculus epithelium of ventriculus stomach epithelial tissue stomach epithelium ventriculus epithelial tissue ventriculus epithelium uberon gastric epithelium UBERON:0001276 epithelium of stomach The epithelial layer of the stomach . MP:0000471 in FMA this is classified as simple columnar, MA divides this into squamous and glandular FMA epithelial tissue of stomach OBOL:automatic epithelial tissue of ventriculus OBOL:automatic epithelium of ventriculus OBOL:automatic stomach epithelial tissue OBOL:automatic stomach epithelium OBOL:automatic ventriculus epithelial tissue OBOL:automatic ventriculus epithelium OBOL:automatic gastric epithelium BTO:0000500 Epithelial layer that lines the intestine. Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] BTO:0000781 EMAPA:32873 FMA:17229 MA:0001536 NCIT:C49240 SCTID:266135004 TAO:0005124 UMLS:C0226890 Wikipedia:Intestinal_epithelium ZFA:0005124 bowel epithelial tissue bowel epithelium epithelial tissue of bowel epithelial tissue of intestine epithelium of bowel epithelium of intestine intestine epithelial tissue villous epithelium uberon intestine epithelium UBERON:0001277 intestinal epithelium Epithelial layer that lines the intestine. UBERON:cjm Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] 2012-08-14 TAO:0005124 TAO ZFIN:curator UMLS:C0226890 ncithesaurus:Intestinal_Epithelium bowel epithelial tissue OBOL:automatic bowel epithelium OBOL:automatic epithelial tissue of bowel OBOL:automatic epithelial tissue of intestine OBOL:automatic epithelium of bowel OBOL:automatic epithelium of intestine OBOL:automatic intestine epithelial tissue OBOL:automatic villous epithelium ZFA:0005124 An epithelium that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2105 EMAPA:35466 FMA:17301 MA:0001545 epithelial tissue of large intestine large intestinal epithelium large intestine epithelial tissue large intestine epithelium uberon UBERON:0001278 epithelium of large intestine An epithelium that is part of a large intestine [Automatically generated definition]. OBOL:automatic epithelial tissue of large intestine OBOL:automatic large intestine epithelial tissue OBOL:automatic A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver. FMA:17523 MA:0002499 NCIT:C33342 SCTID:362192000 UMLS:C0227514 Wikipedia:Portal_triad trias hepatica uberon trias hepatica UBERON:0001279 portal triad https://upload.wikimedia.org/wikipedia/commons/6/62/Portal_triad.JPG A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. ISBN:0-683-40008-8 MGI:csmith MP:0008993 http://orcid.org/0000-0002-6601-2165 UMLS:C0227514 ncithesaurus:Portal_Triad trias hepatica Wikipedia:Portal_triad The functional units of the liver including the lobules. the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG] UBERON:0003223 AAO:0010405 EHDAA2:0001004 EHDAA:2201 EMAPA:17203 FMA:17540 MA:0000366 NCIT:C32735 SCTID:363535004 UMLS:C0736268 VHOG:0000539 XAO:0000454 hepatic parenchyma liver parenchyme parenchyma of liver uberon hepatic parenchyme UBERON:0001280 liver parenchyma XAO The functional units of the liver including the lobules. MP:0008986 the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG] 2012-09-17 VHOG:0000539 VHOG DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007) http://bgee.unil.ch/ hepatic parenchyma FMA:17540 liver parenchyme XAO:0000454 parenchyma of liver FMA:17540 hepatic parenchyme VHOG:0000539 Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers. (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] UBERON:0003275 EHDAA2:0000999 EMAPA:17365 FMA:17543 MA:0000367 NCIT:C32733 SCTID:67435004 TAO:0005091 UMLS:C0227523 VHOG:0000708 Wikipedia:Hepatic_sinusoid ZFA:0005091 liver hepatic sinusoids liver sinusoid liver sinusoidal blood vessel sinusoid of liver sinusoidal blood vessel of liver vas capillare sinusoideum vas sinusoideum uberon hepatic sinusoids UBERON:0001281 hepatic sinusoid https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers. Wikipedia:Hepatic_sinusoid ZFIN:curator (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] 2012-09-17 VHOG:0000708 VHOG DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) http://bgee.unil.ch/ UMLS:C0227523 ncithesaurus:Hepatic_Sinusoid liver hepatic sinusoids EHDAA2:0000999 liver sinusoidal blood vessel OBOL:automatic sinusoid of liver OBOL:automatic sinusoidal blood vessel of liver OBOL:automatic vas sinusoideum Wikipedia:Hepatic_sinusoid The tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule. Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct) FMA:17545 MA:0002669 NCIT:C32255 SCTID:227002 SCTID:269922006 UMLS:C0227517 Wikipedia:Canals_of_Hering canal of Herring cholangiole ductus interlobularis bilifer uberon canal of Hering canals of Hering duct of Herring intrahepatic bile ductule UBERON:0001282 intralobular bile duct FMA FMA FMA The tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule. MGI:csmith MP:0009499 UMLS:C0227517 ncithesaurus:Canal_of_Hering canal of Herring FMA:17545 cholangiole FMA:17545 ductus interlobularis bilifer FMA:17545 FMA:TA canals of Hering Wikipedia:Canals_of_Hering duct of Herring Wikipedia:Canals_of_Hering intrahepatic bile ductule Wikipedia:Canals_of_Hering Muscle (organ) which is a part of the pelvis. Examples: levator ani,. EMAPA:18184 EMAPA:37481 FMA:19086 MA:0000534 muscle organ of pelvis pelvic muscle pelvis muscle pelvis muscle organ uberon UBERON:0001325 muscle of pelvis FMAdef MA Muscle (organ) which is a part of the pelvis. Examples: levator ani,. FMA:19086 EMAPA:37481 MA:th muscle organ of pelvis OBOL:automatic pelvic muscle FMA:19086 pelvis muscle organ OBOL:automatic The anus and surrounding regions. Encompasses both internal and external regions, where present. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 EMAPA:16831 MA:0000329 MAT:0000042 MIAA:0000042 NCIT:C32069 SCTID:362680001 UMLS:C0230120 VHOG:0000395 WBbt:0006919 uberon posterior posterior end of organism UBERON:0001353 anal region https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png cjm The anus and surrounding regions. Encompasses both internal and external regions, where present. https://orcid.org/0000-0002-6601-2165 Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000395 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0230120 ncithesaurus:Anal_Region The outer layer of peritoneum that is attached to the abdominal and pelvic walls. Peritoneum attached to the abdominal wall.[AAO] UBERON:0004459 AAO:0010816 EMAPA:16591 FMA:21451 SCTID:362700006 TAO:0005131 VHOG:0001527 Wikipedia:Parietal_peritoneum ZFA:0005131 parietal serous membrane of peritoneum uberon peritoneal cavity lining UBERON:0001366 parietal peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png The outer layer of peritoneum that is attached to the abdominal and pelvic walls. Wikipedia:Peritoneum#Types http://orcid.org/0000-0002-6601-2165 Peritoneum attached to the abdominal wall.[AAO] 2012-06-20 AAO:0010816 AAO AAO:JMG parietal serous membrane of peritoneum UBERON:cjm A zone of skin that is part of a pelvis [Automatically generated definition]. EMAPA:37282 FMA:22984 MA:0000546 SCTID:181517009 pelvic skin pelvis skin pelvis zone of skin zone of skin of pelvis uberon UBERON:0001415 skin of pelvis A zone of skin that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37282 MA:th pelvis zone of skin OBOL:automatic zone of skin of pelvis OBOL:automatic A zone of skin that is part of an abdomen [Automatically generated definition]. EFO:0000214 FMA:22988 FMA:23000 MA:0000523 NCIT:C52758 SCTID:361707007 UMLS:C0222166 abdomen skin abdomen zone of skin abdominal skin skin of abdomen proper zone of skin of abdomen uberon UBERON:0001416 skin of abdomen A zone of skin that is part of an abdomen [Automatically generated definition]. OBOL:automatic UMLS:C0222166 ncithesaurus:Abdominal_Skin abdomen zone of skin OBOL:automatic skin of abdomen proper FMA:22988 zone of skin of abdomen OBOL:automatic A zone of skin that is part of a neck [Automatically generated definition]. EMAPA:37277 FMA:23021 FMA:23022 MA:0000590 NCIT:C52756 SCTID:361705004 UMLS:C0205030 neck (volume) zone of skin neck skin neck zone of skin zone of skin of neck zone of skin of neck (volume) uberon UBERON:0001417 skin of neck A zone of skin that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37277 MA:th UMLS:C0205030 ncithesaurus:Neck_Skin neck (volume) zone of skin OBOL:automatic neck zone of skin OBOL:automatic zone of skin of neck OBOL:automatic zone of skin of neck (volume) OBOL:automatic A zone of skin that is part of a thorax [Automatically generated definition]. EMAPA:37765 FMA:23028 FMA:23029 MA:0000564 SCTID:281723000 thoracic skin thorax skin thorax zone of skin zone of skin of thorax uberon upper body skin UBERON:0001418 skin of thorax A zone of skin that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37765 MA:th thorax zone of skin OBOL:automatic zone of skin of thorax OBOL:automatic An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO] Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO] EMAPA:37856 FMA:23217 SCTID:229759004 VSAO:0000305 galen:ShoulderGirdle cingulum membri superioris girdle - pectoral cingulum membri superioris shoulder girdle upper limb girdle uberon pectoral girdle pectoral region UBERON:0001421 pectoral girdle region An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. FMA:23217 UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO] 2012-08-14 VSAO:0000305 VSAO https://orcid.org/0000-0002-6601-2165 Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO] 2012-09-06 VSAO:0000305 VSAO Curator EMAPA:37856 MA:th cingulum membri superioris FMA:23217 FMA:TA cingulum membri superioris FMA:TA shoulder girdle FMA:23217 upper limb girdle FMA:23217 Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] System that provides physical support to the organism.[AAO] By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] skeletal GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 EFO:0000806 EHDAA2:0003168 EMAPA:35773 FMA:23881 MA:0000018 NCIT:C12788 TAO:0000434 UMLS:C0037253 VHOG:0001254 VSAO:0000027 XAO:0003060 ZFA:0000434 skeleton system set of all bones and joints uberon Skelettsystem UBERON:0001434 skeletal system https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. GO_REF:0000034 VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] 2012-08-14 TAO:0000434 TAO TAO:wd Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] 2012-08-14 VSAO:0000027 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 System that provides physical support to the organism.[AAO] 2012-06-20 AAO:0000566 AAO AAO:LAP By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] 2012-09-17 VHOG:0001254 VHOG DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) http://bgee.unil.ch/ GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates GO UMLS:C0037253 ncithesaurus:Skeletal_System set of all bones and joints Skelettsystem BTO:0001486 FMA:24218 SCTID:123852005 XAO:0000040 head subdivision uberon head region region of head UBERON:0001444 subdivision of head A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. The area that extends from the median ocellus to the oral foramen[HAO]. facial The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) BTO:0003369 CALOHA:TS-2216 EMAPA:32763 FMA:24728 GAID:64 HAO:0000316 MA:0002473 MESH:D005145 NCIT:C13071 SCTID:302549007 UMLS:C0015450 Wikipedia:Face galen:Face uberon facia/facies visage UBERON:0001456 face http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). http://orcid.org/0000-0002-6601-2165 Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. FMA:24728 The area that extends from the median ocellus to the oral foramen[HAO]. HAO:0000316 http://api.hymao.org/api/ref/67791 NCBITaxon:7399 The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf UMLS:C0015450 ncithesaurus:Face facia/facies Wikipedia:Face visage BTO:0003369 A zone of skin that is part of a lip [Automatically generated definition]. EMAPA:37643 FMA:24764 MA:0001579 NCIT:C12291 SCTID:244092005 UMLS:C0222101 lip skin lip zone of skin zone of skin of lip uberon skin of lips UBERON:0001458 skin of lip A zone of skin that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37643 MA:th UMLS:C0222101 ncithesaurus:Skin_of_the_Lip lip zone of skin OBOL:automatic zone of skin of lip OBOL:automatic skin of lips Skeletal element that is composed of bone tissue. Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] Skeletal element that is composed of bone tissue.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 CALOHA:TS-0088 EFO:0000298 EHDAA2:0003082 EMAPA:32782 ENVO:00002039 EV:0100140 FMA:30317 FMA:5018 GAID:92 MA:0001459 MAT:0000299 MIAA:0000299 NCIT:C12366 SCTID:90780006 TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 Wikipedia:Bone XAO:0000169 ZFA:0001514 galen:Bone bone organ uberon bone bones UBERON:0001474 bone element VSAO-modified Skeletal element that is composed of bone tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000057 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/277 Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] 2012-06-20 AAO:0000047 AAO AAO:LAP Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] 2012-08-14 TAO:0001514 TAO ZFIN:curator Skeletal element that is composed of bone tissue.[VSAO] 2012-08-14 VSAO:0000057 VSAO PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000047 AAO The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] 2012-09-17 VHOG:0001190 VHOG DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) http://bgee.unil.ch/ UMLS:C0262950 ncithesaurus:Bone bone organ FMA:5018 bone AEO:0000082 BTO:0000140 MA:0001459 VHOG:0001190 bones ZFA:0001514 An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita EMAPA:37621 FMA:34836 GAID:263 MA:0001519 MESH:D017746 NCIT:C32259 NCIT:C84388 SCTID:182238002 UMLS:C0206207 Wikipedia:Articular_capsule galen:JointCapsule capsula articularis fibrous capsule of joint joint capsule joint fibrous capsule uberon capsulae articulares UBERON:0001484 articular capsule http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. Wikipedia:Articular_capsule check ncita ncit EMAPA:37621 MA:th UMLS:C0206207 ncithesaurus:Joint_Capsule capsula articularis FMA:34836 FMA:TA capsulae articulares Wikipedia:Articular_capsule The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]. EHDAA2:0000147 EHDAA:9828 EMAPA:17014 FMA:3736 MA:0002570 NCIT:C32150 SCTID:181299009 UMLS:C0003956 Wikipedia:Ascending_aorta ascending thoracic aorta pars ascendens aortae uberon aorta ascendens pars ascendens aortae UBERON:0001496 ascending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb EHDAA2 The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]. GO:0035905 Wikipedia:Ascending_aorta UMLS:C0003956 ncithesaurus:Ascending_Aorta ascending thoracic aorta EMAPA:17014 aorta ascendens Wikipedia:Ascending_aorta pars ascendens aortae Wikipedia:Ascending_aorta Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. UBERON:0003271 EHDAA:8326 EMAPA:18184 EMAPA:18185 FMA:37367 MA:0000537 RETIRED_EHDAA2:0001430 girdle-pelvic muscle organ muscle organ of girdle-pelvic muscle organ of pelvic girdle muscle organ of pelvic girdle bone pelvic girdle muscle pelvic girdle muscle organ pelvic girdle skeletal muscle uberon UBERON:0001497 muscle of pelvic girdle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. MA girdle-pelvic muscle organ OBOL:automatic muscle organ of girdle-pelvic OBOL:automatic muscle organ of pelvic girdle OBOL:automatic muscle organ of pelvic girdle bone OBOL:automatic pelvic girdle muscle organ OBOL:automatic pelvic girdle skeletal muscle EMAPA:18185 The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery. Do not confuse with aortic arch The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG] The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG] birds have right aortic arch, mammals left. BTO:0000157 EFO:0002526 EHDAA2:0000132 EMAPA:17613 FMA:3768 GAID:471 MA:0000475 SCTID:181300001 VHOG:0001196 Wikipedia:Arch_of_aorta arcus aortae uberon aortic arch thoracic aorta UBERON:0001508 arch of aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb left arch 4 in human embryology.ch The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery. ISBN:0-683-40008-8 MP:0004113 The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG] 2012-09-17 VHOG:0001196 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/arch+of+aorta The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG] 2012-09-17 VHOG:0001196 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20 http://bgee.unil.ch/ arcus aortae FMA:3768 FMA:TA aortic arch FMA:3768 thoracic aorta GAID:471 The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. results from fusion of left and right dorsal aortae EMAPA:18606 FMA:3784 MA:0002571 NCIT:C32455 SCTID:261399002 UMLS:C0011666 Wikipedia:Descending_aorta pars descendens aortae uberon aorta descendens pars descendens aortae UBERON:0001514 descending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA Wikipedia The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. GO:0035906 Wikipedia:Descending_aorta UMLS:C0011666 ncithesaurus:Descending_Aorta pars descendens aortae FMA:3784 aorta descendens Wikipedia:Descending_aorta pars descendens aortae Wikipedia:Descending_aorta The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest. BTO:0000157 EFO:0002525 EMAPA:18603 FMA:3786 GAID:471 MA:0002569 MESH:D001013 NCIT:C33766 SCTID:302510009 UMLS:C1522460 Wikipedia:Thoracic_aorta galen:ThoracicAorta aorta thoracica thoracic part of aorta uberon aorta thoracalis pars thoracica aortae UBERON:0001515 thoracic aorta http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png FMA The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest. MP:0010468 http://www.medterms.com UMLS:C1522460 ncithesaurus:Thoracic_Aorta aorta thoracica FMA:3786 FMA:TA aorta thoracalis Wikipedia:Thoracic_aorta pars thoracica aortae Wikipedia:Thoracic_aorta Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates BTO:0002976 EFO:0002524 EMAPA:17856 FMA:3789 GAID:470 MA:0000474 MESH:D001012 NCIT:C32038 SCTID:244231007 UMLS:C0003484 Wikipedia:Abdominal_aorta galen:AbdominalAorta abdominal part of aorta descending abdominal aorta pars abdominalis aortae uberon abdominal part of aorta aorta abdominalis pars abdominalis aortae UBERON:0001516 abdominal aorta http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png FMA Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. BTO:0002976 Wikipedia:Abdominal_aorta UMLS:C0003484 ncithesaurus:Abdominal_Aorta abdominal part of aorta FMA:3789 descending abdominal aorta FMA:3789 pars abdominalis aortae FMA:3789 abdominal part of aorta BTO:0002976 aorta abdominalis BTO:0002976 Wikipedia:Abdominal_aorta pars abdominalis aortae BTO:0002976 Wikipedia:Abdominal_aorta The short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery. innominate EFO:0002550 EHDAA2:0000835 EMAPA:17615 FMA:3932 GAID:476 MA:0001922 MESH:D016122 NCIT:C32814 SCTID:244244002 UMLS:C0006094 Wikipedia:Brachiocephalic_artery galen:BrachioCephalicArtery brachiocephalic trunk innominate artery truncus brachiocephalicus uberon truncus brachiocephalicus UBERON:0001529 brachiocephalic artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery. MGI:csmith MP:0010663 innominate Wikipedia:Brachiocephalic_artery UMLS:C0006094 ncithesaurus:Innominate_Artery brachiocephalic trunk MA:0001922 innominate artery Wikipedia:Brachiocephalic_artery truncus brachiocephalicus FMA:3932 FMA:TA truncus brachiocephalicus Wikipedia:Brachiocephalic_artery A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery' This class represents the adult and developing structures' in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae carotid artery CALOHA:TS-0116 EHDAA2:0000217 EHDAA:7331 EMAPA:17855 FMA:3939 GAID:479 MA:0001926 MESH:D017536 NCIT:C32352 SCTID:362041005 UMLS:C0162859 VHOG:0000272 Wikipedia:Common_carotid_artery carotid artery system common carotid artery trunk of common carotid tree uberon a. carotis communis UBERON:0001530 common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA Wikipedia A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. Wikipedia:Common_carotid_artery carotid artery FMA:3939 UMLS:C0162859 ncithesaurus:Common_Carotid_Artery carotid artery system EHDAA2:0000217 common carotid artery FMA:3939 trunk of common carotid tree FMA:3939 a. carotis communis Wikipedia:Common_carotid_artery One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta. Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO) Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO] In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP] The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO] AAO:0010232 EHDAA2:0001933 EHDAA:4357 EMAPA:17617 FMA:3951 GAID:511 MA:0002045 MESH:D013348 NCIT:C33643 SCTID:265790007 TAO:0005086 UMLS:C0038530 Wikipedia:Subclavian_artery XAO:0000365 ZFA:0005086 arteria subclavia arterial tree of upper limb pectoral artery subclavian arterial tree uberon PA arteria subclavia UBERON:0001533 subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg EHDAA2 EHDAA2 One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta. ISBN:0073040584 https://orcid.org/0000-0002-6601-2165 Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO] 2012-06-20 AAO:0010232 AAO AAO:BJB In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP] Wikipedia:Subclavian_artery The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO] 2012-08-14 TAO:0005086 TAO ZFIN:curator UMLS:C0038530 ncithesaurus:Subclavian_Artery arteria subclavia XAO:0000365 PA arteria subclavia Wikipedia:Subclavian_artery The subclavian artery that supplies the right pectoral appendage. in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery proximal part arises from right 4th aortic arch in humans EHDAA2:0004514 EMAPA:37384 FMA:3953 MA:0002047 NCIT:C33490 SCTID:244246000 UMLS:C0226261 Wikipedia:Subclavian_artery arteria subclavia dextra uberon UBERON:0001534 right subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg The subclavian artery that supplies the right pectoral appendage. http://orcid.org/0000-0002-6601-2165 EMAPA:37384 MA:th UMLS:C0226261 ncithesaurus:Right_Subclavian_Artery arteria subclavia dextra FMA:3953 FMA:TA A tube extending from the mouth to the anus. The alimentary or digestive tract, and associated organs.[TAO] The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] FMA also has a term 'gastrointestinal tract', but this includes the liver. we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 BTO:0000511 BTO:0000545 EHDAA2:0000726 EHDAA:518 EMAPA:16247 FBbt:00003125 FMA:45615 MA:0000917 MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 UMLS:C0017189 VHOG:0000309 WBbt:0005743 ZFA:0000112 galen:AlimentaryTract digestive tube enteric tract alimentary canal alimentary tract uberon digestive canal gut tube UBERON:0001555 digestive tract NCBIBook:NBK10107 A tube extending from the mouth to the anus. Wikipedia:Talk:Human_gastrointestinal_tract https://github.com/geneontology/go-ontology/issues/7549 Wikipedia:Acoelomorpha DOI:10.1371/journal.pone.0016309 The alimentary or digestive tract, and associated organs.[TAO] 2012-08-14 TAO:0000112 TAO ZFIN:curator The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000309 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ FMA also has a term 'gastrointestinal tract', but this includes the liver. FMA we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 MA FBbt:00003125 MESH:D041981 https://github.com/biopragmatics/biomappings UMLS:C0017189 ncithesaurus:Gastrointestinal_Tract enteric tract ZFA:0000112 digestive canal BTO:0000058 The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. EHDAA2:0001036 EMAPA:16738 FMA:45662 MA:0000435 SCTID:281488008 VHOG:0000382 Wikipedia:Lower_respiratory_tract lower respiratory system uberon UBERON:0001558 lower respiratory tract http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. Wikipedia:Lower_respiratory_tract http://orcid.org/0000-0002-6601-2165 The subclavian artery that supplies the left pectoral appendage. in humans, branches off the arch of aorta arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans EMAPA:37100 FMA:4694 MA:0002046 NCIT:C32972 SCTID:244245001 UMLS:C0226262 Wikipedia:Subclavian_artery arteria subclavia (sinistra) uberon UBERON:0001584 left subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The subclavian artery that supplies the left pectoral appendage. http://orcid.org/0000-0002-6601-2165 EMAPA:37100 MA:th UMLS:C0226262 ncithesaurus:Left_Subclavian_Artery arteria subclavia (sinistra) FMA:4694 FMA:TA A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green). BTO:0002683 EHDAA2:0001962 EHDAA:8726 EMAPA:18417 FMA:4720 GAID:549 MA:0000481 MESH:D014683 NCIT:C12816 SCTID:181368006 UMLS:C0042459 VHOG:0001195 Wikipedia:Superior_vena_cava galen:SuperiorVenaCava superior caval vein superior vena cava uberon cranial vena cava precava vena cava superior vena maxima UBERON:0001585 anterior vena cava http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png lexical A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart. Wikipedia:Superior_vena_cava http://orcid.org/0000-0002-6601-2165 Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] 2012-09-17 VHOG:0001195 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 http://bgee.unil.ch/ UMLS:C0042459 ncithesaurus:Superior_Vena_Cava superior caval vein http://orcid.org/0000-0002-6601-2165 superior vena cava FMA:4720 cranial vena cava VHOG:0001195 vena cava superior BTO:0002683 Wikipedia:Superior_vena_cava vena maxima Wikipedia:Superior_vena_cava One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] AAO:0010236 EHDAA2:0000877 EHDAA:5407 EMAPA:17620 FMA:4724 MA:0002157 NCIT:C32849 RETIRED_EHDAA2:0000878 SCTID:181372005 UMLS:C0226550 Wikipedia:Internal_jugular_vein XAO:0000382 galen:InternalJugularVein internal jugular internal jugular venous tree uberon vena jugularis interna UBERON:0001586 internal jugular vein http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Wikipedia:Internal_jugular_vein Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] 2012-06-20 AAO:0010236 AAO AAO:BJB UMLS:C0226550 ncithesaurus:Internal_Jugular_Vein internal jugular EHDAA2:0000877 vena jugularis interna Wikipedia:Internal_jugular_vein The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 EMAPA:35240 FMA:49151 MA:0001269 NCIT:C32315 SCTID:280862009 UMLS:C0559230 Wikipedia:Ciliary_muscle musculus ciliarus uberon Bowman`s muscles ciliaris musculus ciliaris UBERON:0001605 ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png MA FMA FMA The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. Wikipedia:Ciliary_muscle UMLS:C0559230 ncithesaurus:Ciliary_Muscle musculus ciliarus BTO:0000654 Bowman`s muscles BTO:0000654 ciliaris Wikipedia:Ciliary_muscle musculus ciliaris Wikipedia:Ciliary_muscle revisit this, see issue #331 The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP] in aves, stromal mesenchymal cells may migrate to the iris and become skeletal EMAPA:35448 FMA:49154 MA:0001287 SCTID:280888007 Wikipedia:Iris_muscle iris muscle iris muscle organ muscle organ of iris uberon UBERON:0001606 muscle of iris FMA iris muscle organ OBOL:automatic muscle organ of iris OBOL:automatic A sphincter muscle that is part of the iris. In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted] WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure constricts iris BTO:0000656 EMAPA:35788 FMA:49157 MA:0001289 NCIT:C33586 SCTID:280889004 UMLS:C0229189 Wikipedia:Iris_sphincter_muscle M. sphincter pupillae iris sphincter muscle musculus sphincter pupillae sphincter muscle of pupil uberon circular fibers constrictor pupillae iris constrictor iris constrictor muscle iris sphincter m. sphincter pupillae pupillary constrictor muscle pupillary sphincter pupillary sphincter muscle sphincter pupillae sphincter pupillae muscle spincter pupillae UBERON:0001607 sphincter pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png BTO ISBN:0781772214 encircles iris dbpedia encircles iris dbpedia dbpedia A sphincter muscle that is part of the iris. Wikipedia:Iris_sphincter_muscle UMLS:C0229189 ncithesaurus:Sphincter_Pupillae_Muscle iris sphincter muscle BTO:0000656 musculus sphincter pupillae BTO:0000656 sphincter muscle of pupil BTO:0000656 circular fibers Wikipedia:Iris_sphincter_muscle constrictor pupillae Wikipedia:Iris_sphincter_muscle iris constrictor muscle Wikipedia:Iris_sphincter_muscle iris sphincter Wikipedia:Iris_sphincter_muscle m. sphincter pupillae Wikipedia:Iris_sphincter_muscle pupillary constrictor muscle Wikipedia:Iris_sphincter_muscle pupillary sphincter Wikipedia:Iris_sphincter_muscle pupillary sphincter muscle Wikipedia:Iris_sphincter_muscle sphincter pupillae Wikipedia:Iris_sphincter_muscle sphincter pupillae muscle Wikipedia:Iris_sphincter_muscle spincter pupillae Wikipedia:Iris_sphincter_muscle A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]. It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina BTO:0001371 EMAPA:35286 FMA:49158 MA:0001288 NCIT:C32463 SCTID:280890008 UMLS:C0229190 Wikipedia:Iris_dilator_muscle dilator muscle of pupil dilator of pupil dilator pupillae dilator pupillae muscle iris dilator muscle musculus dilatator pupillae pupillary dilator muscle radial muscle of iris uberon dilator pupillae muscle iris dilator musculus dilatator pupillae musculus dilator pupillae pupil dilator pupil dilator muscle pupillary dilator pupillary muscle radial muscle radiating fibers UBERON:0001608 dilatator pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png BTO ISBN:0781772214 outer margins of iris dbpedia inner margins of iris dbpedia dbpedia A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]. Wikipedia:Iris_dilator_muscle UMLS:C0229190 ncithesaurus:Dilator_Pupillae_Muscle dilator pupillae muscle Wikipedia:Iris_dilator_muscle iris dilator muscle BTO:0001371 musculus dilatator pupillae FMA:49158 FMA:TA pupillary dilator muscle Wikipedia:Iris_dilator_muscle radial muscle of iris Wikipedia:Iris_dilator_muscle dilator pupillae muscle BTO:0001371 iris dilator Wikipedia:Iris_dilator_muscle musculus dilatator pupillae Wikipedia:Iris_dilator_muscle musculus dilator pupillae BTO:0001371 pupil dilator Wikipedia:Iris_dilator_muscle pupil dilator muscle Wikipedia:Iris_dilator_muscle pupillary dilator Wikipedia:Iris_dilator_muscle pupillary muscle Wikipedia:Iris_dilator_muscle radial muscle Wikipedia:Iris_dilator_muscle radiating fibers Wikipedia:Iris_dilator_muscle A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. EMAPA:19213 FMA:49549 MA:0001950 NCIT:C32578 SCTID:181328007 UMLS:C0226109 Wikipedia:Facial_artery uberon arteria maxillaris externa external maxillary artery UBERON:0001612 facial artery http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. Wikipedia:Facial_artery UMLS:C0226109 ncithesaurus:Facial_Artery arteria maxillaris externa Wikipedia:Facial_artery An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries EHDAA2:0001069 EHDAA:7357 EMAPA:17311 FMA:49675 GAID:498 MA:0001919 MESH:D008438 NCIT:C34205 SCTID:181326006 UMLS:C0024949 Wikipedia:Maxillary_artery uberon arteria maxillaris internal maxillary artery UBERON:0001616 maxillary artery http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. Wikipedia:Maxillary_artery ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries http://download.videohelp.com/vitualis/med/Vascular_Devt.html UMLS:C0024949 ncithesaurus:Maxillary_Artery arteria maxillaris Wikipedia:Maxillary_artery Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Portion of tissue composed of contractile fibers.[TAO] It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] muscular muscle AAO:0011066 EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 GAID:131 MA:0000015 SCTID:71616004 TAO:0005145 VHOG:0001245 XAO:0000172 ZFA:0005145 galen:Muscle uberon UBERON:0001630 muscle organ Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 Portion of tissue composed of contractile fibers.[TAO] 2012-08-14 TAO:0005145 TAO ZFIN:curator It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] 2012-09-17 VHOG:0001245 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 http://bgee.unil.ch/ muscle ZFA:0005145 EMAPA:37474 MA:th An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] arterial Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system. AAO:0010211 AEO:0000208 BTO:0000573 CALOHA:TS-0054 EFO:0000814 EHDAA2:0000143 EHDAA2:0003253 EMAPA:35147 EV:0100026 FMA:50720 GAID:468 MA:0000064 MAT:0000034 MESH:D001158 MIAA:0000034 NCIT:C12372 SCTID:362877004 TAO:0000005 UMLS:C0003842 VHOG:0001251 Wikipedia:Artery XAO:0000114 ZFA:0000005 galen:Artery arterial subtree arterial tree organ part arteries uberon arterial system arterial vessel UBERON:0001637 artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. AEO:JB Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] 2012-06-20 AAO:0010211 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001251 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0003842 ncithesaurus:Artery arteries TAO:0000005 Any of the tubular branching vessels that carry blood from the capillaries toward the heart. TODO - check with MA - vein vs venous blood vessel Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] venous venous subtree venous vessel AAO:0010212 AEO:0000209 BTO:0000234 CALOHA:TS-1108 EFO:0000816 EHDAA2:0003254 EMAPA:35906 EV:0100031 FMA:50723 GAID:492 MA:0000067 MAT:0000037 MESH:D014680 MIAA:0000037 NCIT:C12814 SCTID:181367001 TAO:0000082 UMLS:C0042449 VHOG:0001743 Wikipedia:Vein XAO:0000115 ZFA:0000082 galen:Vein venous tree organ part uberon vascular element vena venae UBERON:0001638 vein http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg Any of the tubular branching vessels that carry blood from the capillaries toward the heart. Wikipedia:Vein Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] 2012-06-20 AAO:0010212 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001743 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0042449 ncithesaurus:Vein vascular element EMAPA:th vena Wikipedia:Vein venae VHOG:0001743 A portal vein that transports nutrients from the digestive tract to the liver[Kardong]. Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG] In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted] AAO:0010214 FMA:50735 MA:0002132 TAO:0005090 VHOG:0000642 Wikipedia:Hepatic_portal_vein ZFA:0005090 hepatic portal tree liver portal vein portal vein of liver uberon HPV portal vein primary hepatic portal vein primary hepatic portal veins vena portae hepatis UBERON:0001639 hepatic portal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb MA A portal vein that transports nutrients from the digestive tract to the liver[Kardong]. ISBN:0073040584 Wikipedia:Hepatic_portal_vein http://sourceforge.net/tracker/?func=detail&aid=3091300&group_id=76834&atid=1205376 Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG] 2012-09-17 VHOG:0000642 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.265 http://bgee.unil.ch/ liver portal vein OBOL:automatic portal vein of liver OBOL:automatic portal vein primary hepatic portal vein ZFA:0005090 vena portae hepatis Wikipedia:Hepatic_portal_vein The first major branch of the abdominal aorta. EHDAA2:0004519 EMAPA:35202 FMA:50737 GAID:483 MA:0001931 MESH:D002445 NCIT:C52846 SCTID:181340007 UMLS:C0007569 Wikipedia:Celiac_artery celiac tree coeliac artery uberon arteria coeliaca arteria cœliaca celiac trunk coeliac axis coeliac trunck coeliac trunk truncus coeliacus truncus cœliacus UBERON:0001640 dorsal aorta in Kardong celiac artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png ISBN:0073040584 ISBN:0073040584 ISBN:0073040584 ISBN:0073040584 The first major branch of the abdominal aorta. Wikipedia:Celiac_artery UMLS:C0007569 ncithesaurus:Coeliac_Artery coeliac artery Wikipedia:Celiac_artery arteria coeliaca Wikipedia:Celiac_artery arteria cœliaca Wikipedia:Celiac_artery celiac trunk Wikipedia:Celiac_artery coeliac axis Wikipedia:Celiac_artery coeliac trunck Wikipedia:Celiac_artery coeliac trunk Wikipedia:Celiac_artery truncus coeliacus Wikipedia:Celiac_artery truncus cœliacus Wikipedia:Celiac_artery Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls 5n AAO:0010470 BAMS:5n BAMS:Vn BAMS:nV BIRNLEX:869 BM:VN BTO:0001072 EFO:0001402 EHDAA2:0002084 EHDAA:3738 EMAPA:17576 FMA:50866 GAID:726 HBA:9322 MA:0001100 MBA:901 MESH:D014276 MFMO:0000093 NCIT:C12806 SCTID:362459002 TAO:0000697 UMLS:C0040996 VHOG:0000704 Wikipedia:Trigeminal_nerve XAO:0003092 ZFA:0000697 neuronames:549 fifth cranial nerve nervus trigeminus nervus trigeminus [v] trigeminal V trigeminal nerve [V] trigeminal nerve tree trigeminal v nerve uberon CN-V cranial nerve V nerve V nervus trigeminus trigeminus UBERON:0001645 trigeminal nerve https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png Wikipedia Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). ISBN:0471209627 Wikipedia:Trigeminal_nerve Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] 2012-06-20 AAO:0010470 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000704 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 http://bgee.unil.ch/ the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls ISBN:0471888893 5n BIRNLEX:869 NIFSTD:NeuroNames_abbrevSource UMLS:C0040996 BIRNLEX:869 ncithesaurus:Trigeminal_Nerve neuronames:549 BIRNLEX:869 nervus trigeminus Wikipedia:Trigeminal_nerve nervus trigeminus [v] FMA:50866 FMA:TA trigeminal V EHDAA2:0002084 nerve V NeuroNames:549 nervus trigeminus BTO:0001072 trigeminus BTO:0001072 The pulmonary artery that supplies the right lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37378 FMA:50872 MA:0002500 NCIT:C33489 SCTID:244235003 UMLS:C0923924 Wikipedia:Right_pulmonary_artery galen:RightPulmonaryArtery right main pulmonary artery right pulmonary arterial tree uberon arteria pulmonalis dextra UBERON:0001651 right pulmonary artery http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png The pulmonary artery that supplies the right lung. UBERON:cjm EMAPA:37378 MA:th UMLS:C0923924 ncithesaurus:Right_Pulmonary_Artery arteria pulmonalis dextra Wikipedia:Right_pulmonary_artery The pulmonary artery that supplies the left lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37097 FMA:50873 MA:0002032 NCIT:C32971 SCTID:244234004 UMLS:C0923925 Wikipedia:Left_pulmonary_artery galen:LeftPulmonaryArtery left main pulmonary artery left pulmonary arterial tree uberon arteria pulmonalis sinistra UBERON:0001652 left pulmonary artery http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png The pulmonary artery that supplies the left lung. UBERON:cjm EMAPA:37097 MA:th UMLS:C0923925 ncithesaurus:Left_Pulmonary_Artery arteria pulmonalis sinistra Wikipedia:Left_pulmonary_artery The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] MA and NCITA also has 'anterior facial vein' AAO:0010513 EMAPA:19220 FMA:50874 MA:0002115 NCIT:C32579 SCTID:181374006 UMLS:C0226532 Wikipedia:Facial_vein face vein vein of face uberon anterior facial vein vena facialis anterior UBERON:0001653 facial vein http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png FMA The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Wikipedia:Facial_vein Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] 2012-06-20 AAO:0010513 AAO AAO:BJB MA and NCITA also has 'anterior facial vein' MA UMLS:C0226532 ncithesaurus:Facial_Vein face vein OBOL:automatic vein of face OBOL:automatic anterior facial vein Wikipedia:Facial_vein vena facialis anterior Wikipedia:Facial_vein The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks) A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. AAO:0011107 BAMS:5Gn BAMS:GV BTO:0001231 EFO:0000903 EHDAA2:0002085 EHDAA:2113 EMAPA:16797 FMA:52618 GAID:725 MA:0001080 MAT:0000511 MESH:D012668 NCIT:C62642 SCTID:244449009 TAO:0000295 UMLS:C0040995 VHOG:0000694 Wikipedia:Trigeminal_ganglion XAO:0000427 XAO:0000428 ZFA:0000295 neuronames:1402 5th ganglion Gasserian ganglion fifth ganglion ganglion of trigeminal complex semilunar ganglion trigeminal V ganglion fused trigeminal ganglion uberon Gasser's ganglion Gasserian ganglia gV ganglion of trigeminal nerve ganglion semilunare ganglion trigeminale trigeminal ganglia trigeminus ganglion UBERON:0001675 trigeminal ganglion http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png ncithesaurus Bgee:AN The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. http://orcid.org/0000-0002-6601-2165 http://www.ncbi.nlm.nih.gov/books/NBK53171 https://github.com/obophenotype/uberon/issues/693 A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000295 TAO ZFIN:curator In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. PMID:21452441 XAO:0004093 UMLS:C0040995 ncithesaurus:Trigeminal_Ganglion 5th ganglion ZFA:0000295 Gasserian ganglion Wikipedia:Trigeminal_ganglion fifth ganglion ZFA:0000295 ganglion of trigeminal complex http://orcid.org/0000-0002-6601-2165 semilunar ganglion ISBN:0471888893 trigeminal V ganglion MA:0001080 fused trigeminal ganglion NCBITaxon:32524 Gasser's ganglion BTO:0001231 Gasserian ganglia Wikipedia:Trigeminal_ganglion ganglion of trigeminal nerve BTO:0001231 ganglion semilunare Wikipedia:Trigeminal_ganglion ganglion trigeminale BTO:0001231 Wikipedia:Trigeminal_ganglion trigeminal ganglia The bone at the lower, posterior part of the skull. formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII fusion of basi-, exo- and supra-occipitals (and maybe tabular) EMAPA:25112 FMA:52735 GAID:227 MA:0001468 MESH:D009777 NCIT:C12757 SCTID:181796003 UMLS:C0028784 Wikipedia:Occipital_bone uberon occipital complex occipital squama os occipitale UBERON:0001676 occipital bone http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png FMA FMA basi paired exo and supra occipital bones MA-modified interparietal (postparietal) WP PMID:11523816 The bone at the lower, posterior part of the skull. ISBN:0-683-40008-8 MP:0005269 formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII PMID:11523816 fusion of basi-, exo- and supra-occipitals (and maybe tabular) Kardong UMLS:C0028784 ncithesaurus:Occipital_Bone occipital complex http://palaeos.com/vertebrates/bones/braincase/occiput.html os occipitale Wikipedia:Occipital_bone An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended. part of viscerocranium (facial skeleton) in FMA CALOHA:TS-2343 EMAPA:18340 FMA:52736 GAID:230 MA:0001472 MESH:D013100 NCIT:C12790 SCTID:272676008 UMLS:C0037884 Wikipedia:Sphenoid_bone os sphenoidale sphenoid sphenoidal bone uberon butterfly bone os sphenoidale os sphenoidum sphenoid complex UBERON:0001677 sphenoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg FMA orbito pre and basi sphenoid pterygoid process alisphenoid cjm An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended. Wikipedia:Sphenoid_bone part of viscerocranium (facial skeleton) in FMA FMA UMLS:C0037884 ncithesaurus:Sphenoid_Bone os sphenoidale FMA:52736 FMA:TA butterfly bone Wikipedia:Sphenoid_bone os sphenoidale Wikipedia:Sphenoid_bone os sphenoidum Wikipedia:Sphenoid_bone A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP]. A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG] The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG] ethmoidal todo - homology e.g. mesethmoid of teleost Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA BTO:0004140 EMAPA:19018 FMA:52740 GAID:212 MA:0001483 MESH:D005004 NCIT:C12711 SCTID:272674006 UMLS:C0015027 VHOG:0001317 Wikipedia:Ethmoid_bone ethmoid ethmoidal bone os ethmoidale uberon UBERON:0001679 ethmoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg ISBN:0073040584 definitional A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP]. Wikipedia:Ethmoid_bone A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG] 2012-09-17 VHOG:0001317 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/ethmoid+bone The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG] 2012-09-17 VHOG:0001317 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.259 http://bgee.unil.ch/ Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA MA UMLS:C0015027 ncithesaurus:Ethmoid_Bone ethmoid FMA:52740 ethmoidal bone MP:0000101 os ethmoidale FMA:52740 FMA:TA Wikipedia:Ethmoid Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball. Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO] in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit BTO:0004687 FMA:53074 GAID:223 MA:0002482 MESH:D009915 NCIT:C12347 TAO:0001410 UMLS:C0029180 Wikipedia:Orbit_(anatomy) XAO:0003171 ZFA:0001410 galen:Orbit bony orbit eye socket orbit of skull uberon orbit UBERON:0001697 orbit of skull FMA-abduced-lr Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball. TAO:0001410 Wikipedia:Orbit_(anatomy) http://orcid.org/0000-0002-6601-2165 Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO] 2012-08-14 TAO:0001410 TAO TAO:MAH in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit FMA UMLS:C0029180 ncithesaurus:Orbit orbit of skull FMA:53074 orbit ZFA:0001410 Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] neurocranial It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... AAO:0010153 EHDAA2:0000243 EMAPA:17681 FMA:53672 MA:0000317 SCTID:361731002 TAO:0001580 Wikipedia:Neuroranium XAO:0003170 ZFA:0001580 brain box uberon brain case brain pan braincase UBERON:0001703 neurocranium FMA Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. PMID:11523816 TAO:MAH Wikipedia:Neuroranium ZFA:0001580 Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] 2012-08-14 TAO:0001580 TAO TAO:MAH The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. WP It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... MA brain case ZFA:0001580 brain pan http://www.thefreedictionary.com/braincase braincase ZFA:0001580 Subdivision of skeleton which includes upper and lower jaw skeletons. TODO - move ZFA:0001227 (it is the entire jaw skeleton). Skeletal and cartilage elements of the first pharyngeal arch.[TAO] There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates AAO:0000988 BTO:0001749 EMAPA:35455 FMA:54396 GAID:214 MA:0001905 MESH:D007568 NCIT:C48821 SCTID:181811001 TAO:0001227 UMLS:C0022359 Wikipedia:Jaw ZFA:0001227 galen:Jaw jaw jaw cartilage mandibular arch skeleton uberon anterior splanchnocranium jaws mandibular arch oral jaw skeleton pharyngeal arch 1 skeleton visceral arch 1 UBERON:0001708 jaw skeleton cjm Subdivision of skeleton which includes upper and lower jaw skeletons. Wikipedia:Jaw https://orcid.org/0000-0002-6601-2165 Skeletal and cartilage elements of the first pharyngeal arch.[TAO] 2012-08-14 TAO:0001227 TAO ZFIN:curator in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates FMA UMLS:C0022359 ncithesaurus:Jaw jaw MA:0001905 jaw cartilage ZFA:0001227 mandibular arch skeleton ZFA:0001227 mandibular arch TAO:0001227 Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO] Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] Note isa/partof difference MA/FMA AAO:0000620 EHDAA2:0002118 EHDAA2:0004607 EHDAA:8025 EMAPA:17924 FMA:59399 SCTID:362636001 VHOG:0000454 Wikipedia:Upper_jaw ncithesaurus:Upper_Jaw maxillary part of mouth uberon alveolodental arch of bimaxilla dorsal mandibular arch dorsal pharyngeal arch 1 maxillary part of mouth proper palatoquadrate arch upper pharyngeal jaws UBERON:0001709 See notes for jaw w.r.t skeletal element vs subdivision of head. upper jaw region http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray189.png Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Wikipedia:Upper_jaw http://orcid.org/0000-0002-6601-2165 Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO] 2012-06-20 AAO:0000620 AAO AAO:LAP Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000454 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ Note isa/partof difference MA/FMA MA maxillary part of mouth FMA:59399 alveolodental arch of bimaxilla FMA:59399 dorsal pharyngeal arch 1 maxillary part of mouth proper FMA:59399 palatoquadrate arch Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] Note isa/partof difference MA/FMA AAO:0000272 EFO:0003660 EHDAA2:0001018 EHDAA:7995 EMAPA:17906 FMA:59398 MESH:D008334 SCTID:362637005 VHOG:0000453 Wikipedia:Lower_jaw ncithesaurus:Lower_Jaw mandibular part of mouth uberon lower part of mouth mandibular series UBERON:0001710 See notes for jaw w.r.t skeletal element vs subdivision of head lower jaw region http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png Wikipedia:Mandibular_prominence Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Wikipedia:Lower_jaw Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] 2012-06-20 AAO:0000272 AAO AAO:LAP Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000453 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ Note isa/partof difference MA/FMA MA mandibular part of mouth FMA:59398 The groups of nerve cell bodies associated with the twelve cranial nerves. Ganglion which is located in the head.[TAO] UBERON:0003213 UBERON:0026601 BIRNLEX:2597 BTO:0000106 EFO:0000902 EMAPA:16659 FMA:54502 MA:0000213 MA:0000214 MAT:0000200 MIAA:0000200 SCTID:244448001 TAO:0000013 VHOG:0000076 Wikipedia:Cranial_nerve_ganglion XAO:0000027 ZFA:0000013 cranial ganglion cranial ganglion part of peripheral nervous system cranial ganglion/nerve cranial nerve ganglion cranial neural ganglion cranial neural tree organ ganglion ganglion of cranial nerve ganglion of cranial neural tree organ uberon cranial ganglia head ganglion presumptive cranial ganglia UBERON:0001714 cranial ganglion The groups of nerve cell bodies associated with the twelve cranial nerves. ISBN:0-683-40008-8 MGI:csmith MP:0001081 PMID:9362461 Ganglion which is located in the head.[TAO] 2012-08-14 TAO:0000013 TAO ZFIN:curator cranial ganglion part of peripheral nervous system BIRNLEX:2597 cranial neural tree organ ganglion OBOL:automatic ganglion of cranial nerve FMA:54502 ganglion of cranial neural tree organ OBOL:automatic presumptive cranial ganglia ZFA:0000013 An anatomical space that is enclosed by a pharynx. See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship TOODO check AAO:0010435 BSA:0000113 BTO:0002097 EMAPA:18381 FMA:54935 SCTID:180543003 XAO:0000105 lumen of pharynx pharyngeal cavity uberon cavitas pharyngealis cavitas pharyngis UBERON:0001731 cavity of pharynx XAO An anatomical space that is enclosed by a pharynx. OBOL:automatic cavitas pharyngealis cavitas pharyngis BTO:0002097 The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens. The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball BTO:0002084 EHDAA2:0000129 EHDAA:9033 EMAPA:18231 FMA:58078 GAID:889 MA:0000262 MESH:D000867 NCIT:C12667 SCTID:181160009 UMLS:C0003151 VHOG:0001431 Wikipedia:Anterior_chamber_of_eyeball anterior chamber anterior chamber of eye camera anterior eye anterior chamber uberon camera anterior bulbi camera anterior bulbi oculi camera oculi anterior UBERON:0001766 anterior chamber of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens. MESH:A09.371.060.067 MP:0005205 The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] 2012-09-17 VHOG:0001431 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/anterior+chamber space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball EHDAA2 UMLS:C0003151 ncithesaurus:Anterior_Chamber_of_the_Eye anterior chamber HP:0000593 MP:0010709 camera anterior bulbi BTO:0002084 camera anterior bulbi oculi Wikipedia:Anterior_chamber_of_eyeball camera oculi anterior BTO:0002084 The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus uveal CALOHA:TS-2228 EMAPA:35901 FMA:58103 GAID:912 MA:0002480 MESH:D014602 NCIT:C12811 SCTID:280648000 UMLS:C0042160 Wikipedia:Uvea tunica vasculosa of eyeball uvea uveal tract uberon pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi vascular layer of eyeball UBERON:0001768 uvea http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png FMA The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. MP:0005197 Wikipedia:Uvea DOI:10.1177/0192623311409597 UMLS:C0042160 ncithesaurus:Uvea tunica vasculosa of eyeball FMA:58103 uvea FMA:58103 uveal tract FMA:58103 pars iridica retinae Wikipedia:Uvea tunica vasculatis oculi Wikipedia:Uvea tunica vasculosa bulbi Wikipedia:Uvea vascular layer of eyeball FMA:58103 The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye. The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] iridial The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019] AAO:0010347 BTO:0000653 CALOHA:TS-0491 EFO:0004245 EMAPA:19154 EV:0100345 FMA:58235 GAID:917 MA:0000273 MESH:D007498 NCIT:C12737 SCTID:181164000 TAO:0001238 UMLS:C0022077 VHOG:0000101 Wikipedia:Iris_(anatomy) XAO:0000185 ZFA:0001238 uberon anterior uvea irides irises UBERON:0001769 iris XAO The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye. ISBN:0-683-40008-8 MP:0001322 The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000101 VHOG http://bgee.unil.ch/ The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000101 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0022077 ncithesaurus:Iris irides irises VHOG:0000101 The smooth stratified squamous epithelium that covers the outer surface of the cornea. Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals BTO:0000287 CALOHA:TS-0173 EFO:0001917 EHDAA2:0000319 EMAPA:17162 FMA:58263 GAID:895 MA:0001243 MESH:D019573 NCIT:C12928 SCTID:368825001 TAO:0002187 UMLS:C0459875 Wikipedia:Corneal_epithelium ZFA:0001683 anterior corneal epithelium cornea epithelial tissue cornea epithelium epithelial tissue of cornea epithelium anterius (cornea) epithelium anterius corneae epithelium corneæ anterior layer epithelium of cornea external epithelium of cornea uberon anterior endothelium of cornea e. anterius corneae endothelium anterius corneae endothelium camerae anterioris bulbi endothelium corneale epithelium posterius corneae UBERON:0001772 corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png ISBN:0781772214 The smooth stratified squamous epithelium that covers the outer surface of the cornea. MESH:A09.371.060.217.325 MGI:smb MP:0006000 Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] 2012-08-14 TAO:0002187 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0459875 ncithesaurus:Corneal_Epithelium cornea epithelial tissue OBOL:automatic cornea epithelium OBOL:automatic epithelial tissue of cornea OBOL:automatic epithelium anterius corneae FMA:58263 FMA:TA anterior endothelium of cornea BTO:0000287 e. anterius corneae Wikipedia:Corneal_epithelium endothelium anterius corneae BTO:0000287 endothelium camerae anterioris bulbi BTO:0000287 endothelium corneale BTO:0000287 epithelium posterius corneae BTO:0000287 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] scleral in fish, reptiles and monotremes the connective tissue of the sclera is skeletal continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]. AAO:0010354 BTO:0001606 EMAPA:19027 EV:0100342 FMA:58269 GAID:911 MA:0000280 MESH:D012590 NCIT:C12784 SCTID:181163006 UMLS:C0036410 VHOG:0001274 Wikipedia:Sclera XAO:0000183 ZFA:0005563 uberon scleral capsule UBERON:0001773 Disease notes: implicated in rheumatoid arthritis. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA ZFA ISBN:0781772214 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. Wikipedia:Sclera ZFIN:ZDB-PUB-050701-15 The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. Wikipedia:Sclera The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] 2012-09-17 VHOG:0001274 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/sclera UMLS:C0036410 ncithesaurus:Sclera A skeletal muscle organ that is part of the trunk region. Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'. Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here. AAO:0000611 EMAPA:35888 FMA:58274 MA:0000514 TAO:0000473 XAO:0003230 ZFA:0000473 body musculature muscle of trunk muscle organ of torso muscle organ of trunk torso muscle organ trunk muscle trunk muscle organ trunk musculature uberon UBERON:0001774 skeletal muscle of trunk prolog A skeletal muscle organ that is part of the trunk region. http://orcid.org/0000-0002-6601-2165 body musculature ZFA:0000473 muscle of trunk FMA:58274 muscle organ of torso OBOL:automatic muscle organ of trunk OBOL:automatic torso muscle organ OBOL:automatic trunk muscle organ OBOL:automatic The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] AAO:0010341 BTO:0000260 CALOHA:TS-0694 EMAPA:19065 EV:0100346 FMA:58295 GAID:916 MA:0000264 MESH:D002924 NCIT:C12345 SCTID:263340007 UMLS:C0008779 VHOG:0000102 Wikipedia:Ciliary_body XAO:0000186 neuronames:1571 ocular ciliary body uberon anterior uvea ciliary bodies corpus ciliare UBERON:0001775 ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg ISBN:0781772214 The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes. ISBN:0-683-40008-8 MP:0005099 Wikipedia:Ciliary_body The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000102 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0008779 ncithesaurus:Ciliary_Body ciliary bodies VHOG:0000102 corpus ciliare Wikipedia:Ciliary_body Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA choroidal MP treats posterior uvea and optic choroid as distinct BTO:0001829 CALOHA:TS-2054 EMAPA:19077 EV:0100347 FMA:58298 GAID:913 MA:0000263 MESH:D002829 NCIT:C12344 SCTID:181172003 TAO:0005229 UMLS:C0008520 VHOG:0001568 Wikipedia:Choroid ZFA:0005229 choroid choroid coat choroidea eye choroid posterior uvea uberon chorioid choroidea optic choroid UBERON:0001776 optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg MA Wikipedia lexical Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. Wikipedia:Choroid MP treats posterior uvea and optic choroid as distinct MP UMLS:C0008520 ncithesaurus:Choroid choroid MA:0000263 choroid coat Wikipedia:Choroid choroidea Wikipedia:Choroid eye choroid VHOG:0001568 posterior uvea Wikipedia:Uvea#Regions chorioid BTO:0001829 choroidea Wikipedia:Choroid optic choroid ZFA:0005229 The lamellated connective tissue of the cornea between the Bowman and Descemet membranes. Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] substantia propria CALOHA:TS-1138 EFO:0002514 EMAPA:17602 FMA:58306 GAID:893 MA:0001245 MESH:D003319 NCIT:C12699 SCTID:362511000 TAO:0002189 UMLS:C0010040 Wikipedia:Corneal_stroma ZFA:0001685 corneal stroma stroma of cornea substantia propria corneae uberon UBERON:0001777 substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png cjm ISBN:0781772214 Wikipedia The lamellated connective tissue of the cornea between the Bowman and Descemet membranes. ISBN:0-683-40008-8 MESH:A09.371.060.217.228 MP:0005300 Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] 2012-08-14 TAO:0002189 TAO ZFIN:ZDB-PUB-061010-3 relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] 2012-08-14 TAO:0002189 TAO relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] 2012-08-14 TAO:0002189 TAO UMLS:C0010040 ncithesaurus:Corneal_Stroma corneal stroma MA:0001245 substantia propria corneae FMA:58306 FMA:TA A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 CALOHA:TS-0695 EMAPA:35239 FMA:58464 MA:0001238 NCIT:C32314 SCTID:280870004 UMLS:C0459736 Wikipedia:Ciliary_body#Ciliary_epithelium ciliary body epithelium epithelium of ciliary body ocular ciliary epithelium uberon UBERON:0001778 ciliary epithelium FMA MA MP Wikipedia A double layer covering the ciliary body that produces aqueous humor. Wikipedia:Ciliary_body#Ciliary_epithelium UMLS:C0459736 ncithesaurus:Ciliary_Epithelium ciliary body epithelium FMA:58464 epithelium of ciliary body FMA:58464 The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. EMAPA:35451 FMA:58526 MA:0002777 SCTID:280882008 Wikipedia:Iris_stroma ZFA:0005569 iridial stroma stroma of iris uberon UBERON:0001779 iris stroma http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. Wikipedia:Iris_stroma http://www.drugs.com/dict/stroma-of-iris.html The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]. Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] AAO:0011101 BAMS:spin BTO:0000870 EHDAA2:0001898 EMAPA:16989 FMA:5858 GAID:841 MA:0000233 MESH:D013127 NCIT:C12792 SCTID:361099009 UMLS:C0037941 VHOG:0000824 Wikipedia:Spinal_nerve XAO:0003101 neuronames:1228 backbone nerve nerve of backbone nerve of spinal column nerve of spine nerve of vertebral column spinal column nerve spinal nerve tree spine nerve vertebral column nerve uberon nervi spinales spinal nerves UBERON:0001780 spinal nerve https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]. MESH:A08.800.800.720 MP:0001077 Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] 2012-09-17 VHOG:0000824 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/spinal+nerve UMLS:C0037941 ncithesaurus:Spinal_Nerve backbone nerve OBOL:automatic nerve of backbone OBOL:automatic nerve of spinal column OBOL:automatic nerve of spine OBOL:automatic nerve of vertebral column OBOL:automatic spinal column nerve OBOL:automatic spine nerve OBOL:automatic vertebral column nerve OBOL:automatic nervi spinales Wikipedia:Spinal_nerve spinal nerves BAMS:spin Any of the layers that make up the retina[MP]. MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers AAO:0010353 EMAPA:35742 FMA:58617 MA:0001319 NCIT:C49328 SCTID:280657006 UMLS:C0459649 XAO:0000266 retina layer retina neuronal layer retinal layer retinal neuronal layer uberon UBERON:0001781 layer of retina Any of the layers that make up the retina[MP]. MP:0003727 MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers MA UMLS:C0459649 ncithesaurus:Retina_Layer retina neuronal layer MP:0006069 retinal neuronal layer MP:0006069 Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6 AAO:0000108 BAMS:cran BIRNLEX:1623 BTO:0001104 EHDAA2:0000323 EMAPA:17264 FMA:5865 GAID:802 HBA:9299 MA:0000215 MBA:967 MESH:D003391 NCIT:C12700 SCTID:244447006 TAO:0000641 UMLS:C0010268 UMLS:C1269897 VHOG:0000279 Wikipedia:Cranial_nerve XAO:0000429 XAO:0003089 ZFA:0000641 neuronames:1227 cranial neural tree organ uberon cranial nerves nervus cranialis UBERON:0001785 cranial nerve http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. Wikipedia:Cranial_nerve Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] 2012-08-14 TAO:0000641 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] 2012-09-17 VHOG:0000279 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ UMLS:C0010268 BIRNLEX:1623 ncithesaurus:Cranial_Nerve UMLS:C1269897 BIRNLEX:1623 nervus cranialis Wikipedia:Cranial_nerve A thick watery refractive medium that fills the space between the lens and the cornea[WP]. The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. EHDAA2:0000139 EHDAA:10196 EMAPA:18232 ENVO:02000024 FMA:58819 GAID:890 MA:0001236 MESH:D001082 NCIT:C13190 SCTID:280587006 UMLS:C0003662 VHOG:0000548 Wikipedia:Aqueous_humor ZFA:0005564 aqueous humor aqueous humour humor aquosus uberon UBERON:0001796 aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA def states A and P located_in in EHDAA2 VHOG A thick watery refractive medium that fills the space between the lens and the cornea[WP]. Wikipedia:Aqueous_humor The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] 2012-09-17 VHOG:0000548 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/aqueous+humour (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000548 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 http://bgee.unil.ch/ FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. FMA UMLS:C0003662 ncithesaurus:Aqueous_Humor aqueous humour EHDAA2:0000139 humor aquosus FMA:58819 FMA:TA The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. AEO:0001000 BTO:0005630 EMAPA:36596 FMA:5885 MA:0002566 MESH:D017950 NCIT:C13060 UMLS:C0206429 ganglion sensorium uberon UBERON:0001800 sensory ganglion The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. MP:0000960 UMLS:C0206429 ncithesaurus:Sensory_Ganglion ganglion sensorium Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive). EMAPA:36594 FMA:58865 MA:0002484 MESH:D000869 NCIT:C12668 SCTID:280658001 UMLS:C0003153 Wikipedia:Anterior_segment_of_eyeball ZFA:0005566 anterior eye segment anterior segment eye anterior segment of eye anterior segment of the eye eye anterior segment segmentum anterius (bulbus oculi) uberon segmentum anterius bulbi oculi UBERON:0001801 anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png FMA cjm lexical Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive). ISBN:0-683-40008-8 MESH:A09.371.060 MP:0005193 ZFA https://github.com/obophenotype/uberon/issues/378 pending UMLS:C0003153 ncithesaurus:Anterior_Eye_Segment anterior segment eye ZFA:0005566 segmentum anterius bulbi oculi Wikipedia:Anterior_segment_of_eyeball Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive). EMAPA:36595 FMA:58868 MA:0002485 NCIT:C12906 SCTID:280659009 UMLS:C0278450 Wikipedia:Posterior_segment_of_eyeball ZFA:0005567 eye posterior segment posterior eye segment posterior segment eye posterior segment of eye posterior segment of the eye segmentum posterius (bulbus oculi) uberon segmentum posterius bulbi oculi UBERON:0001802 posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA cjm lexical Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive). ISBN:0-683-40008-8 MP:0005195 UMLS:C0278450 ncithesaurus:Posterior_Eye_Segment posterior segment eye ZFA:0005567 segmentum posterius bulbi oculi Wikipedia:Posterior_segment_of_eyeball A layer of epithelial cells that is part of the eye. this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former BTO:0001873 CALOHA:TS-0543 EMAPA:32871 FMA:58871 MA:0001301 SCTID:362523006 TAO:0001326 Wikipedia:Lens_(anatomy)#Lens_Epithelium XAO:0004094 ZFA:0001326 epithelial tissue of eye lens epithelial tissue of lens epithelium lentis epithelium of eye lens eye lens epithelial tissue eye lens epithelium lens epithelial tissue lens epithelium uberon UBERON:0001803 epithelium of lens A layer of epithelial cells that is part of the eye. http://orcid.org/0000-0002-6601-2165 epithelial tissue of eye lens OBOL:automatic epithelial tissue of lens OBOL:automatic epithelium lentis FMA:58871 FMA:TA epithelium of eye lens OBOL:automatic eye lens epithelial tissue OBOL:automatic eye lens epithelium OBOL:automatic lens epithelial tissue OBOL:automatic The elastic, clear, membrane-like structure, that is outer most layer of the lens. The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular EHDAA2:0000977 EMAPA:18237 FMA:58881 MA:0001300 NCIT:C32975 SCTID:244500004 UMLS:C0229232 VHOG:0000550 Wikipedia:Lens_(anatomy)#Lens_capsule ZFA:0005574 capsula lentis lens capsule uberon UBERON:0001804 capsule of lens http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png EHDAA2 The elastic, clear, membrane-like structure, that is outer most layer of the lens. MGI:smb MP:0003236 PMID:15483628 The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000550 VHOG http://bgee.unil.ch/ (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000550 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 http://bgee.unil.ch/ FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular FMA UMLS:C0229232 ncithesaurus:Lens_Capsule capsula lentis Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. AEO:0001001 CALOHA:TS-2340 EMAPA:17157 EMAPA:18221 FMA:5889 MA:0000220 MESH:D005725 NCIT:C12720 UMLS:C0017068 Wikipedia:Autonomic_ganglion autonomic nervous system ganglion ganglion of autonomic nervous system ganglion of visceral nervous system visceral nervous system ganglion uberon ganglion autonomicum UBERON:0001805 autonomic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. Wikipedia:Autonomic_ganglion UMLS:C0017068 ncithesaurus:Autonomic_Ganglion autonomic nervous system ganglion OBOL:automatic ganglion of autonomic nervous system OBOL:automatic ganglion of visceral nervous system OBOL:automatic visceral nervous system ganglion OBOL:automatic ganglion autonomicum Wikipedia:Autonomic_ganglion A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia. AAO:0010773 BTO:0001333 CALOHA:TS-0994 EHDAA2:0001969 EMAPA:17157 FMA:5890 MA:0000226 MESH:D005728 NCIT:C12467 SCTID:362485003 UMLS:C0017071 Wikipedia:Sympathetic_ganglion ganglion of sympathetic nervous system ganglion of sympathetic part of autonomic division of nervous system ganglion sympatheticum sympathetic nervous system ganglion sympathetic part of autonomic division of nervous system ganglion uberon ganglion sympathicum UBERON:0001806 sympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png DOI:10.1101/gr.157586.113 ISBN:0073040584 A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia. MP:0001008 http://orcid.org/0000-0002-6601-2165 MESH:D005728 https://github.com/biopragmatics/biomappings UMLS:C0017071 ncithesaurus:Sympathetic_Ganglion ganglion of sympathetic nervous system OBOL:automatic ganglion of sympathetic part of autonomic division of nervous system OBOL:automatic sympathetic nervous system ganglion OBOL:automatic sympathetic part of autonomic division of nervous system ganglion OBOL:automatic ganglion sympathicum BTO:0001333 Wikipedia:Sympathetic_ganglion One of the two fleshy folds which surround the opening of the mouth. Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] labial BTO:0001647 CALOHA:TS-0558 EMAPA:32839 FMA:59816 GAID:76 MA:0000343 MESH:D008046 NCIT:C12220 SCTID:181221003 TAO:0007006 UMLS:C0023759 VHOG:0000677 Wikipedia:Lip ZFA:0007006 galen:Lip uberon labia oris lips UBERON:0001833 lip http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg ZFA BTO FMA-implicit VHOG ZFA cjm One of the two fleshy folds which surround the opening of the mouth. Wikipedia:Lip http://www.medterms.com/script/main/art.asp?articlekey=9458 Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] 2012-08-14 TAO:0007006 TAO ZFIN:curator http//:www.medterms.com/script/main/art.asp?articlekey=9458 UMLS:C0023759 ncithesaurus:Lip labia oris Wikipedia:Lip Lip that covers the upper portion of the mouth.[TAO]. Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG] Lip that covers the upper portion of the mouth.[TAO] UBERON:0003391 EMAPA:17925 FMA:59817 MA:0000919 SCTID:245776003 TAO:0001970 VHOG:0001750 Wikipedia:Upper_lip ZFA:0005226 upper jaw lip uberon labium superius oris UBERON:0001834 upper lip http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg Lip that covers the upper portion of the mouth.[TAO]. TAO:0001970 Wikipedia:Upper_lip Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG] 2012-09-17 VHOG:0001750 VHOG http://bgee.unil.ch/ Lip that covers the upper portion of the mouth.[TAO] 2012-08-14 TAO:0001970 TAO TAO:wd upper jaw lip https://orcid.org/0000-0002-6601-2165 labium superius oris Wikipedia:Upper_lip Lip that covers the lower portion of the mouth.[TAO]. Lip that covers the lower portion of the mouth.[TAO] UBERON:0003392 EHDAA2:0001020 EMAPA:17909 FMA:59818 MA:0000921 NCIT:C94572 SCTID:245777007 TAO:0002060 UMLS:C0458583 Wikipedia:Lower_lip ZFA:0005225 lower jaw lip uberon labium inferius oris UBERON:0001835 lower lip http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg Lip that covers the lower portion of the mouth.[TAO]. TAO:0002060 Wikipedia:Lower_lip Lip that covers the lower portion of the mouth.[TAO] 2012-08-14 TAO:0002060 TAO TAO:wd UMLS:C0458583 ncithesaurus:Lower_Lip lower jaw lip https://orcid.org/0000-0002-6601-2165 labium inferius oris Wikipedia:Lower_lip A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] BAMS:phn BTO:0001063 EHDAA:4677 EMAPA:17813 FMA:6191 GAID:848 MA:0001170 MESH:D010791 NCIT:C52813 SCTID:280344009 UMLS:C0031774 VHOG:0000728 Wikipedia:Phrenic_nerve uberon diaphragmatic nerve nervus phrenicus phrenic UBERON:0001884 phrenic nerve http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. VHOG:0000728 A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] 2012-09-17 VHOG:0000728 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/phrenic+nerve UMLS:C0031774 ncithesaurus:Phrenic_Nerve diaphragmatic nerve BTO:0001063 nervus phrenicus BTO:0001063 Wikipedia:Phrenic_nerve phrenic BTO:0001063 The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised Middle part of the brain composed of the optic tectum and penducular region.[AAO] The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] mesencephalic part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships MB AAO:0010149 BAMS:MES BIRNLEX:1667 BM:MB BTO:0000138 CALOHA:TS-0630 DHBA:10648 DMBA:16649 EFO:0000919 EHDAA2:0001162 EHDAA:3694 EMAPA:16974 EV:0100242 FMA:61993 HBA:9001 MA:0000207 MAT:0000106 MBA:313 MESH:D008636 MIAA:0000106 NCIT:C12510 RETIRED_EHDAA2:0001104 SCTID:279099009 TAO:0000128 UMLS:C0025462 VHOG:0000069 Wikipedia:Midbrain XAO:0000014 ZFA:0000128 neuronames:462 uberon mesencephalon UBERON:0001891 midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG definitional Bgee:AN The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. GO:0030901 ZFA https://github.com/obophenotype/uberon/issues/378 ABA pending ZFA ABA pending Middle part of the brain composed of the optic tectum and penducular region.[AAO] 2012-06-20 AAO:0010149 AAO AAO:BJB The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000128 TAO ZFIN:curator Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000069 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships ABA MB BIRNLEX:1667 NIFSTD:NeuroNames_abbrevSource UMLS:C0025462 BIRNLEX:1667 ncithesaurus:Mesencephalon neuronames:462 BIRNLEX:1667 mesencephalon Wikipedia:Midbrain A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] In human embryonic development, the rhombomeres are present by day 29 DHBA divides this into A(1-3),B(4),C(5-7) and D(8) hindbrain segment segment of hindbrain DHBA:12664 EFO:0003617 EMAPA:16148 FMA:295666 MAT:0000272 MIAA:0000272 RETIRED_EHDAA2:0000669 TAO:0001064 VHOG:0000672 Wikipedia:Rhombomere XAO:0004079 ZFA:0001064 hindbrain neuromere hindbrain neuromeres rhombomere uberon future rhombencephalon rhombomeres UBERON:0001892 rhombomere A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. Wikipedia:Rhombomere ZFIN:curator A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001064 TAO ZFIN:curator Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] 2012-09-17 VHOG:0000672 VHOG DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002) http://bgee.unil.ch/ hindbrain segment ZFA:0001064 segment of hindbrain ZFA:0001064 hindbrain neuromeres DHBA:HNM future rhombencephalon MIAA:0000272 rhombomeres VHOG:0000672 Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] epencephalon BAMS:Met BIRNLEX:965 BTO:0000673 CALOHA:TS-2029 DHBA:10655 EHDAA2:0001149 EHDAA:5498 EMAPA:17071 FMA:62003 GAID:594 HBA:4833 MA:0000197 MESH:D020540 NCIT:C32741 UMLS:C0376353 UMLS:C1516904 VHOG:0000741 Wikipedia:Metencephalon neuronames:543 epencephalon-2 uberon UBERON:0001895 the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA]. metencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Wikipedia:Metencephalon https://github.com/obophenotype/uberon/issues/300 Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. BIRNLEX:965 The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] 2012-09-17 VHOG:0000741 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/metencephalon The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000741 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ epencephalon ncithesaurus:Epencephalon UMLS:C0376353 BIRNLEX:965 UMLS:C1516904 ncithesaurus:Epencephalon neuronames:543 BIRNLEX:965 epencephalon-2 FMA:62003 Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] bulb medulla AAO:0010486 BAMS:MY BAMS:Md BIRNLEX:957 BM:Me BTO:0000041 CALOHA:TS-0607 DMBA:17352 EFO:0000924 EHDAA2:0001088 EHDAA:7588 EMAPA:17550 EV:0100275 FMA:62004 GAID:590 MA:0000206 MAT:0000111 MAT:0000367 MBA:354 MESH:D008526 MIAA:0000111 NCIT:C12442 SCTID:279104005 TAO:0000545 UMLS:C0025148 UMLS:C1269575 VHOG:0000181 Wikipedia:Bone_marrow_of_ovary_oblongata XAO:0003100 ZFA:0000545 neuronames:698 bulbus uberon medulla oblonzata metepencephalon UBERON:0001896 medulla oblongata http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. FMA:62004 GO:0021550 Wikipedia:Bone_marrow_of_ovary_oblongata Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] 2012-06-20 AAO:0010486 AAO AAO:BJB The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000181 VHOG http://bgee.unil.ch/ Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000181 VHOG DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008) http://bgee.unil.ch/ medulla ABA:MY UMLS:C0025148 BIRNLEX:957 ncithesaurus:Medulla_Oblongata UMLS:C1269575 BIRNLEX:957 neuronames:698 BIRNLEX:957 bulbus FMA:62004 FMA:TA medulla oblonzata Wikipedia:Medulla_oblongata metepencephalon FMA:62004 An epithelium that is part of a small intestine [Automatically generated definition]. Intestinal epithelium which lines the lumen of the mid intestine.[TAO] BTO:0001258 CALOHA:TS-2104 EMAPA:35778 FMA:62017 MA:0001553 SCTID:45480009 TAO:0005127 ZFA:0005127 epithelial tissue of small bowel epithelial tissue of small intestine epithelium of small bowel mid intestine epithelium small bowel epithelial tissue small bowel epithelium small intestinal epithelium small intestine epithelial tissue small intestine epithelium uberon UBERON:0001902 epithelium of small intestine FMA An epithelium that is part of a small intestine [Automatically generated definition]. OBOL:automatic Intestinal epithelium which lines the lumen of the mid intestine.[TAO] 2012-08-14 TAO:0005127 TAO ZFIN:curator epithelial tissue of small bowel OBOL:automatic epithelial tissue of small intestine OBOL:automatic epithelium of small bowel OBOL:automatic mid intestine epithelium ZFA:0005127 small bowel epithelial tissue OBOL:automatic small bowel epithelium OBOL:automatic small intestine epithelial tissue OBOL:automatic An endothelium that is part of a capillary [Automatically generated definition]. BTO:0004954 CALOHA:TS-0112 EMAPA:36292 FMA:62114 MA:0000711 NCIT:C49215 UMLS:C0006904 blood capillary endothelium capillary endothelium capillary vessel endothelium endothelium of blood capillary endothelium of capillary vessel uberon UBERON:0001915 endothelium of capillary An endothelium that is part of a capillary [Automatically generated definition]. OBOL:automatic UMLS:C0006904 ncithesaurus:Capillary_Endothelium blood capillary endothelium OBOL:automatic capillary vessel endothelium OBOL:automatic endothelium of blood capillary OBOL:automatic endothelium of capillary vessel OBOL:automatic An endothelium that is part of an arteriole [Automatically generated definition]. EMAPA:36286 FMA:62115 MA:0000705 NCIT:C49192 UMLS:C1179024 arteriole endothelium uberon UBERON:0001916 endothelium of arteriole An endothelium that is part of an arteriole [Automatically generated definition]. OBOL:automatic UMLS:C1179024 ncithesaurus:Arteriole_Endothelium An endothelium that is part of an artery [Automatically generated definition]. The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011013 BTO:0004757 EMAPA:35148 FMA:62116 MA:0000707 NCIT:C49194 UMLS:C1179025 VHOG:0001215 XAO:0000357 arterial endothelium artery endothelium uberon UBERON:0001917 endothelium of artery An endothelium that is part of an artery [Automatically generated definition]. OBOL:automatic The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] 2012-06-20 AAO:0011013 AAO XAO:curator Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001215 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C1179025 ncithesaurus:Artery_Endothelium An endothelium that is part of a venule [Automatically generated definition]. EMAPA:36290 FMA:62117 MA:0000716 NCIT:C49319 UMLS:C1179026 venule endothelium uberon UBERON:0001918 endothelium of venule An endothelium that is part of a venule [Automatically generated definition]. OBOL:automatic UMLS:C1179026 ncithesaurus:Venule_Endothelium An endothelium that is part of a vein [Automatically generated definition]. Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011110 BTO:0004756 EMAPA:36288 FMA:62118 MA:0000712 NCIT:C49317 UMLS:C1179027 VHOG:0001216 XAO:0000358 vein endothelium venous endothelium uberon veinous endothelium UBERON:0001919 endothelium of vein An endothelium that is part of a vein [Automatically generated definition]. OBOL:automatic Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001216 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C1179027 ncithesaurus:Vein_Endothelium veinous endothelium VHOG:0001216 Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] MTg tegmentum BAMS:MTg BIRNLEX:1200 BTO:0003388 DHBA:12195 EFO:0000921 EHDAA2:0004475 EMAPA:18215 FMA:62393 HBA:9002 MA:0000212 MAT:0000452 MESH:D013681 SCTID:362392007 TAO:0000160 UMLS:C0039441 VHOG:0001367 Wikipedia:Midbrain_tegmentum XAO:0004271 ZFA:0000160 neuronames:491 tegmentum mesencephali tegmentum of midbrain uberon mesencephalic tegmentum tegmentum mesencephalicum UBERON:0001943 'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png ZFA Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. FMA:FMA ISBN:0471888893 Wikipedia:Midbrain_tegmentum Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] 2012-09-17 VHOG:0001367 VHOG DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) http://bgee.unil.ch/ MTg BIRNLEX:1200 NIFSTD:NeuroNames_abbrevSource tegmentum ISBN:0471888893 MESH:D013681 https://github.com/biopragmatics/biomappings UMLS:C0039441 BIRNLEX:1200 neuronames:491 BIRNLEX:1200 tegmentum mesencephali Wikipedia:Midbrain_tegmentum mesencephalic tegmentum VHOG:0001367 tegmentum mesencephalicum NeuroNames:491 A multi-tissue structure that is part of a spinal cord. BIRNLEX:1496 NCIT:C33969 SCTID:244437008 UMLS:C1268166 uberon spinal cord part UBERON:0001948 regional part of spinal cord A multi-tissue structure that is part of a spinal cord. OBOL:automatic UMLS:C1268166 ncithesaurus:Spinal_Cord_Part The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 NCIT:C13356 UMLS:C0032105 Wikipedia:Blood_plasma blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma The liquid component of blood, in which erythrocytes are suspended. http://orcid.org/0000-0002-6601-2165 plasma MA:0002501 portion of plasma FMA:62970 UMLS:C0032105 ncithesaurus:Plasma Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum. aids the process of digestion of lipids in the small intestine bile salts function to emulsify dietary fats and facilitate their intestinal absorption elimination of cholesterol major excretory route for potentially harmful exogenous lipophilic substances many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine BTO:0000121 CALOHA:TS-1172 ENVO:02000023 FMA:62971 GAID:1157 MA:0002513 MESH:D001646 NCIT:C13192 UMLS:C0005388 Wikipedia:Bile ZFA:0005857 galen:Bile uberon fel gall UBERON:0001970 bile 0.3% in humans Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. DOI:10.1002/cphy.c120027 Wikipedia:Bile UMLS:C0005388 ncithesaurus:Bile fel BTO:0000121 gall BTO:0000121 BTO:0000501 FMA:62972 GAID:1160 MA:0002519 MESH:D005750 NCIT:C32661 UMLS:C0017133 Wikipedia:Gastric_juice galen:GastricJuice stomach secretion uberon succus gastricus UBERON:0001971 gastric juice UMLS:C0017133 ncithesaurus:Gastric_Secretion succus gastricus BTO:0000501 A submucosa that is part of a esophagus [Automatically generated definition]. BTO:0002109 EMAPA:35325 FMA:62997 MA:0002724 SCTID:362128009 esophageal submucosa esophagus submucosa gullet submucosa oesophagus submucosa submucosa of esophagus submucosa of gullet submucosa of oesophagus tela submucosa (oesophagus) tela submucosa esophagi tela submucosa oesophageae tela submucosa of esophagus uberon submucous layer of esophagus tela submucosa oesophagi UBERON:0001972 submucosa of esophagus A submucosa that is part of a esophagus [Automatically generated definition]. OBOL:automatic gullet submucosa OBOL:automatic oesophagus submucosa OBOL:automatic submucosa of gullet OBOL:automatic submucosa of oesophagus OBOL:automatic tela submucosa (oesophagus) FMA:62997 FMA:TA tela submucosa esophagi BTO:0002109 tela submucosa oesophageae FMA:62997 FMA:TA submucous layer of esophagus BTO:0002109 tela submucosa oesophagi BTO:0002109 A lamina propria that is part of a esophagus [Automatically generated definition]. EMAPA:26987 FMA:63050 MA:0001568 NCIT:C49223 UMLS:C1707949 esophagus lamina propria esophagus lamina propria mucosa esophagus lamina propria mucosae gullet lamina propria gullet lamina propria mucosa gullet lamina propria mucosae lamina propria mucosa of esophagus lamina propria mucosa of gullet lamina propria mucosa of oesophagus lamina propria mucosae of esophagus lamina propria mucosae of gullet lamina propria mucosae of oesophagus lamina propria of gullet lamina propria of oesophagus oesophagus lamina propria mucosa oesophagus lamina propria mucosae uberon esophageal lamina propria oesophagus lamina propria UBERON:0001974 lamina propria of esophagus FMA A lamina propria that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C1707949 ncithesaurus:Esophageal_Lamina_Propria esophagus lamina propria mucosa OBOL:automatic esophagus lamina propria mucosae OBOL:automatic gullet lamina propria OBOL:automatic gullet lamina propria mucosa OBOL:automatic gullet lamina propria mucosae OBOL:automatic lamina propria mucosa of esophagus OBOL:automatic lamina propria mucosa of gullet OBOL:automatic lamina propria mucosa of oesophagus OBOL:automatic lamina propria mucosae of gullet OBOL:automatic lamina propria mucosae of oesophagus OBOL:automatic lamina propria of gullet OBOL:automatic lamina propria of oesophagus OBOL:automatic oesophagus lamina propria mucosa OBOL:automatic oesophagus lamina propria mucosae OBOL:automatic esophageal lamina propria EMAPA:26987 A serous membrane that is part of a esophagus [Automatically generated definition]. EMAPA:35322 FMA:63057 MA:0001571 esophagus serosa esophagus serous membrane gullet serosa gullet serous membrane oesophagus serous membrane serosa of abdominal part of esophagus serosa of gullet serosa of oesophagus serous coat of oesophagus serous membrane of esophagus serous membrane of gullet serous membrane of oesophagus tunica serosa oesophageae uberon oesophagus serosa UBERON:0001975 serosa of esophagus A serous membrane that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus serous membrane OBOL:automatic gullet serosa OBOL:automatic gullet serous membrane OBOL:automatic oesophagus serous membrane OBOL:automatic serosa of gullet OBOL:automatic serous membrane of esophagus OBOL:automatic serous membrane of gullet OBOL:automatic serous membrane of oesophagus OBOL:automatic tunica serosa oesophageae FMA:63057 FMA:TA The epithelial layer that lines the luminal space of the esophagus. TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO] BTO:0001578 CALOHA:TS-0698 EFO:0003041 EHDAA2:0001287 EMAPA:16835 FMA:63063 MA:0001565 NCIT:C49221 TAO:0001499 UMLS:C1179544 ZFA:0001499 epithelial tissue of esophagus epithelial tissue of gullet epithelial tissue of oesophagus epithelium of gullet epithelium of oesophagus esophageal epithelium esophagus epithelial tissue esophagus epithelium gullet epithelial tissue gullet epithelium oesophagus epithelial tissue uberon oesophagus epithelium UBERON:0001976 epithelium of esophagus FMA The epithelial layer that lines the luminal space of the esophagus. ISBN:0-683-40008-8 MP:0000468 Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001499 TAO ZFIN:curator UMLS:C1179544 ncithesaurus:Esophageal_Epithelium epithelial tissue of esophagus OBOL:automatic epithelial tissue of gullet OBOL:automatic epithelial tissue of oesophagus OBOL:automatic epithelium of gullet OBOL:automatic epithelium of oesophagus OBOL:automatic esophagus epithelial tissue OBOL:automatic gullet epithelial tissue OBOL:automatic gullet epithelium OBOL:automatic oesophagus epithelial tissue OBOL:automatic EMAPA:32925 FMA:63120 MA:0000724 SCTID:371401008 VHOG:0001430 pancreas parenchyma pancreatic parenchyma uberon UBERON:0001978 parenchyma of pancreas One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins. Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] BTO:0002626 EMAPA:35917 FMA:63130 MA:0000071 MESH:D014699 NCIT:C12818 SCTID:341687009 TAO:0005315 UMLS:C0042520 VHOG:0001765 Wikipedia:Venule ZFA:0005315 uberon venula UBERON:0001979 venule https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins. MESH:A07.231.432.952 MP:0004125 Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] 2012-08-14 TAO:0005315 TAO ZFIN:curator UMLS:C0042520 ncithesaurus:Venule venula Wikipedia:Venule The smallest division of the artery located between the muscular arteries and the capillaries[GO]. Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] Small, terminal branch of an artery which generally connects to capillaries.[AAO] AAO:0010253 BTO:0001997 EMAPA:35146 FMA:63182 MA:0000063 MESH:D001160 NCIT:C12672 SCTID:337724002 TAO:0002138 UMLS:C0003847 VHOG:0001763 Wikipedia:Arteriole ZFA:0005255 uberon arteriola UBERON:0001980 arteriole https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg MA The smallest division of the artery located between the muscular arteries and the capillaries[GO]. GO:0014830 Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] 2012-08-14 TAO:0002138 TAO ZFIN:curator Small, terminal branch of an artery which generally connects to capillaries.[AAO] 2012-06-20 AAO:0010253 AAO AAO:BJB UMLS:C0003847 ncithesaurus:Arteriole arteriola Wikipedia:Arteriole A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] annelids have blood vessels, but this class is not applicable to annelids. FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 GAID:169 MA:0000060 MAT:0000393 MESH:D001808 NCIT:C12679 NLXANAT:090901 SCTID:361097006 TAO:0002137 UMLS:C0005847 VHOG:0001250 Wikipedia:Blood_vessel XAO:0001011 ZFA:0005314 region of vascular tree organ vascular tree organ region uberon vas sanguineum UBERON:0001981 blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg AEO EHDAA2 GO:0072360 A vessel through which blood circulates in the body. BTO:0001102 Wikipedia:Blood_vessel Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] 2012-09-17 VHOG:0001250 VHOG http://bgee.unil.ch/ Any of the vessels through which blood circulates in the body.[AAO] 2012-06-20 AAO:0011004 AAO AAO:EJS The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001250 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX FMA vascular element EMAPA:35993 UMLS:C0005847 ncithesaurus:Blood_Vessel region of vascular tree organ FMA:50722 vascular tree organ region FMA:50722 vas sanguineum Wikipedia:Blood_vessel Any of the smallest blood vessels connecting arterioles with venules. not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs AAO:0010252 BTO:0002045 CALOHA:TS-2006 EFO:0001906 EMAPA:35198 EV:0100035 FMA:63194 MA:0000065 MESH:D002196 NCIT:C12685 NLXANAT:090902 TAO:0005250 UMLS:C0935624 VHOG:0001253 Wikipedia:Capillary XAO:0000116 ZFA:0005250 blood capillary capillary vessel uberon UBERON:0001982 capillary https://github.com/obophenotype/uberon/issues/2186 http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg Any of the smallest blood vessels connecting arterioles with venules. ISBN:0073040584 Wikipedia:Capillary https://github.com/obophenotype/uberon/issues/137 Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] 2012-06-20 AAO:0010252 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001253 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0935624 ncithesaurus:Capillary A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. CALOHA:TS-0172 EMAPA:35935 FMA:63882 GAID:891 MA:0001242 MESH:D004728 NCIT:C12707 SCTID:368827009 TAO:0002186 UMLS:C0014259 Wikipedia:Corneal_endothelium ZFA:0001687 cornea endothelium endothelium of cornea uberon epithelium posterius corneae UBERON:0001985 corneal endothelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. Wikipedia:Corneal_endothelium UMLS:C0014259 ncithesaurus:Corneal_Endothelium cornea endothelium OBOL:automatic endothelium of cornea OBOL:automatic epithelium posterius corneae Wikipedia:Corneal_endothelium A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 FMA:63916 GAID:520 MESH:D004727 NCIT:C12481 SCTID:27168002 UMLS:C0014257 galen:Endothelium uberon UBERON:0001986 The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980) endothelium FMA-text-def https://github.com/obophenotype/uberon/issues/225 A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. FMA:63916 MESH:A10.272.491 https://github.com/obophenotype/uberon/issues/225 UMLS:C0014257 ncithesaurus:Endothelium Portion of semisolid bodily waste discharged through the anus[MW,modified]. Excretion in semisolid state processed by the intestine.[FMA] fecal excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 UMLS:C0015733 Wikipedia:Feces galen:Feces faeces fecal material fecal matter piece of shit portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint uberon droppings excrement ordure spoor UBERON:0001988 feces Portion of semisolid bodily waste discharged through the anus[MW,modified]. Wikipedia:Feces http://www.merriam-webster.com/dictionary/feces Excretion in semisolid state processed by the intestine.[FMA] FMA:64183 UMLS:C0015733 ncithesaurus:Feces piece of shit PMID:23285307 portionem cacas cow dung Wikipedia:Cow_dung cow pat Wikipedia:Cow_dung fewmet Wikipedia:Fewmet frass Wikipedia:Frass guano Wikipedia:Guano spraint Wikipedia:Spraint excrement BTO:0000440 An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Major artery which supplies blood to the lungs.[AAO] One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP] AAO:0010221 BTO:0000778 CALOHA:TS-0839 EFO:0001399 EHDAA2:0001575 EHDAA:4351 EMAPA:17008 FMA:66326 GAID:505 MA:0002031 MESH:D011651 NCIT:C12774 SCTID:181380003 UMLS:C0034052 VHOG:0000982 Wikipedia:Pulmonary_artery XAO:0004162 galen:PulmonaryArtery pulmonary arterial tree pulmonary arterial tree organ part uberon arteria pulmonalis pulmonary arterial subtree truncus pulmonalis UBERON:0002012 pulmonary artery https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png Wikipedia EHDAA2 XAO EHDAA2 An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Wikipedia:Pulmonary_artery http://orcid.org/0000-0002-6601-2165 Major artery which supplies blood to the lungs.[AAO] 2012-06-20 AAO:0010221 AAO AAO:BJB One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] 2012-09-17 VHOG:0000982 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+artery On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0000982 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0034052 ncithesaurus:Pulmonary_Artery pulmonary arterial tree FMA:66326 pulmonary arterial tree organ part FMA:66326 arteria pulmonalis Wikipedia:Pulmonary_artery pulmonary arterial subtree FMA:66326 truncus pulmonalis Wikipedia:Pulmonary_artery Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] the veins that return oxygenated blood from the lungs to the left atrium of the heart On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] AAO:0010521 BTO:0001799 CALOHA:TS-0840 EHDAA2:0001579 EHDAA:2629 EMAPA:18645 FMA:66643 GAID:543 MA:0002206 MESH:D011667 NCIT:C12776 SCTID:430160002 UMLS:C0034090 VHOG:0001133 Wikipedia:Pulmonary_vein XAO:0000394 galen:PulmonaryVein pulmonary venous tree organ part uberon venae pulmonales UBERON:0002016 pulmonary vein https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. GO:0060577 Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] 2012-06-20 AAO:0010521 AAO AAO:BJB One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] 2012-09-17 VHOG:0001133 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+vein the veins that return oxygenated blood from the lungs to the left atrium of the heart MP:0002726,MGI:cwg On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0001133 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0034090 ncithesaurus:Pulmonary_Vein venae pulmonales Wikipedia:Pulmonary_vein A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. BTO:0001792 CALOHA:TS-0814 EHDAA2:0001485 EHDAA:6510 EMAPA:17349 FMA:66645 GAID:540 MA:0002198 MESH:D011169 NCIT:C33343 SCTID:362064007 UMLS:C0032718 VHOG:0000656 XAO:0000392 galen:PortalVein portal venous tree organ part uberon UBERON:0002017 portal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png FMA A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. BTO:0001792 UMLS:C0032718 ncithesaurus:Portal_Vein portal venous tree organ part FMA:66645 A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 EMAPA:37596 FMA:67242 HBA:4006 MA:0001112 MESH:D066128 NCIT:C32695 TAO:0002197 UMLS:C0018220 VHOG:0001768 Wikipedia:Gray_matter ZFA:0001681 neuronames:2869 gray matter gray matter of neuraxis grey matter grey matter of neuraxis grey substance neuronal grey matter substantia grisea uberon gray mater grisea UBERON:0002020 gray matter https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Wikipedia:Gray_matter http://orcid.org/0000-0002-6601-2165 Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] 2012-08-14 TAO:0002197 TAO ZFIN:curator EMAPA:37596 MA:th MESH:D066128 https://github.com/biopragmatics/biomappings UMLS:C0018220 ncithesaurus:Gray_Matter gray matter of neuraxis FMA:67242 neuronal grey matter AEO:0001012 substantia grisea FMA:67242 FMA:TA gray mater ZFA:0001681 grisea The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] rhombencephalic in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps AAO:0010150 BAMS:HB BIRNLEX:942 BTO:0000672 CALOHA:TS-0457 DHBA:10653 DMBA:16808 EFO:0000923 EHDAA2:0000746 EHDAA:3514 EHDAA:6487 EMAPA:16916 FMA:67687 MA:0000195 MAT:0000107 MBA:1065 MESH:D012249 MIAA:0000107 NCIT:C40336 SCTID:303456008 TAO:0000029 UMLS:C0035507 UMLS:C1522180 VHOG:0000070 Wikipedia:Rhombencephalon XAO:0000015 ZFA:0000029 neuronames:540 uberon rhombencephalon UBERON:0002028 hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg modified-source-relation ABA Bgee:AN The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. Wikipedia:Rhombencephalon ZFA:0000029 ZFIN:curator ZFA ABA https://github.com/obophenotype/uberon/issues/378 pending ABA PMID:8932866 Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] 2012-06-20 AAO:0010150 AAO AAO:BJB The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000029 TAO ZFIN:curator relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] 2012-08-14 TAO:0000029 TAO Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000070 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps MA UMLS:C0035507 BIRNLEX:942 ncithesaurus:Hind-Brain UMLS:C1522180 BIRNLEX:942 neuronames:540 BIRNLEX:942 The simple columnar epithelial lining of the gall bladder. BTO:0001449 CALOHA:TS-1304 EMAPA:35370 FMA:67711 MA:0001632 NCIT:C49227 UMLS:C1180206 epithelial tissue of gall bladder epithelial tissue of gallbladder epithelium of gallbladder gall bladder epithelial tissue gall bladder epithelium gallbladder epithelial tissue gallbladder epithelium uberon biliary epithelium UBERON:0002029 epithelium of gall bladder The simple columnar epithelial lining of the gall bladder. MP:0009492 UMLS:C1180206 ncithesaurus:Gallbladder_Epithelium epithelial tissue of gall bladder OBOL:automatic epithelial tissue of gallbladder OBOL:automatic epithelium of gallbladder OBOL:automatic gall bladder epithelial tissue OBOL:automatic gallbladder epithelial tissue OBOL:automatic gallbladder epithelium OBOL:automatic Muscle tissue that contains fibers that are divided by transverse bands into striations. Voluntary muscle tissue arranged in bundles of fibers.[AAO] AAO:0010762 AEO:0000140 CALOHA:TS-2047 EHDAA2:0003140 EMAPA:36390 FMA:67905 MA:0002438 NCIT:C12436 UMLS:C1331262 WBbt:0005779 Wikipedia:Striated_muscle galen:StriatedMuscle striated muscle uberon UBERON:0002036 striated muscle tissue Muscle tissue that contains fibers that are divided by transverse bands into striations. CL:0000737 GOC:dph GOC:mtg_muscle Voluntary muscle tissue arranged in bundles of fibers.[AAO] 2012-06-20 AAO:0010762 AAO AAO:CAM UMLS:C1331262 ncithesaurus:Striated_Muscle_Tissue A systemic artery that supplies the lung with with oxygenated blood. EMAPA:18608 FMA:68109 GAID:477 MA:0001923 MESH:D001981 NCIT:C32230 SCTID:244247009 UMLS:C0006257 Wikipedia:Bronchial_artery bronchial arterial tree uberon arteriae bronchiales rami bronchiales partis thoracicae aortae UBERON:0002040 Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. bronchial artery http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png A systemic artery that supplies the lung with with oxygenated blood. UBERON:cjm Wikipedia:Bronchial_artery UMLS:C0006257 ncithesaurus:Bronchial_Artery arteriae bronchiales Wikipedia:Bronchial_artery rami bronchiales partis thoracicae aortae Wikipedia:Bronchial_artery The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. BAMS:PnR BAMS:RA-PONS BAMS:RPn BIRNLEX:1110 DHBA:12471 DHBA:12475 FMA:68875 HBA:9159 MA:0001022 MBA:238 UMLS:C0175423 Wikipedia:Pontine_raphe_nucleus neuronames:589 raphe of pons raphe pontis uberon nucleus raphe pontis nucleus raphes pontis raphe (mediana pontina) raphe pontis nucleus UBERON:0002047 pontine raphe nucleus Wikipedia The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. Wikipedia:Pontine_raphe_nucleus ABA ABA ABA ABA UMLS:C0175423 BIRNLEX:1110 neuronames:589 BIRNLEX:1110 raphe pontis FMA:68875 FMA:TA nucleus raphe pontis NeuroNames:589 nucleus raphes pontis Wikipedia:Pontine_raphe_nucleus raphe (mediana pontina) NeuroNames:589 Respiration organ that develops as an outpocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 SCTID:181216001 UMLS:C0024109 VHOG:0000310 Wikipedia:Lung XAO:0000119 galen:Lung pulmo uberon UBERON:0002048 Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung https://github.com/obophenotype/uberon/issues/701 https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb some species only have a single lung Respiration organ that develops as an outpocketing of the esophagus. http://orcid.org/0000-0002-6601-2165 https://orcid.org/0000-0002-9415-5104 https://github.com/obophenotype/uberon/issues/701 https://orcid.org/0000-0002-9415-5104 https://github.com/obophenotype/uberon/issues/701 Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] 2012-06-20 AAO:0010567 AAO AAO:SBH Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000310 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011) http://bgee.unil.ch/ UMLS:C0024109 ncithesaurus:Lung pulmo An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? vascular BTO:0003718 FMA:69050 TAO:0005249 ZFA:0005249 vascular network uberon UBERON:0002049 vasculature http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg FMA An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. ZFA:0005249 vascular network FMA:69050 Anatomical structure that is part of an embryo. Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 NCIT:C13229 RETIRED_EHDAA2:0003169 SCTID:667009 TAO:0001105 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure embryonic anatomical structure uberon developing structure embryonale Struktur embryonic structures UBERON:0002050 embryonic structure Anatomical structure that is part of an embryo. BTO:0000174 ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] 2012-06-20 AAO:0000138 AAO AAO:BJB Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] 2012-08-14 TAO:0001105 TAO ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] 2012-08-14 VSAO:0000178 VSAO ZFIN:curator in FMA embryo is_a embryonic structure FMA FBbt:00004208 UMLS:C0013948 ncithesaurus:Embryonic_Structure developing embryonic structure FBbt:00004208 embryonic anatomical structure RETIRED_EHDAA2:0003169 embryonale Struktur BTO:0000174 embryonic structures ZFA:0001105 An artery that supplies the diaphragm. In humans this includes the superior and inferior phrenic arteries EMAPA:37108 FMA:69330 MA:0002019 NCIT:C33320 UMLS:C1181536 uberon UBERON:0002057 phrenic artery An artery that supplies the diaphragm. https://orcid.org/0000-0002-6601-2165 EMAPA:37108 MA:th UMLS:C1181536 ncithesaurus:Phrenic_Artery The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit EHDAA2:0004143 EMAPA:35887 FMA:70301 GAID:554 MA:0000103 MESH:D014338 NCIT:C34317 SCTID:308828009 UMLS:C1519589 Wikipedia:Truncus_arteriosus_(embryology) uberon UBERON:0002061 truncus arteriosus EHDAA2 FMA MA EHDAA2 EHDAA2 The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. Wikipedia:Truncus_arteriosus_(embryology) assume spelling error for ncit ncit UMLS:C1519589 ncithesaurus:Trancus_Arteriosus The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] EHDAA2:0000434 EHDAA2:0004028 EHDAA:2586 EMAPA:16696 FMA:70302 MA:0000078 MESH:D054089 TAO:0001317 VHOG:0000932 Wikipedia:Atrioventricular_cushions XAO:0004189 ZFA:0001317 AV cushion atrioventricular cushion cardiac cushion endocardial cushion tissue uberon atrioventricular canal cushion endocardial cushions UBERON:0002062 GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form endocardial cushion http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png ZFA The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. GO:0003197 Wikipedia:Atrioventricular_cushions ZFIN:curator Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] 2012-08-14 TAO:0001317 TAO ZFIN:curator relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] 2012-08-14 TAO:0001317 TAO (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] 2012-09-17 VHOG:0000932 VHOG DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3 http://bgee.unil.ch/ MESH:D054089 https://github.com/biopragmatics/biomappings atrioventricular cushion Wikipedia:Endocardial_cushion cardiac cushion PMID:15797462 endocardial cushion tissue EHDAA2:0000434 atrioventricular canal cushion FMA:70302 endocardial cushions The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616] In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract inflow tract AAO:0010505 EHDAA2:0001839 EHDAA:480 EMAPA:16237 FMA:70303 NCIT:C34299 NCIT:C34300 TAO:0000154 UMLS:C0225857 UMLS:C0231084 VHOG:0000177 Wikipedia:Sinus_venosus ZFA:0000154 uberon sinus venarum sinus venosus cordis venarum venarum sinus venosus UBERON:0002063 sinus venosus http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png VHOG Bgee:AN The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. PMID:20735616 Wikipedia:Sinus_venosus Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000154 TAO ZFIN:curator Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] 2012-06-20 AAO:0010505 AAO AAO:BJB In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] 2012-09-17 VHOG:0000177 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract ZFA:0000154 inflow tract ZFA:0000154 UMLS:C0225857 ncithesaurus:Sinus_Venarum UMLS:C0231084 ncithesaurus:Sinus_Venosus sinus venarum Wikipedia:Sinus_venosus sinus venosus cordis Wikipedia:Sinus_venosus venarum Wikipedia:Sinus_venosus venarum sinus Wikipedia:Sinus_venosus venosus Wikipedia:Sinus_venosus The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Consider adding a layer-of-skin grouping class for all skin layers A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] dermal AAO:0000128 BTO:0000294 CALOHA:TS-2076 EFO:0000953 EMAPA:17527 EV:0100154 FMA:70323 GAID:1321 MA:0000152 MAT:0000153 MESH:D020405 MIAA:0000153 NCIT:C12701 SCTID:361696001 TAO:0001119 UMLS:C0011646 VHOG:0000108 Wikipedia:Dermis XAO:0000217 ZFA:0001119 vertebrate dermis uberon corium cutis UBERON:0002067 dermis http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg FMA definitional The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Wikipedia:Dermis ZFIN:curator A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001119 TAO ZFIN:curator When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] 2012-09-17 VHOG:0000108 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1 http://bgee.unil.ch/ UMLS:C0011646 ncithesaurus:Dermis corium BTO:0000294 Wikipedia:Dermis cutis BTO:0000294 Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. hypodermal subcutaneous subcutaneus BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO:0001314 CALOHA:TS-2366 EMAPA:37505 FMA:70544 MESH:D040521 NCIT:C33645 TAO:0001136 UMLS:C0278403 Wikipedia:Hypodermis ZFA:0001136 hypoderm vertebrate hypodermis uberon sub-tegumental tissue subcutaneous tissue subcutis subtegumental tissue superficial fascia tela subcutanea UBERON:0002072 hypodermis http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg ZFA FMA-modified Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. Wikipedia:Hypodermis A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001136 TAO ZFIN:curator A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. FMA:70544 BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO EMAPA:37505 MA:th MESH:D040521 https://github.com/biopragmatics/biomappings UMLS:C0278403 ncithesaurus:Subcutis sub-tegumental tissue BTO:0004525 subcutaneous tissue Wikipedia:Hypodermis subtegumental tissue BTO:0004525 superficial fascia tela subcutanea Wikipedia:Hypodermis An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 NCIT:C28287 RETIRED_EHDAA2:0002201 SCTID:118760003 UMLS:C0042779 Wikipedia:Viscus XAO:0003034 visceral organ visceral organ system uberon splanchnic tissue viscera visceral tissue UBERON:0002075 viscus An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. BTO:0001491 Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] 2012-06-20 AAO:0010386 AAO BTO:0001491 general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. FMA UMLS:C0042779 ncithesaurus:Viscera visceral organ RETIRED_EHDAA2:0002201 visceral organ system MA:0000019 splanchnic tissue BTO:0001491 visceral tissue BTO:0001491 A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010248 BTO:0001703 EHDAA2:0000290 EMAPA:17321 FMA:7096 MA:0000075 NCIT:C12868 SCTID:244383003 UMLS:C0225844 VHOG:0000328 Wikipedia:Right_atrium XAO:0003192 galen:RightAtrium cardiac right atrium heart right atrium right atrium right atrium of heart right cardiac atrium uberon atrium dextrum UBERON:0002078 right cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. Wikipedia:Right_atrium http://orcid.org/0000-0002-6601-2165 Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] FMA:7096 The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000328 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225844 ncithesaurus:Right_Atrium heart right atrium MA:0000075 right atrium VHOG:0000328 atrium dextrum Wikipedia:Right_atrium A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] The chamber of the heart that receives blood from the lungs[XAO:EJS]. The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010247 BTO:0001702 EHDAA2:0000275 EMAPA:17315 FMA:7097 MA:0000074 NCIT:C12869 SCTID:244387002 UMLS:C0225860 VHOG:0000369 Wikipedia:Left_atrium XAO:0003191 galen:LeftAtrium atrium sinistrum cardiac left atrium heart left atrium left atrium left atrium of heart left cardiac atrium uberon UBERON:0002079 left cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. Wikipedia:Left_atrium http://orcid.org/0000-0002-6601-2165 Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] FMA:7097 The chamber of the heart that receives blood from the lungs[XAO:EJS]. XAO:EJS The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000369 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225860 ncithesaurus:Left_Atrium atrium sinistrum Wikipedia:Left_atrium heart left atrium MA:0000074 left atrium VHOG:0000369 A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with the pulmonary arteries BTO:0001630 CALOHA:TS-0443 EHDAA2:0000196 EMAPA:17340 FMA:7098 MA:0000093 NCIT:C12870 SCTID:244384009 UMLS:C0225883 VHOG:0000717 Wikipedia:Right_ventricle galen:RightVentricle cardiac right ventricle right ventricle right ventricle of heart uberon right cardiac ventricle ventriculus dexter UBERON:0002080 heart right ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb PMID:17276708 cjm A cardiac ventricle that is in the right side of the heart. http://orcid.org/0000-0002-6601-2165 The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] 2012-09-17 VHOG:0000717 VHOG http://bgee.unil.ch/ UMLS:C0225883 ncithesaurus:Right_Ventricle right ventricle FMA:7098 right cardiac ventricle EMAPA:17340 ventriculus dexter Wikipedia:Right_ventricle Cardiac chamber in which blood enters the heart. One of four heart chambers.[TAO] One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] AAO:0010246 BTO:0000903 CALOHA:TS-0437 EFO:0000277 EHDAA2:0000154 EHDAA:1265 EMAPA:16688 EV:0100019 FMA:7099 GAID:555 MA:0000073 MAT:0000496 MESH:D006325 NCIT:C12728 SCTID:261405004 TAO:0000471 UMLS:C0018792 VHOG:0000175 Wikipedia:Heart_atrium ZFA:0000471 galen:Atrium atria atrium atrium of heart cardiac atria heart atrium uberon atrial tissue UBERON:0002081 cardiac atrium Cardiac chamber in which blood enters the heart. Wikipedia:Heart_atrium http://orcid.org/0000-0002-6601-2165 One of four heart chambers.[TAO] 2012-08-14 TAO:0000471 TAO ZFIN:curator One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] 2012-06-20 AAO:0010246 AAO AAO:BJB In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] 2012-09-17 VHOG:0000175 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ UMLS:C0018792 ncithesaurus:Cardiac_Atrium atria atrium ZFA:0000471 cardiac atria atrial tissue BTO:0000903 Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] One of four heart chambers.[TAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] ventricle AAO:0010249 BTO:0000862 CALOHA:TS-0444 EFO:0000317 EHDAA2:0004164 EHDAA:1912 EMAPA:17331 EV:0100020 FMA:7100 GAID:568 MA:0000091 MAT:0000497 MESH:D006352 NCIT:C12730 SCTID:277699000 TAO:0000009 UMLS:C0018827 VHOG:0000435 Wikipedia:Ventricle_(heart) XAO:0003193 ZFA:0000009 galen:Ventricle heart ventricle lower chamber of heart ventricle of heart uberon UBERON:0002082 cardiac ventricle Bgee:AN Cardiac chamber through which blood leaves the heart. Wikipedia:Ventricle_(heart) http://orcid.org/0000-0002-6601-2165 A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] 2012-06-20 AAO:0010249 AAO AAO:BJB One of four heart chambers.[TAO] 2012-08-14 TAO:0000009 TAO ZFIN:curator In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] 2012-09-17 VHOG:0000435 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ UMLS:C0018827 ncithesaurus:Cardiac_Ventricle A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with aorta BTO:0001629 CALOHA:TS-0439 EHDAA2:0002178 EMAPA:17337 FMA:7101 MA:0000092 NCIT:C12871 SCTID:244385005 UMLS:C0225897 VHOG:0000718 Wikipedia:Left_ventricle galen:LeftVentricle cardiac left ventricle left cardiac ventricle left ventricle left ventricle of heart uberon ventriculus sinister cordis UBERON:0002084 heart left ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb GO A cardiac ventricle that is in the left side of the heart. http://orcid.org/0000-0002-6601-2165 Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000718 VHOG http://bgee.unil.ch/ The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] 2012-09-17 VHOG:0000718 VHOG DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010) http://bgee.unil.ch/ UMLS:C0225897 ncithesaurus:Left_Ventricle left ventricle FMA:7101 ventriculus sinister cordis Wikipedia:Left_ventricle A cardiac septum that divides the left and right atria of the heart. The partition separating the right and left atria of the heart. [TFD][VHOG] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] EHDAA2:0000838 EHDAA:1896 EMAPA:17011 FMA:7108 MA:0000084 NCIT:C32818 SCTID:362016003 UMLS:C0225836 VHOG:0000385 Wikipedia:Interatrial_septum galen:InteratrialSeptum atrial septum atrium septum interatrial septal wall uberon UBERON:0002085 interatrial septum http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png A cardiac septum that divides the left and right atria of the heart. http://orcid.org/0000-0002-6601-2165 The partition separating the right and left atria of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000385 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/interatrial+septum The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000385 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225836 ncithesaurus:Interatrial_Septum The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 MESH:D013131 MIAA:0000148 TAO:0000317 VHOG:0000317 VSAO:0000093 XAO:0003073 ZFA:0000317 post-cranial axial skeleton uberon UBERON:0002090 previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. postcranial axial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. ZFA:0000317 https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000093 VSAO PSPUB:0000170 The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] 2012-06-20 AAO:0000034 AAO AAO:LAP The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] 2012-08-14 TAO:0000317 TAO ZFIN:curator The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0000317 VHOG DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) http://bgee.unil.ch/ axial skeleton FMA:71221 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton EMAPA:37721 MA:th MESH:D013131 https://github.com/biopragmatics/biomappings Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. AAO:0000747 EFO:0000951 EMAPA:32729 FMA:71222 MA:0000290 MAT:0000278 MIAA:0000278 NCIT:C49477 SCTID:322050006 UMLS:C0222646 VHOG:0001666 VSAO:0000076 Wikipedia:Appendicular_skeleton XAO:0003166 appendicular skeleton entire appendicular skeleton paired fin skeleton uberon skeleton appendiculare UBERON:0002091 appendicular skeleton https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. UBERONREF:0000003 Wikipedia:Appendicular_skeleton https://orcid.org/0000-0002-6601-2165 Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] 2012-08-14 VSAO:0000076 VSAO PSPUB:0000170 https://orcid.org/0000-0002-6601-2165 Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] 2012-08-14 TAO:0000027 TAO TAO:wd The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] 2012-06-20 AAO:0000747 AAO AAO:LAP ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. FMA UMLS:C0222646 ncithesaurus:Appendicular_Skeleton entire appendicular skeleton https://github.com/obophenotype/uberon/issues/59 paired fin skeleton skeleton appendiculare Wikipedia:Appendicular_skeleton Cardiac septum which separates the right ventricle from the left ventricle.[FMA]. The partition separating the right and left ventricles of the heart. [TFD][VHOG] The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) BTO:0002483 EFO:0001956 EHDAA:2603 EMAPA:17333 FMA:7133 MA:0000085 NCIT:C32874 SCTID:362019005 UMLS:C0225870 VHOG:0000386 Wikipedia:Interventricular_septum galen:InterventricularSeptum heart interventricular septum heart ventricular septum uberon interventricular septum of heart interventriculare cordis intraventricular septum s. interventriculare cordis septum inferius septum membranaceum ventricle septum ventricular septum UBERON:0002094 interventricular septum http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb Cardiac septum which separates the right ventricle from the left ventricle.[FMA]. FMA:7133 The partition separating the right and left ventricles of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000386 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/interventricular+septum The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] 2012-09-17 VHOG:0000386 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430 http://bgee.unil.ch/ involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) ISBN:0124020607 UMLS:C0225870 ncithesaurus:Interventricular_Septum heart interventricular septum MA:0000085 heart ventricular septum MA:0000085 interventricular septum of heart BTO:0002483 interventriculare cordis BTO:0002483 intraventricular septum Wikipedia:Interventricular_septum s. interventriculare cordis Wikipedia:Interventricular_septum septum inferius Wikipedia:Interventricular_septum septum membranaceum Wikipedia:Interventricular_septum ventricular septum MA:0000085 Wikipedia:Interventricular_septum Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon. mesenteric in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery. AAO:0011061 BTO:0001380 EV:0100083 FMA:7144 GAID:21 MESH:D008643 NCIT:C33103 SCTID:362707009 UMLS:C0025474 Wikipedia:Mesentery#Mesentery_.28general.29 galen:Mesentery generic mesentery mesentery (generic) uberon UBERON:0002095 mesentery http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png PMID:28192867 Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon. FMA:7144 Wikipedia:Mesentery Wikipedia:Mesentery#Mesentery_.28general.29 https://github.com/obophenotype/uberon/issues/85 in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery. FMA UMLS:C0025474 ncithesaurus:Mesentery generic mesentery Wikipedia:Mesentery mesentery (generic) Wikipedia:Mesentery The organ covering the body that consists of the dermis and epidermis. consider 'integumentary system' for invertebrates MA uses the term skin to refer to what is called here: zone of skin BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:D012867 MFMO:0000099 NCIT:C12470 SCTID:181469002 UMLS:C1123023 Wikipedia:Skin XAO:0000023 galen:Skin entire skin skin organ uberon entire integument integument integumental organ pelt skin UBERON:0002097 skin of body http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Skin.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb Wikipathways:WP2062 The organ covering the body that consists of the dermis and epidermis. UBERON:cjm MA uses the term skin to refer to what is called here: zone of skin FMA UMLS:C1123023 ncithesaurus:Skin The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. 'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations' in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this EMAPA:35400 FMA:7180 GAID:562 MA:0000083 MESH:D006346 NCIT:C49485 SCTID:362014000 UMLS:C0018819 cardiac septa heart septa heart septum septum of heart uberon spiral septa UBERON:0002099 cardiac septum The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. MESH:A07.541.459 in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this GO UMLS:C0018819 ncithesaurus:Heart_Septum cardiac septa heart septa spiral septa XAO:0004141 Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 CALOHA:TS-1071 EFO:0000966 EMAPA:31857 FMA:7181 MA:0000004 MAT:0000296 MIAA:0000296 NCIT:C33816 SCTID:262225004 TAO:0001115 UMLS:C0460005 Wikipedia:Torso XAO:0000054 XAO:0003025 ZFA:0001115 galen:Trunk thoracolumbar region torso trunk region uberon Rumpf UBERON:0002100 trunk Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. TAO:0001115 UBERONREF:0000006 Wikipedia:Torso ZFA https://github.com/obophenotype/uberon/issues/378 pending Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] 2012-06-20 AAO:0010339 AAO AAO:BJB Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] 2012-08-14 TAO:0001115 TAO ZFIN:curator UMLS:C0460005 ncithesaurus:Trunk trunk region XAO:0000054 Rumpf BTO:0001493 The sensory system subserving the sense of vision. The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 FMA:7191 MA:0002444 NCIT:C12888 SCTID:281831001 TAO:0001127 UMLS:C0587900 Wikipedia:Visual_system XAO:0003198 ZFA:0001127 http://uri.neuinfo.org/nif/nifstd/FMAID_7191 photosensory system visual organ system uberon UBERON:0002104 visual system The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 The sensory system used for sight.[AAO] 2012-06-20 AAO:0000632 AAO AAO:EJS UMLS:C0587900 ncithesaurus:Visual_System photosensory system BILA:0000140 Sensory system responsible for the perception of spatial orientation and auditory stimuli. The sensory system used for balance and hearing.[AAO] AAO:0000631 EMAPA:36002 EMAPA:37985 FMA:78500 TAO:0001138 XAO:0003195 ZFA:0001138 auditory organ system vestibuloauditory system uberon auditory system auditory/vestibular system vestibuloauditory system UBERON:0002105 vestibulo-auditory system http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg Sensory system responsible for the perception of spatial orientation and auditory stimuli. ZFA:0001138 The sensory system used for balance and hearing.[AAO] 2012-06-20 AAO:0000631 AAO AAO:EJS EMAPA:37985 MA:th The organ that functions to filter blood and to store red corpuscles and platelets. An organ involved in red blood cell filtration and immune response.[AAO] With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG] lienal splenic In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells AAO:0010395 BTO:0001281 CALOHA:TS-0956 EFO:0000869 EMAPA:18767 EV:0100055 FMA:7196 GAID:1289 MA:0000141 MAT:0000085 MESH:D013154 MIAA:0000085 NCIT:C12432 SCTID:181279003 TAO:0000436 UMLS:C0037993 VHOG:0000120 Wikipedia:Spleen XAO:0000328 ZFA:0000436 galen:Spleen uberon lien UBERON:0002106 spleen https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Spleen.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spleen.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg multiple sources - true spleen appear in jawed vertebrates The organ that functions to filter blood and to store red corpuscles and platelets. ISBN:0-683-40008-8 MP:0000689 An organ involved in red blood cell filtration and immune response.[AAO] 2012-06-20 AAO:0010395 AAO AAO:BMZ With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG] 2012-09-17 VHOG:0000120 VHOG ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94 http://bgee.unil.ch/ Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) PMID:20959416 UMLS:C0037993 ncithesaurus:Spleen lien Wikipedia:Spleen An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Organ which secretes bile and participates in formation of certain blood proteins.[AAO] relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] hepatic An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. AAO:0010111 BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 NCIT:C12392 SCTID:181268008 TAO:0000123 UMLS:C0023884 VHOG:0000257 Wikipedia:Liver XAO:0000133 ZFA:0000123 galen:Liver uberon iecur jecur UBERON:0002107 liver https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg BTO EHDAA2 GO-def ZFA ZFA-weakened EHDAA2 http://www.stembook.org/node/512 An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. BTO:0000759 Wikipedia:Liver Organ which secretes bile and participates in formation of certain blood proteins.[AAO] 2012-06-20 AAO:0010111 AAO AAO:BJB relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] 2012-06-20 AAO:0010111 AAO All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000257 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. ZFA UMLS:C0023884 ncithesaurus:Liver iecur Wikipedia:Liver jecur Wikipedia:Liver Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010397 BTO:0000651 CALOHA:TS-0942 EFO:0000841 EMAPA:32834 EV:0100072 FMA:7200 GAID:313 MA:0000337 MAT:0000047 MESH:D007421 MIAA:0000047 NCIT:C12386 SCTID:181250005 TAO:0001323 UMLS:C0021852 VHOG:0000055 Wikipedia:Small_intestine XAO:0000130 ZFA:0001323 galen:SmallIntestine small bowel small intestine uberon anterior intestine intestinum tenue mid intestine UBERON:0002108 small intestine http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb 2 cjm Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. ISBN:0073040584 Wikipedia:Small_intestine The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0001323 TAO ZFIN:curator Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000055 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 http://bgee.unil.ch/ UMLS:C0021852 ncithesaurus:Small_Intestine intestinum tenue BTO:0000651 Wikipedia:Small_intestine An organ that aids digestion and stores bile produced by the liver[WP]. Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO] relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG] AAO:0010114 BTO:0000493 CALOHA:TS-0394 EFO:0000853 EHDAA2:0000699 EHDAA:8062 EMAPA:17202 EV:0100090 FMA:7202 MA:0000356 MAT:0000072 MESH:D005704 MIAA:0000072 NCIT:C12377 SCTID:181269000 TAO:0000208 UMLS:C0016976 VHOG:0000221 Wikipedia:Gallbladder XAO:0000135 ZFA:0000208 galen:Gallbladder cholecyst gall bladder uberon vesica biliaris vesica fellea UBERON:0002110 Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988) gallbladder https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg BTO definitional An organ that aids digestion and stores bile produced by the liver[WP]. Wikipedia:Gallbladder ISBN:9780120749034 GOC:mr ISBN:9781840761122 GOC:mr ISBN:9781840761122 Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000221 VHOG http://bgee.unil.ch/ Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO] 2012-06-20 AAO:0010114 AAO AAO:BJB relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] 2012-06-20 AAO:0010114 AAO The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG] 2012-09-17 VHOG:0000221 VHOG DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997) http://bgee.unil.ch/ UMLS:C0016976 ncithesaurus:Gallbladder cholecyst WikipediaVersioned:Gallbladder&oldid=1092217922 vesica biliaris Wikipedia:Gallbladder vesica fellea Wikipedia:Gallbladder A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. BTO:0000087 CALOHA:TS-1198 EMAPA:36285 FMA:72024 MA:0000708 NCIT:C49195 UMLS:C1706851 arterial smooth muscle artery smooth muscle artery smooth muscle tissue smooth muscle of artery uberon arterial smooth muscle cell UBERON:0002111 artery smooth muscle tissue A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. OBOL:automatic UMLS:C1706851 ncithesaurus:Artery_Smooth_Muscle_Tissue arterial smooth muscle BTO:0000087 smooth muscle of artery FMA:72024 arterial smooth muscle cell BTO:0000087 A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]. EMAPA:35323 FMA:72025 MA:0001573 esophageal smooth muscle esophagus involuntary muscle esophagus non-striated muscle esophagus smooth muscle esophagus smooth muscle tissue gullet involuntary muscle gullet non-striated muscle gullet smooth muscle gullet smooth muscle tissue involuntary muscle of esophagus involuntary muscle of gullet involuntary muscle of oesophagus non-striated muscle of esophagus non-striated muscle of gullet non-striated muscle of oesophagus oesophagus involuntary muscle oesophagus non-striated muscle oesophagus smooth muscle tissue smooth muscle of gullet smooth muscle of oesophagus smooth muscle tissue of esophagus smooth muscle tissue of gullet smooth muscle tissue of oesophagus uberon oesophagus smooth muscle UBERON:0002112 smooth muscle of esophagus A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus involuntary muscle OBOL:automatic esophagus non-striated muscle OBOL:automatic esophagus smooth muscle tissue OBOL:automatic gullet involuntary muscle OBOL:automatic gullet non-striated muscle OBOL:automatic gullet smooth muscle OBOL:automatic gullet smooth muscle tissue OBOL:automatic involuntary muscle of esophagus OBOL:automatic involuntary muscle of gullet OBOL:automatic involuntary muscle of oesophagus OBOL:automatic non-striated muscle of esophagus OBOL:automatic non-striated muscle of gullet OBOL:automatic non-striated muscle of oesophagus OBOL:automatic oesophagus involuntary muscle OBOL:automatic oesophagus non-striated muscle OBOL:automatic oesophagus smooth muscle tissue OBOL:automatic smooth muscle of gullet OBOL:automatic smooth muscle of oesophagus OBOL:automatic smooth muscle tissue of esophagus OBOL:automatic smooth muscle tissue of gullet OBOL:automatic smooth muscle tissue of oesophagus OBOL:automatic The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] duodenal In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. AAO:0010402 BTO:0000365 CALOHA:TS-0214 EFO:0000851 EMAPA:18852 EV:0100073 FMA:7206 GAID:284 MA:0000338 MAT:0000044 MESH:D004386 MIAA:0000044 NCIT:C12263 SCTID:181247007 UMLS:C0013303 VHOG:0000052 Wikipedia:Duodenum XAO:0000236 galen:Duodenum uberon proximal intestine upper intestine UBERON:0002114 duodenum http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb 3 cjm The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). ISBN:0815318960 Wikipedia:Duodenum ZFA:0000348 The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000052 VHOG http://bgee.unil.ch/ In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. NCBITaxon:32443 Wikipedia:Duodenum In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. NCBITaxon:9606 Wikipedia:Duodenum UMLS:C0013303 ncithesaurus:Duodenum proximal intestine BTO:0000365 upper intestine BTO:0000365 An ovary that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37367 FMA:7213 MA:0001705 NCIT:C33487 SCTID:280123002 UMLS:C0227873 uberon UBERON:0002118 right ovary An ovary that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37367 MA:th UMLS:C0227873 ncithesaurus:Right_Ovary An ovary that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo EMAPA:37366 FMA:7214 MA:0001704 NCIT:C32969 SCTID:280124008 UMLS:C0227874 uberon UBERON:0002119 left ovary An ovary that is part of a left side of organism [Automatically generated definition]. OBOL:automatic In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo Wikipedia:Ovary#In_other_animals EMAPA:37366 MA:th UMLS:C0227874 ncithesaurus:Left_Ovary A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718] The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates. BAMS:SOC BIRNLEX:1307 DHBA:12462 EMAPA:35840 EV:0100263 FMA:72247 HBA:9177 MA:0001026 MBA:398 MESH:D065832 UMLS:C0175427 VHOG:0001381 Wikipedia:Superior_olivary_complex neuronames:569 nucleus olivaris superior superior olivary nuclei uberon regio olivaris superioris superior olivary nucleus superior olivary nucleus (Barr & Kiernan) superior olive UBERON:0002128 superior olivary complex http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png NIFSTD A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. ISBN:0-19-502694-2 Wikipedia:Superior_olivary_complex ABA ABA ABA MESH:D065832 https://github.com/biopragmatics/biomappings UMLS:C0175427 BIRNLEX:1307 neuronames:569 BIRNLEX:1307 nucleus olivaris superior FMA:72247 FMA:TA superior olivary nuclei FMA:72247 regio olivaris superioris NeuroNames:569 superior olivary nucleus FMA:72247 superior olivary nucleus (Barr & Kiernan) NeuroNames:569 superior olive FMA:72247 ISBN:0-19-502694-2 The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. TODO - check ZFA/pons. also GO says part of dorsorostral pons BAMS:CAE BAMS:LC BIRNLEX:905 BM:Pons-LC BTO:0001408 DHBA:12819 DMBA:16972 EFO:0001963 EMAPA:35502 FMA:72478 GAID:577 HBA:9148 MA:0001017 MBA:147 MESH:D008125 NCIT:C97333 SCTID:369016004 TAO:0000539 UMLS:C0023951 Wikipedia:Locus_ceruleus ZFA:0000539 neuronames:583 Noradrenergic cell group A6 blue nucleus caerulean nucleus locus caeruleus locus coeruleu locus coeruleus nucleus caeruleus nucleus of locus caeruleus nucleus pigmentosus pontis substantia ferruginea uberon loci coeruleus locus cinereus locus coeruleus (Vicq d'Azyr) nucleus loci caerulei UBERON:0002148 locus ceruleus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png check ZFA NIFSTD The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. GAID:577 GO:0021703 Wikipedia:Locus_ceruleus ABA ABA ABA ABA UMLS:C0023951 BIRNLEX:905 ncithesaurus:Locus_Coeruleus neuronames:583 BIRNLEX:905 Noradrenergic cell group A6 Noradrenergic_cell_group_A6&oldid=981960774 blue nucleus BIRNLEX:905 locus caeruleus BIRNLEX:905 nucleus caeruleus FMA:72478 FMA:TA nucleus pigmentosus pontis BIRNLEX:905 substantia ferruginea BIRNLEX:905 loci coeruleus ZFA:0000539 locus cinereus BTO:0001408 locus coeruleus (Vicq d'Azyr) NeuroNames:583 nucleus loci caerulei NeuroNames:583 Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BAMS:SSN BAMS:SuS BIRNLEX:1131 DHBA:12435 EHDAA2:0004646 EMAPA:37756 FMA:72482 HBA:9194 MA:0001027 MBA:462 SCTID:369028007 UMLS:C0175447 Wikipedia:Superior_salivatory_nucleus neuronames:590 superior salivary nucleus uberon nucleus salivarius superior nucleus salivatorius cranialis nucleus salivatorius rostralis nucleus salivatorius superior UBERON:0002149 superior salivatory nucleus http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png definitional Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BIRNLEX:1131 ABA ABA ABA ABA ABA ABA ABA ABA ABA EMAPA:37756 MA:th UMLS:C0175447 BIRNLEX:1131 neuronames:590 BIRNLEX:1131 superior salivary nucleus GO:0021753 nucleus salivarius superior NeuroNames:590 nucleus salivatorius cranialis NeuroNames:590 nucleus salivatorius rostralis NeuroNames:590 nucleus salivatorius superior NeuroNames:590 The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. Layer that lines the lumen of the heart.[TAO] Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. UBERON:0006225 AAO:0010408 BTO:0000387 CALOHA:TS-2075 EFO:0000821 EHDAA2:0004153 EMAPA:17868 EMAPA:32686 EV:0100021 FMA:7280 GAID:550 MA:0000076 MAT:0000455 MESH:D004699 NCIT:C13004 SCTID:362013006 TAO:0001320 UMLS:C0014124 VHOG:0000084 Wikipedia:Endocardium XAO:0000066 ZFA:0001320 galen:Endocardium endocardial lining endocardial tissue heart endocardium uberon heart endocardial tissue UBERON:0002165 fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 endocardium http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png Bgee:AN The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. GO:0003157 Layer that lines the lumen of the heart.[TAO] 2012-08-14 TAO:0001320 TAO ZFIN:curator Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] 2012-06-20 AAO:0010408 AAO AAO:BJB Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. FMA:7280 UMLS:C0014124 ncithesaurus:Endocardium endocardial lining EMAPA:32686 endocardial tissue EMAPA:17868 heart endocardial tissue VHOG:0000084 Endocardium that is part of the atrium. EMAPA:32745 FMA:7284 MA:0000077 SCTID:192001005 TAO:0002169 VHOG:0000606 ZFA:0001614 Cardiac atria endocardium atrial endocardium atrium endocardium atrium of heart endocardium cardiac atrium endocardium endocardium of Cardiac atria endocardium of atrium of heart endocardium of cardiac atrium endocardium of heart atrium heart atrium endocardium uberon atrium endocardial tissue UBERON:0002166 endocardium of atrium Endocardium that is part of the atrium. ZFIN:curator Cardiac atria endocardium OBOL:automatic atrium of heart endocardium OBOL:automatic cardiac atrium endocardium OBOL:automatic endocardium of Cardiac atria OBOL:automatic endocardium of atrium of heart OBOL:automatic endocardium of cardiac atrium OBOL:automatic endocardium of heart atrium OBOL:automatic heart atrium endocardium OBOL:automatic atrium endocardial tissue VHOG:0000606 Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]. Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 MA:0000426 NCIT:C33483 SCTID:361967000 UMLS:C0225706 VHOG:0000301 Wikipedia:Right_lung uberon UBERON:0002167 right lung http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]. FMA:FMA Wikipedia:Right_lung Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000301 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 http://bgee.unil.ch/ UMLS:C0225706 ncithesaurus:Right_Lung Lung which consists of the left upper lobe and left lower lobe.[FMA]. Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000943 EHDAA:4947 EMAPA:17653 FMA:7310 MA:0000425 NCIT:C32967 SCTID:361982005 UMLS:C0225730 VHOG:0000618 Wikipedia:Left_lung uberon UBERON:0002168 left lung http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb Lung which consists of the left upper lobe and left lower lobe.[FMA]. FMA:FMA Wikipedia:Left_lung Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000618 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 http://bgee.unil.ch/ UMLS:C0225730 ncithesaurus:Left_Lung A portion of adipose tissue that is part of the hypodermis, beneath the dermis. the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] UBERON:0008875 panniculus adiposus BTO:0004042 EMAPA:35829 FMA:74315 MA:0000473 MESH:D015434 fatty layer of subcutaneous tissue hypodermis fat layer panniculus adiposus (tela subcutanea) panniculus adiposus telae subcutaneae subcutaneous fat layer uberon fatty layer of superficial fascia subcutaneous fat UBERON:0002190 subcutaneous adipose tissue A portion of adipose tissue that is part of the hypodermis, beneath the dermis. http://orcid.org/0000-0002-6601-2165 the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] MP:0011156 panniculus adiposus MP:0011156 MESH:D015434 https://github.com/biopragmatics/biomappings fatty layer of subcutaneous tissue FMA:74315 hypodermis fat layer MP:0011156 panniculus adiposus (tela subcutanea) FMA:74315 FMA:TA panniculus adiposus telae subcutaneae FMA:74315 FMA:TA subcutaneous fat layer MP:0011156 fatty layer of superficial fascia FMA:74315 subcutaneous fat BTO:0004042 Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. CALOHA:TS-2018 EHDAA2:0004615 EMAPA:18765 FMA:74562 MA:0000013 hematolymphoid system lymphomyeloid complex uberon haemolymphoid system UBERON:0002193 hemolymphoid system MA Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. http://orcid.org/0000-0002-6601-2165 The dermis, epidermis and hypodermis. in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition. Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] Surface structure that is the outer protective covering of the body.[VSAO] The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] integumental integumentary AAO:0000239 BTO:0000634 EMAPA:37504 FMA:74657 TAO:0000368 VSAO:0000029 Wikipedia:Integument ZFA:0000368 galen:Integument dermis plus epidermis plus hypodermis integumentum commune skin and subcutaneous tissue skin plus hypodermis the integument uberon dermal system dermoid system skin tegument vertebrate integument UBERON:0002199 integument FMA FMA The dermis, epidermis and hypodermis. Wikipedia:Integument Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] 2012-06-20 AAO:0000239 AAO AAO:EJS Surface structure that is the outer protective covering of the body.[VSAO] 2012-08-14 VSAO:0000029 VSAO PSPUB:0000170 The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000368 TAO ZFIN:curator EMAPA:37504 MA:th integumentum commune FMA:74657 FMA:TA the integument FMA:74657 dermal system BTO:0000634 dermoid system BTO:0000634 tegument BTO:0000634 Vasculature that is part of a head [Automatically generated definition]. EFO:0003656 FMA:74710 TAO:0001267 XAO:0004152 ZFA:0001267 adult head vascular network adult head vasculature cranial vasculature head vascular network vascular network of adult head vascular network of head vasculature of adult head uberon head vasculature UBERON:0002200 vasculature of head Vasculature that is part of a head [Automatically generated definition]. OBOL:automatic adult head vascular network OBOL:automatic adult head vasculature OBOL:automatic head vascular network OBOL:automatic vascular network of adult head OBOL:automatic vascular network of head OBOL:automatic vasculature of adult head OBOL:automatic A vasculature that is part of a trunk [Automatically generated definition]. FMA:74712 TAO:0005024 ZFA:0005024 torso vascular network torso vasculature trunk vascular network trunk vasculature vascular network of torso vascular network of trunk vasculature of torso uberon UBERON:0002201 vasculature of trunk A vasculature that is part of a trunk [Automatically generated definition]. OBOL:automatic torso vascular network OBOL:automatic torso vasculature OBOL:automatic trunk vascular network OBOL:automatic vascular network of torso OBOL:automatic vascular network of trunk OBOL:automatic vasculature of torso OBOL:automatic Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA FMA:74743 SCTID:123846009 TAO:0007057 ZFA:0007057 eye vascular network ocular blood vessel ocular vasculature vascular network of eye uberon eye vasculature optic vasculature UBERON:0002203 vasculature of eye https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb ISBN:0781772214 Vasculature that is part of the eye region. OBOL:automatic https://sourceforge.net/tracker/?func=detail&aid=3489658&group_id=76834&atid=994726 not part of the eye in ZFA. Note this changed to a blood vessel in ZFA ZFA eye vascular network OBOL:automatic ocular blood vessel ZFA:0007057 vascular network of eye OBOL:automatic Anatomical system that consists of the muscular and skeletal systems. Anatomical system that provides locomotion and physical support to the organism.[AAO] There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 EV:0100139 FMA:7482 GAID:98 MA:0002418 MESH:D009141 NCIT:C12754 SCTID:278858007 UMLS:C0026860 VHOG:0001275 VSAO:0000031 Wikipedia:Musculoskeletal_system XAO:0000168 musculo-skeletal system uberon UBERON:0002204 musculoskeletal system check ctenophore Anatomical system that consists of the muscular and skeletal systems. VSAO:0000031 VSAO:curator https://github.com/obophenotype/uberon/issues/77 Anatomical system that provides locomotion and physical support to the organism.[AAO] 2012-06-20 AAO:0010546 AAO AAO:EJS There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] 2012-09-17 VHOG:0001275 VHOG DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) http://bgee.unil.ch/ UMLS:C0026860 ncithesaurus:Musculoskeletal_System Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]. EMAPA:36581 FMA:7496 MA:0000320 SCTID:58442004 TAO:0005155 Wikipedia:Cartilaginous_joint ZFA:0005155 articulatio cartilaginea uberon junctura cartilaginea UBERON:0002213 cartilaginous joint FMA Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]. FMA:FMA Wikipedia:Cartilaginous_joint junctura cartilaginea Wikipedia:Cartilaginous_joint Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]. Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 FMA:7501 MA:0000322 NCIT:C32461 SCTID:113234001 TAO:0005153 Wikipedia:Synovial_joint ZFA:0005153 galen:SynovialJoint articulatio synoviale diarthroses diarthrosis diarthrosis joint uberon diarthrodial joints UBERON:0002217 synovial joint Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]. FMA:7501 Wikipedia:Synovial_joint Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] 2012-08-14 TAO:0005153 TAO ZFIN:Curator diarthroses ZFA:0005153 diarthrodial joints ZFA:0005153 The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 MA:0000032 MESH:D035423 NCIT:C12905 SCTID:243949006 UMLS:C0230139 Wikipedia:Thoracic_cavity cavitas thoracis cavity of chest cavity of thorax chest cavity pectoral cavity space of thoracic compartment thoracic lumen uberon UBERON:0002224 thoracic cavity http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. UBERON:cjm Wikipedia:Thoracic_cavity UMLS:C0230139 ncithesaurus:Thoracic_Cavity cavitas thoracis Wikipedia:Thoracic_cavity space of thoracic compartment FMA:7565 Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). TODO - add superclass to unify with VNC? Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010151 BAMS:SP BAMS:Spinal BIRNLEX:1709 BM:SpC BTO:0001279 CALOHA:TS-0953 DHBA:12890 DMBA:17651 EFO:0000110 EHDAA2:0001255 EHDAA:2863 EMAPA:17577 EV:0100316 FMA:7647 GAID:695 MA:0000216 MAT:0000183 MESH:D013116 MIAA:0000183 NCIT:C12464 SCTID:180959008 TAO:0000075 UMLS:C0037925 VHOG:0000601 Wikipedia:Spinal_cord XAO:0000020 ZFA:0000075 neuronames:22 uberon SpC cerebro-cerebellar fissure cerebrocerebellar fissure fissura cerebro-cerebellaris fissura cerebrocerebellaris medulla spinalis spinal cord structure spinal medulla UBERON:0002240 spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb ZFA definitional definitional Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). BIRNLEX:1709 ZFA https://github.com/obophenotype/uberon/issues/378 pending Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] 2012-06-20 AAO:0010151 AAO AAO:BJB (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000601 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 http://bgee.unil.ch/ UMLS:C0037925 BIRNLEX:1709 ncithesaurus:Spinal_Cord neuronames:22 BIRNLEX:1709 SpC cerebro-cerebellar fissure NeuroNames:22 cerebrocerebellar fissure NeuroNames:22 fissura cerebro-cerebellaris NeuroNames:22 fissura cerebrocerebellaris NeuroNames:22 medulla spinalis BTO:0001279 Wikipedia:Spinal_cord spinal cord structure ZFA:0000075 spinal medulla BTO:0001279 Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal) Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] chondrocranial covers the brain dorsally in chondrichthyans AAO:0010169 EHDAA2:0000243 EMAPA:17681 TAO:0001424 VHOG:0000288 Wikipedia:Chondrocranium ZFA:0001424 uberon calvarium neurocranium UBERON:0002241 chondrocranium Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. Wikipedia:Chondrocranium http://medical-dictionary.thefreedictionary.com/chondrocranium Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] 2012-06-20 AAO:0010169 AAO AAO:BJB Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] 2012-08-14 TAO:0001424 TAO ZFIN:curator calvarium MA:0000317 neurocranium MA:0000317 The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO]. The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord]. BAMS:VH BIRNLEX:2668 BTO:0005151 EMAPA:18575 EMAPA:35794 FMA:256541 MA:0001134 NCIT:C33859 SCTID:279443000 TAO:0000702 UMLS:C0228569 UMLS:C0228590 VHOG:0001288 Wikipedia:Anterior_horn_of_spinal_cord ZFA:0000702 neuronames:1751 anterior gray column of spinal cord anterior gray horn of spinal cord anterior grey column of spinal cord anterior horn columna grisea anterior medullae spinalis spinal cord anterior horn spinal cord ventral horn ventral gray column of spinal cord ventral gray matter of spinal cord ventral grey column of spinal cord ventral grey horn ventral horn spinal cord ventral region of spinal cord ventral spinal cord uberon anterior column anterior column of the spinal cord anterior horn (spinal cord) cornu anterius medullae spinalis ventral horn of the spinal cord ventral horns spinal cord UBERON:0002257 ventral horn of spinal cord FMA-abduced-lr The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO]. GO:0021517 MP:0005112 Wikipedia:Anterior_horn_of_spinal_cord https://sourceforge.net/tracker/?group_id=36855&atid=440764 The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord]. Wikipedia:Anterior_horn_of_spinal_cord UMLS:C0228569 BIRNLEX:2668 UMLS:C0228590 ncithesaurus:Ventral_Horn_of_the_Spinal_Cord anterior gray column of spinal cord FMA:256541 anterior gray horn of spinal cord FMA:256541 anterior horn BIRNLEX:2668 columna grisea anterior medullae spinalis FMA:256541 FMA:TA spinal cord anterior horn BIRNLEX:2668 ventral gray column of spinal cord FMA:256541 ventral gray matter of spinal cord FMA:256541 ventral grey horn BIRNLEX:2668 ventral horn spinal cord ZFA:0000702 anterior column Wikipedia:Anterior_horn_of_spinal_cord anterior column of the spinal cord Wikipedia:Anterior_horn_of_spinal_cord anterior horn (spinal cord) Wikipedia:Anterior_horn_of_spinal_cord cornu anterius medullae spinalis Wikipedia:Anterior_horn_of_spinal_cord ventral horn of the spinal cord BAMS:VH ventral horns spinal cord VHOG:0001288 A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation. It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain. FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure BAMS:RET EMAPA:35188 FMA:77719 MA:0003185 MESH:D012154 NLX:143558 SCTID:361552007 Wikipedia:Reticular_formation neuronames:1223 brain stem reticular formation brainstem reticular formation reticular formation (classical) reticular formation of the brainstem uberon UBERON:0002275 reticular formation http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). NeuroNames:1223 FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure FMA brain stem reticular formation NeuroNames:1223 brainstem reticular formation MA:0003185 NeuroNames:1223 reticular formation (classical) NeuroNames:1223 reticular formation of the brainstem NeuroNames:1223 Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). FMA:79646 GAID:279 MA:0001273 MESH:D001659 NCIT:C12678 SCTID:361354009 Wikipedia:Biliary_system biliary apparatus uberon biliary tract UBERON:0002294 biliary system http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). Wikipedia:Biliary_system biliary apparatus FMA:79646 biliary tract FMA:79646 MA:0001273 The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]. The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO] EHDAA2:0004560 EHDAA:3019 EHDAA:3033 EHDAA:3921 EHDAA:3934 EHDAA:3957 EHDAA:3971 FMA:79795 SCTID:308823000 TAO:0005130 Wikipedia:Mesentery#Development ZFA:0005130 uberon dorsal mesogastrium mesenterium dorsale commune UBERON:0002296 dorsal mesentery http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png EHDAA2 The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]. Wikipedia:Dorsal_mesentery Wikipedia:Mesentery#Development ZFIN:curator The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO] 2012-08-14 TAO:0005130 TAO ZFIN:curator dorsal mesogastrium Wikipedia:Dorsal_mesentery mesenterium dorsale commune Wikipedia:Dorsal_mesentery Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] BAMS:BS BIRNLEX:1565 BTO:0000146 CALOHA:TS-0093 EFO:0001962 EMAPA:32678 EV:0100241 FMA:79876 MA:0000169 MBA:343 MESH:D001933 NCIT:C12441 SCTID:180925009 TAO:0002156 UMLS:C0006121 VHOG:0001457 Wikipedia:Brainstem ZFA:0001707 neuronames:236 brain stem truncus encephali uberon accessory medullary lamina of pallidum lamella pallidi incompleta lamina medullaris accessoria lamina medullaris incompleta pallidi lamina pallidi incompleta truncus encephalicus UBERON:0002298 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). brainstem http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. ISBN:0471888893 MP:0005277 Wikipedia:Brainstem ZFA:0001707 we apply a strict definition ZFA ABA https://github.com/obophenotype/uberon/issues/378 pending we apply a strict definition Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] 2012-08-14 TAO:0002156 TAO ISBN:3764351209 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. ZFA:0001707 the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] MP:0005277 UMLS:C0006121 BIRNLEX:1565 ncithesaurus:Brain_Stem neuronames:236 BIRNLEX:1565 brain stem ABA:BS truncus encephali Wikipedia:Brainstem accessory medullary lamina of pallidum NeuroNames:236 lamella pallidi incompleta NeuroNames:236 lamina medullaris accessoria NeuroNames:236 lamina medullaris incompleta pallidi NeuroNames:236 lamina pallidi incompleta NeuroNames:236 truncus encephalicus BTO:0000146 The atrial part of middle layer of the heart, comprised of involuntary muscle. As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003087 EMAPA:32746 FMA:83509 MA:0000081 SCTID:191910002 TAO:0001374 VHOG:0000602 ZFA:0001374 atrial myocardium atrium myocardium uberon atrium cardiac muscle UBERON:0002302 myocardium of atrium The atrial part of middle layer of the heart, comprised of involuntary muscle. ISBN:0-683-40008-8 MP:0010493 As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000602 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ atrial myocardium ZFA:0001374 atrium cardiac muscle VHOG:0000602 A neural nucleus that is part of the brain. EMAPA:35185 FMA:83840 MA:0000811 NCIT:C49346 SCTID:426465002 UMLS:C1706993 ZFA:0005575 brain nucleus uberon brain nuclei UBERON:0002308 nucleus of brain A neural nucleus that is part of the brain. http://orcid.org/0000-0002-6601-2165 UMLS:C1706993 ncithesaurus:Brain_Nucleus brain nuclei ZFA:0005575 The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. BAMS:Scgrey DHBA:146035048 EMAPA:35792 FMA:256580 MA:0000002 NCIT:C32696 NLXANAT:100204 SCTID:279441003 UMLS:C0475853 neuronames:2619 gray matter of spinal cord gray substance of spinal cord grey matter of spinal cord grey substance of spinal cord spinal cord gray matter spinal cord grey matter spinal cord grey substance substantia grisea medullae spinalis uberon UBERON:0002315 gray matter of spinal cord The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. MP:0008503 UMLS:C0475853 ncithesaurus:Gray_Matter_of_the_Spinal_Cord gray matter of spinal cord OBOL:automatic gray substance of spinal cord FMA:256580 spinal cord gray matter OBOL:automatic spinal cord grey substance OBOL:automatic substantia grisea medullae spinalis FMA:256580 FMA:TA The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 SCTID:361348008 TAO:0001438 UMLS:C0333343 ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen main body cavity space of body compartment ventral body cavity uberon celom coelom coelome hemocoel UBERON:0002323 EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen definitional The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. 2012-09-12 ZFA:0001438 ZFA ZFIN:curator The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. 2012-09-12 BTO:0001707 BTO BTO body cavity BTO:0001707 FBbt:00005060 UMLS:C0333343 ncithesaurus:Cavity coelomic cavity EHDAA2:0000267 coelomic cavity lumen EHDAA2:0000267 space of body compartment FMA:85006 ventral body cavity NCBITaxon:7742 celom BTO:0001707 coelome BTO:0001707 hemocoel FBbt:00005060 Any muscle organ that is part of a back [Automatically generated definition]. EMAPA:35161 FMA:85216 MA:0000496 back muscle back muscle organ muscle organ of back uberon UBERON:0002324 muscle of back prolog Any muscle organ that is part of a back [Automatically generated definition]. OBOL:automatic back muscle organ OBOL:automatic muscle organ of back OBOL:automatic A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] notochordal In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 EHDAA2:0001277 EHDAA:1241 EHDAA:6021 EMAPA:16191 EV:0100002 FMA:85521 GAID:1311 MAT:0000281 MESH:D009672 NCIT:C12463 SCTID:308820002 TAO:0000135 UMLS:C0028439 VHOG:0000199 VSAO:0000032 Wikipedia:Notochord XAO:0000055 ZFA:0000135 http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg embryonic notocord notocord uberon notochorda UBERON:0002328 The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png PMID:15890825 VSAO http://tolweb.org/Chordata/2499 ZFA EHDAA2 A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. ISBN:0815318960 Wikipedia:Notochord http://tolweb.org/Chordata/2499 https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] 2012-08-14 VSAO:0000032 VSAO PSPUB:0000170 Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000135 TAO ZFIN:curator Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] 2012-06-20 AAO:0000327 AAO AAO:LAP relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] 2012-06-20 AAO:0000327 AAO (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000199 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ UMLS:C0028439 ncithesaurus:Notochord notocord ZFA:0000135 notochorda Wikipedia:Notochord Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] somitic mesodermal cluster AAO:0010569 AEO:0001015 BTO:0001558 EHDAA2:0003436 EHDAA:366 EHDAA:699 EMAPA:31169 FMA:85522 GAID:1306 MAT:0000068 MESH:D019170 MIAA:0000068 NCIT:C34302 TAO:0000155 UMLS:C0376449 VHOG:0000191 Wikipedia:Somite XAO:0000058 ZFA:0000155 uberon epimere epimere mesoderm epithelial somite somites somitic mesoderm somitus UBERON:0002329 When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 GOTAX:0000352 ZFA Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. DOI:10.1111/j.1439-0426.2012.01987.x Wikipedia:Somite PMID:17237766 Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] 2012-06-20 AAO:0010569 AAO AAO:EJS Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000155 TAO ZFIN:curator relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] 2012-06-20 AAO:0010569 AAO (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000191 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) http://bgee.unil.ch/ mesodermal cluster GO:0001756 UMLS:C0376449 ncithesaurus:Somite epimere ISBN:0073040584 epithelial somite https://github.com/obophenotype/uberon/wiki/The-neural-crest somites somitus Wikipedia:Somite Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. CALOHA:TS-2057 EHDAA2:0002225 EMAPA:35329 FMA:85539 MA:0002411 NCIT:C12957 UMLS:C1516995 Wikipedia:Exocrine_gland WikipediaCategory:Exocrine_system exocrine glandular system uberon UBERON:0002330 exocrine system Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. Wikipedia:Exocrine_gland UMLS:C1516995 ncithesaurus:Exocrine_System exocrine glandular system EHDAA2:0002225 An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] EHDAA2:0001576 EHDAA:9831 EMAPA:17015 FMA:8612 MA:0002033 NCIT:C116918 VHOG:0001134 galen:PulmonaryTrunk pulmonary artery (trunk) trunk of pulmonary arterial tree uberon main pulmonary artery UBERON:0002333 pulmonary trunk https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png MA An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. http://orcid.org/0000-0002-6601-2165 An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] 2012-09-17 VHOG:0001134 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+trunk As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] 2012-09-17 VHOG:0001134 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ main pulmonary artery Wikipedia:Pulmonary_artery A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 EHDAA2:0004419 EMAPA:32737 FMA:86666 GAID:1310 MAT:0000066 MESH:D009432 MIAA:0000066 NCIT:C34222 SCTID:361462002 TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest XAO:0000048 ZFA:0000045 neuronames:1366 NC uberon crista neuralis neural crest material UBERON:0002342 Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. neural crest http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 BTO PMID:11523831 pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest PMID:11523831 A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 ISBN:0073040584 PMID:17377535 A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000045 TAO ZFIN:curator Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] 2012-06-20 AAO:0010578 AAO AAO:EJS A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] PMID:11523831 We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] 2012-09-17 VHOG:0000057 VHOG DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) http://bgee.unil.ch/ UMLS:C0027789 ncithesaurus:Neural_Crest NC XAO:0000048 crista neuralis Wikipedia:Neural_crest neural crest material VHOG:0000057 Set of all muscles in abdomen. distinction between abdomen muscle and abdomen musculature FMA:71294 FMA:86917 TAO:0001327 ZFA:0001327 abdominal musculature muscle group of abdomen muscles of abdomen musculature of abdomen musculature of abdominal wall set of muscles of abdomen uberon UBERON:0002343 abdomen musculature Set of all muscles in abdomen. OBOL:automatic muscle group of abdomen FMA:71294 muscles of abdomen FMA:71294 musculature of abdominal wall FMA:86917 set of muscles of abdomen FMA:71294 The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest. EFO:0002527 EMAPA:18605 FMA:87217 MA:0002572 SCTID:181301002 uberon UBERON:0002345 descending thoracic aorta The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest. MP:0009868 Embryonic ectoderm that gives rise to nervous tissue. (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] neurectodermal we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 EHDAA2:0001248 EHDAA:1498 EHDAA:255 EMAPA:16073 EV:0100004 FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 NCIT:C34228 TAO:0001120 UMLS:C1518271 VHOG:0000150 Wikipedia:Neuroectoderm XAO:0000042 ZFA:0001120 neural ectoderm neuroectoderm uberon epithelium tubi neuralis; neuroectoderma neuaral ectoderm presumptive central nervous system ventral neurogenic region UBERON:0002346 neurectoderm Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] 2012-09-17 VHOG:0000150 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ FBbt:00001057 UMLS:C1518271 ncithesaurus:Neuroectoderm epithelium tubi neuralis; neuroectoderma Wikipedia:Neuroectoderm ventral neurogenic region VHOG:0000150 A thoracic vertebra endochondral element that is composed primarily of a bone tissue. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs EMAPA:18011 FMA:9139 GAID:244 MA:0000314 MESH:D013904 NCIT:C12798 SCTID:181821009 UMLS:C0039987 Wikipedia:Thoracic_vertebrae dorsal vertebra thorax vertebra vertebra of thorax vertebra thoracica uberon UBERON:0002347 thoracic vertebra http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png A thoracic vertebra endochondral element that is composed primarily of a bone tissue. OBOL:automatic UMLS:C0039987 ncithesaurus:Thoracic_Vertebra thorax vertebra OBOL:automatic vertebra of thorax OBOL:automatic A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. External layer of the heart.[TAO] The inner layer of the pericardium that is in contact with the surface of the heart.[AAO] The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium] AAO:0010409 EHDAA2:0002202 FMA:9461 NCIT:C13164 TAO:0005057 UMLS:C0225968 VHOG:0000119 Wikipedia:Epicardium XAO:0000316 ZFA:0005057 galen:Epicardium heart epicardium visceral serous pericardium of heart visceral serous pericardium proper uberon pericardium visceral mesothelium UBERON:0002348 EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer. epicardium multiple FMA-inferred FMA A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. http://orcid.org/0000-0002-6601-2165 External layer of the heart.[TAO] 2012-08-14 TAO:0005057 TAO ZFIN:curator The inner layer of the pericardium that is in contact with the surface of the heart.[AAO] 2012-06-20 AAO:0010409 AAO AAO:BJB UMLS:C0225968 ncithesaurus:Epicardium visceral serous pericardium of heart FMA:9461 visceral serous pericardium proper FMA:9461 pericardium visceral mesothelium EMAPA:16589 The middle layer of the heart, comprised mainly of striated cardiac muscle fibers. Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The middle layer of the heart, consisting of cardiac muscle.[AAO] myocardial AAO:0010410 BSA:0000089 BTO:0000901 CALOHA:TS-0440 EFO:0000819 EHDAA2:0004150 EMAPA:32688 EV:0100022 FMA:9462 GAID:173 MA:0000164 MAT:0000453 MESH:D009206 NCIT:C12371 RETIRED_EHDAA2:0001220 SCTID:362012001 TAO:0001319 UMLS:C0027061 VHOG:0000083 Wikipedia:Myocardium XAO:0000065 ZFA:0001319 galen:Myocardium heart myocardium muscle of heart uberon cardiac muscle heart muscle UBERON:0002349 EDITOR_NOTE TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium myocardium http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg The middle layer of the heart, comprised mainly of striated cardiac muscle fibers. ISBN:0-683-40008-8 MP:0005329 Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000083 VHOG http://bgee.unil.ch/ The middle layer of the heart, consisting of cardiac muscle.[AAO] 2012-06-20 AAO:0010410 AAO AAO:BJB UMLS:C0027061 ncithesaurus:Myocardium muscle of heart FMA:9462 cardiac muscle ZFA:0001319 heart muscle FMA:9462 ZFA:0001319 The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]. EHDAA2 divides the system from the tissue The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] EFO:0003909 EHDAA2:0004185 EMAPA:35428 EV:0100025 FMA:9476 MA:0000094 MESH:D006329 SCTID:281489000 TAO:0005063 VHOG:0001271 ZFA:0005063 cardiac conducting system cardiac conduction system cardiac impulse conducting system cardionector complexus stimulans cordis heart conduction system impulse conducting system systema conducente cordis uberon central conduction system UBERON:0002350 conducting system of heart FMA FMA FMA FMA FMA FMA The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]. GO:0003161 The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] 2012-09-17 VHOG:0001271 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) http://bgee.unil.ch/ cardiac conducting system VHOG:0001271 cardiac impulse conducting system GO:0003161 complexus stimulans cordis FMA:9476 FMA:TA heart conduction system GO:0003161 impulse conducting system MA:0000094 systema conducente cordis FMA:9476 FMA:TA The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. BTO:0004358 EHDAA2:0004184 EMAPA:35772 FMA:9477 GAID:561 MA:0000097 MESH:D012849 NCIT:C33555 SCTID:277687007 TAO:0005069 UMLS:C0037189 Wikipedia:Sinoatrial_node ZFA:0005069 Koch's node SA nodal muscle tissue SA node cardiac pacemaker node of Keith-Flack nodus sinuatrialis sinoatrial node sinu-atrial node sinuatrial nodal muscle tissue sinuatrial node sinus node sinus node of Keith and Flack uberon nodus sinuatrialis UBERON:0002351 WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node. sinoatrial node http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg cjm ZFA The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. GO:0003163 Wikipedia:Sinoatrial_node UMLS:C0037189 ncithesaurus:Sinoatrial_Node Koch's node FMA:9477 SA nodal muscle tissue FMA:9477 SA node FMA:9477 cardiac pacemaker FMA:9477 node of Keith-Flack FMA:9477 nodus sinuatrialis FMA:9477 FMA:TA sinoatrial node FMA:9477 sinu-atrial node FMA:9477 sinuatrial nodal muscle tissue FMA:9477 sinuatrial node FMA:9477 sinus node FMA:9477 sinus node of Keith and Flack FMA:9477 nodus sinuatrialis Wikipedia:Sinoatrial_node An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles. Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG] BTO:0005689 EFO:0000276 EHDAA2:0004183 EMAPA:35153 FMA:9478 GAID:558 MA:0000095 MAT:0000498 MESH:D001283 NCIT:C32161 SCTID:277688002 TAO:0005070 UMLS:C0004247 VHOG:0001474 Wikipedia:Atrioventricular_node ZFA:0005070 AV nodal muscle tissue AV node Aschoff-Tawara node atrioventricular nodal muscle tissue node of Tawara nodus atrioventricularis uberon A-V node atrio-ventricular node atriovetricular node downstream pacemaker nodus atrioventricularis UBERON:0002352 atrioventricular node http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png cjm An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles. UBERON:cjm Wikipedia:Atrioventricular_node Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG] 2012-09-17 VHOG:0001474 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) http://bgee.unil.ch/ UMLS:C0004247 ncithesaurus:Atrioventricular_Node AV nodal muscle tissue FMA:9478 AV node FMA:9478 MA:0000095 Aschoff-Tawara node FMA:9478 atrioventricular nodal muscle tissue FMA:9478 node of Tawara FMA:9478 nodus atrioventricularis FMA:TA A-V node EMAPA:35153 atrio-ventricular node EMAPA:35153 atriovetricular node TAO:0005070 downstream pacemaker ZFA:0005070 nodus atrioventricularis Wikipedia:Atrioventricular_node The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle. UBERON:0004147 BTO:0001735 EMAPA:35718 FMA:9492 GAID:560 MA:0000096 MESH:D011690 NCIT:C33430 UMLS:C0034144 Wikipedia:Purkinje_fiber Purkinje fiber cardiac Purkinje fiber myofibra conducens cardiacus subendocardial branch uberon heart Purkinje fiber UBERON:0002354 cardiac Purkinje fiber http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png FMA https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 FMA The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle. GO:0003165 UMLS:C0034144 ncithesaurus:Purkinje_Fiber Purkinje fiber FMA:9492 MA:0000096 cardiac Purkinje fiber BTO:0001735 GO:0003165 myofibra conducens cardiacus subendocardial branch Wikipedia:Purkinje_fiber heart Purkinje fiber BTO:0001735 The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. pelvic MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs BTO:0001006 CALOHA:TS-2227 EFO:0002805 EMAPA:35931 EV:0100012 FMA:9578 GAID:87 MA:0000030 MESH:D010388 NCIT:C12767 SCTID:229765004 UMLS:C0030797 Wikipedia:Pelvis galen:Pelvis lesser pelvis pelvic region pelvis pelvis region true pelvis uberon UBERON:0002355 pelvic region of trunk The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. Wikipedia:Pelvis http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/720 MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs MA UMLS:C0030797 ncithesaurus:Pelvis lesser pelvis FMA:9578 pelvis FMA:9578 MA:0000030 true pelvis FMA:9578 Serous membrane which is divided into parietal and visceral serous pericardium. EMAPA:19030 FMA:9582 MA:0002739 SCTID:243954002 Wikipedia:Serous_pericardium serous portion of pericardium uberon pericardium serosum UBERON:0002357 serous pericardium FMA FMA Serous membrane which is divided into parietal and visceral serous pericardium. Wikipedia:Serous_pericardium http://orcid.org/0000-0002-6601-2165 serous portion of pericardium FMA:9582 pericardium serosum Wikipedia:Serous_pericardium A serous membrane that lines the peritoneal cavity[VHOG,modified]. TODO - in ZFA is_a epithelium An epithelium that lines the peritoneal cavity.[TAO] Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] peritoneal todo: check MA/EMAPA. AAO:0010814 BTO:0001472 CALOHA:TS-2072 EV:0100087 FMA:9584 GAID:18 MA:0000449 MESH:D010537 NCIT:C12770 TAO:0005120 UMLS:C0031153 VHOG:0001257 Wikipedia:Peritoneum XAO:0000139 ZFA:0005120 galen:Peritoneum uberon peritonaeum UBERON:0002358 peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png MP A serous membrane that lines the peritoneal cavity[VHOG,modified]. VHOG:0001257 An epithelium that lines the peritoneal cavity.[TAO] 2012-08-14 TAO:0005120 TAO ZFIN:curator Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] 2012-06-20 AAO:0010814 AAO AAO:JMG todo: check MA/EMAPA. MA UMLS:C0031153 ncithesaurus:Peritoneum peritonaeum VHOG:0001257 Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]. most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium] EMAPA:19029 FMA:9586 MA:0002738 SCTID:243953008 Wikipedia:Fibrous_pericardium fibrous portion of pericardium uberon pericardium fibrosum UBERON:0002359 fibrous pericardium FMA FMA WP Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]. FMA:9586 pericardium fibrosum Wikipedia:Fibrous_pericardium A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas. Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses AEO:0000097 BTO:0000765 CALOHA:TS-2012 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 NCIT:C12712 SCTID:115976003 UMLS:C0015282 Wikipedia:Exocrine_gland ducted gland glandula exocrina uberon UBERON:0002365 exocrine gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas. Wikipedia:Exocrine_gland UMLS:C0015282 ncithesaurus:Exocrine_Gland ducted gland AEO:0000097 glandula exocrina Wikipedia:Exocrine_gland Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 FMA:9602 GAID:335 MA:0002563 MESH:D004702 NCIT:C12704 SCTID:40818001 UMLS:C0014133 Wikipedia:Endocrine_gland ductless gland glandula endocrina uberon ductless gland glandulae endocrinae UBERON:0002368 endocrine gland http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. Wikipedia:Endocrine_gland UMLS:C0014133 ncithesaurus:Endocrine_Gland ductless gland AEO:0000098 ductless gland Wikipedia:Ductless_gland glandulae endocrinae Wikipedia:Endocrine_gland The soft tissue that fills the cavities of bones. TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs consider placement of NCIT:C53466 medullary bone The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] AAO:0011007 BTO:0000141 BTO:0000829 CALOHA:TS-0087 EFO:0000868 EMAPA:32760 EV:0100046 FMA:9608 GAID:1287 MA:0000134 MAT:0000084 MESH:D001853 MIAA:0000084 NCIT:C12431 SCTID:421320006 UMLS:C0005953 VHOG:0001218 Wikipedia:Bone_marrow XAO:0000123 galen:BoneMarrow medulla ossea medulla ossium uberon medulla of bone medullary bone UBERON:0002371 bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg FMA MA The soft tissue that fills the cavities of bones. MGI:cwg MP:0002397 The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] 2012-09-17 VHOG:0001218 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) http://bgee.unil.ch/ UMLS:C0005953 ncithesaurus:Bone_Marrow medulla ossea BTO:0000141 FMA:9608 medulla ossium BTO:0000141 Wikipedia:Bone_marrow medulla of bone BTO:0000141 Any skeletal muscle that is part of the head region. UBERON:0003899 AAO:0000107 BTO:0000021 EFO:0003524 EHDAA2:0000322 EMAPA:18172 FMA:9616 MA:0000578 SCTID:244718003 ZFA:0001652 cephalic muscle cephalic musculature head muscle head muscle organ muscle of head muscle organ of adult head muscle organ of head musculus caput adult head muscle organ uberon cranial muscle head muscles UBERON:0002376 defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) cranial muscle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships EHDAA2-abduced Any skeletal muscle that is part of the head region. http://orcid.org/0000-0002-6601-2165 cephalic muscle ZFA:0001652 head muscle MA:0000578 head muscle organ OBOL:automatic muscle of head FMA:9616 muscle organ of adult head OBOL:automatic muscle organ of head OBOL:automatic adult head muscle organ OBOL:automatic cranial muscle ZFA:0001652 Any muscle that is part of the cervical (neck) region. EMAPA:36050 FMA:9617 GAID:149 MA:0000587 MESH:D009334 NCIT:C33163 UMLS:C0027532 muscle organ of neck muscle organ of neck (volume) neck (volume) muscle organ neck muscle neck muscle organ uberon UBERON:0002377 muscle of neck prolog Any muscle that is part of the cervical (neck) region. http://orcid.org/0000-0002-6601-2165 UMLS:C0027532 ncithesaurus:Neck_Muscle muscle organ of neck OBOL:automatic muscle organ of neck (volume) OBOL:automatic neck (volume) muscle organ OBOL:automatic neck muscle organ OBOL:automatic Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. BTO:0001261 EMAPA:35103 FMA:9620 GAID:89 MA:0000520 MESH:D000009 NCIT:C32040 SCTID:361352008 UMLS:C0000739 Wikipedia:Abdominal_muscle abdomen muscle abdomen muscle organ abdominal muscle abdominal wall muscle muscle organ of abdomen uberon abdominal wall musculature UBERON:0002378 muscle of abdomen prolog Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. Wikipedia:Abdominal_muscle UMLS:C0000739 ncithesaurus:Abdominal_Muscle abdomen muscle organ OBOL:automatic muscle organ of abdomen OBOL:automatic abdominal wall musculature EMAPA:35103 Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 NCIT:C12374 SCTID:361919005 TAO:0001641 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus uberon Bindegewebe UBERON:0002384 connective tissue Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. GO_REF:0000034 PSPUB:0000170 VSAO:0000017 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] 2012-06-20 AAO:0000098 AAO AAO:LAP Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] 2012-08-14 TAO:0001641 TAO TAO:wd Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] 2012-08-14 VSAO:0000017 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 MA also has set of connective tissues MA UMLS:C0009780 ncithesaurus:Connective_Tissue portion of connective tissue FMA:9640 Bindegewebe BTO:0000421 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 NCIT:C12435 SCTID:91727004 UMLS:C2328219 Wikipedia:Muscle_tissue galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis uberon UBERON:0002385 Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. muscle tissue Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. GO:0060537 Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] 2012-06-20 AAO:0000306 AAO AAO:LAP UMLS:C2328219 ncithesaurus:Muscle_Tissue muscular tissue portion of muscle tissue FMA:9641 Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] hematopoietic In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 NCIT:C12909 SCTID:362587009 TAO:0005023 UMLS:C0018957 VHOG:0001624 Wikipedia:Haematopoiesis XAO:0000122 ZFA:0005023 haematological system haemopoietic system organa haemopoietica uberon Blutbildungssystem haematopoietic system hematological system hematolymphoid system hemopoietic system UBERON:0002390 hematopoietic system FMA definitional Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis Anatomical system that consists of the blood and blood forming tissues.[AAO] 2012-06-20 AAO:0011002 AAO AAO:EJS Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] 2012-09-17 VHOG:0001624 VHOG DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) http://bgee.unil.ch/ In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes WP UMLS:C0018957 ncithesaurus:Hematopoietic_System Blutbildungssystem BTO:0000570 Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. A duct that carries bile from the liver to the intestine. Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA AAO:0011019 BTO:0000122 CALOHA:TS-0075 EHDAA2:0000741 EMAPA:35171 EV:0100091 FMA:9706 GAID:280 MA:0000354 MESH:D001652 NCIT:C12376 SCTID:276157007 TAO:0001100 UMLS:C0005400 VHOG:0000212 Wikipedia:Bile_duct XAO:0000134 ZFA:0001100 uberon bile tube biliary duct gall duct hepatic duct UBERON:0002394 bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png EMAPA MA XAO Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. Wikipedia:Bile_duct http://orcid.org/0000-0002-6601-2165 A duct that carries bile from the liver to the intestine. ZFA:0001100, ZFA:curator Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] 2012-09-17 VHOG:0000212 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/bile+duct (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] 2012-09-17 VHOG:0000212 VHOG DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) http://bgee.unil.ch/ we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA ZFA UMLS:C0005400 ncithesaurus:Bile_Duct biliary duct FMA:9706 gall duct BTO:0000122 hepatic duct ZFA:0001100 The triangular flat bone of the nasal septum. Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO] Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO] relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO] relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO] In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP] The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO] AAO:0000633 FMA:9710 MA:0001496 MESH:D055172 NCIT:C33888 SCTID:272678009 TAO:0000308 UMLS:C0242403 Wikipedia:Vomer ZFA:0000308 vomer bone uberon prevomer UBERON:0002396 vomer http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg FMA The triangular flat bone of the nasal septum. ISBN:0-683-40008-8 MP:0000098 Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO] 2012-08-14 TAO:0000308 TAO ZFIN:curator Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO] 2012-06-20 AAO:0000633 AAO AAO:LAP relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO] 2012-08-14 TAO:0000308 TAO relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO] 2012-08-14 TAO:0000308 TAO In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP] Wikipedia:Vomer#In_other_animals The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO] 2012-09-06 TAO:0000308 TAO Curator MESH:D055172 https://github.com/biopragmatics/biomappings UMLS:C0242403 ncithesaurus:Vomer prevomer TAO:0000308 The outer serous membrane of the pulmonary pleural. EMAPA:16776 FMA:9733 MA:0002488 NCIT:C33273 SCTID:361998003 UMLS:C0225777 VHOG:0001495 Wikipedia:Parietal_pleura uberon pleura parietalis UBERON:0002400 the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax parietal pleura The outer serous membrane of the pulmonary pleural. UBERON:cjm Wikipedia:Pulmonary_pleurae UMLS:C0225777 ncithesaurus:Parietal_Pleura pleura parietalis Wikipedia:Parietal_pleura The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. FMA treats this as part of the lungs EHDAA2:0002205 EMAPA:16777 FMA:9734 MA:0002489 NCIT:C33881 SCTID:361997008 UMLS:C0225776 VHOG:0001496 pleura pulmonalis pleura visceralis pleura visceralis (pulmonalis) pulmonary visceral pleura uberon lung mesothelium lung pleura pulmonary pleura UBERON:0002401 visceral pleura FMA The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. UBERON:cjm Wikipedia:Pulmonary_pleurae Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. Wikipedia:Visceral_pleura FMA treats this as part of the lungs FMA UMLS:C0225776 ncithesaurus:Visceral_Pleura pleura pulmonalis FMA:9734 FMA:TA pleura visceralis Wikipedia:Visceral_pleura lung mesothelium EHDAA2:0002205 pulmonary pleura FMA:9734 The fluid-filled cavity that lies between the visceral and parietal pleurae. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 BTO:0004422 EHDAA2:0001475 EMAPA:16773 EMAPA:16774 FMA:9740 GAID:95 MA:0000055 MESH:D035422 NCIT:C12840 SCTID:361999006 UMLS:C0178802 VHOG:0000581 Wikipedia:Pleural_cavity cavitas pleuralis uberon cavitum pleuralae cavitum pleurale UBERON:0002402 pleural cavity http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png Wikipedia The fluid-filled cavity that lies between the visceral and parietal pleurae. Wikipedia:Pleural_cavity https://github.com/obophenotype/uberon/issues/86 In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000581 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 EHDAA2 UMLS:C0178802 ncithesaurus:Pleural_Cavity cavitas pleuralis Wikipedia:Pleural_cavity cavitum pleuralae Wikipedia:Pleural_cavity cavitum pleurale Wikipedia:Pleural_cavity Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 FMA:9825 GAID:328 MA:0002711 MESH:D007107 NCIT:C12735 SCTID:362590003 TAO:0001159 UMLS:C0020962 VHOG:0001247 Wikipedia:Immune_system XAO:0003152 ZFA:0001159 uberon UBERON:0002405 immune system Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. Wikipedia:Immune_system The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] 2012-09-17 VHOG:0001247 VHOG PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010) http://bgee.unil.ch/ UMLS:C0020962 ncithesaurus:Immune_System A double-walled sac containing the heart and the roots of the great vessels. FMA:9868 RETIRED_EHDAA2:0001443 SCTID:361326002 TAO:0000054 uberon pericardium UBERON:0002406 pericardial sac http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png FMA A double-walled sac containing the heart and the roots of the great vessels. Wikipedia:Pericardium https://github.com/obophenotype/uberon/issues/86 The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. Peritoneum that surrounds the heart.[AAO] pericardial In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO) we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium AAO:0010817 BSA:0000090 BTO:0000717 CALOHA:TS-0761 EFO:0000820 EHDAA:5376 EMAPA:16133 EV:0100023 FMA:9869 GAID:569 MA:0000099 MAT:0000454 MESH:D010496 NCIT:C13005 RETIRED_EHDAA2:0001443 SCTID:181295003 TAO:0000054 UMLS:C0031050 VHOG:0001280 Wikipedia:Pericardium XAO:0004182 ZFA:0000054 galen:Pericardium uberon UBERON:0002407 pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png MA The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. Wikipedia:Pericardium http://orcid.org/0000-0002-6601-2165 Peritoneum that surrounds the heart.[AAO] 2012-06-20 AAO:0010817 AAO AAO:JMG In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity FMA this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO) ZFA we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium FMA UMLS:C0031050 ncithesaurus:Pericardium Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. EHDAA:3422 EHDAA:5378 EMAPA:19031 FMA:9870 MA:0000483 NCIT:C94500 SCTID:243956000 UMLS:C0225969 VHOG:0000537 Wikipedia:Parietal_pericardium lamina parietalis (pericardii serosum) lamina parietalis pericardii parietal layer of serous pericardium parietal pericardium uberon pericardial sac UBERON:0002408 parietal serous pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. http://orcid.org/0000-0002-6601-2165 UMLS:C0225969 ncithesaurus:Parietal_Pericardium lamina parietalis pericardii FMA:9870 FMA:TA parietal pericardium VHOG:0000537 pericardial sac DOI:10.5962/bhl.title.1013 Transudate contained in the pericardial cavity.[FMA]. BTO:0001016 FMA:9887 MA:0002530 MESH:D000069236 Wikipedia:Pericardial_fluid uberon UBERON:0002409 pericardial fluid FMA Transudate contained in the pericardial cavity.[FMA]. FMA:9887 Wikipedia:Pericardial_fluid MESH:D000069236 https://github.com/biopragmatics/biomappings The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib AAO:0000033 BIRNLEX:1123 BTO:0002507 CALOHA:TS-2001 EHDA:10095 EHDAA2:0000158 EHDAA:3767 EMAPA:16984 FMA:65553 GAID:706 IDOMAL:0002126 MA:0000219 MESH:D001341 NCIT:C12673 SCTID:362481007 TAO:0001574 UMLS:C0004388 UMLS:C1305381 VHOG:0000396 Wikipedia:Autonomic_nervous_system ZFA:0001574 neuronames:2054 autonomic division of peripheral nervous system autonomic part of peripheral nervous system divisio autonomica systematis nervosi peripherici pars autonomica systematis nervosi peripherici peripheral autonomic nervous system visceral nervous system uberon ANS divisio autonomica systematis nervosi peripherici UBERON:0002410 autonomic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png cjm EMAPA MA NIFSTD ZFA-modified-from-isa The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. GO:0048483 Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000396 VHOG http://bgee.unil.ch/ Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] 2012-06-20 AAO:0000033 AAO AAO:BJB From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] 2012-09-17 VHOG:0000396 VHOG DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000) http://bgee.unil.ch/ FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib FMA IDOMAL:0002126 https://github.com/biopragmatics/biomappings UMLS:C0004388 BIRNLEX:1123 ncithesaurus:Autonomic_Nervous_System UMLS:C1305381 BIRNLEX:1123 autonomic division of peripheral nervous system FMA:65553 autonomic part of peripheral nervous system FMA:65553 divisio autonomica systematis nervosi peripherici FMA:TA pars autonomica systematis nervosi peripherici FMA:TA peripheral autonomic nervous system FMA:65553 ANS divisio autonomica systematis nervosi peripherici Wikipedia:Autonomic_nervous_system The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. Consider changing name to make distinction from inferred superclass 'vertebral element' clear we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO] Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO] AAO:0000691 BTO:0006196 CALOHA:TS-2352 EFO:0001371 EMAPA:32740 FMA:9914 MA:0000309 NCIT:C12933 SCTID:181817002 TAO:0001189 UMLS:C0549207 Wikipedia:Vertebra XAO:0004019 ZFA:0001189 galen:Vertebra vertebra bone vertebrae uberon UBERON:0002412 vertebra FMA The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 Wikipedia Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO] 2012-08-14 TAO:0001189 TAO ZFIN:curator Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO] 2012-06-20 AAO:0000691 AAO AAO:Pugener_and_Maglia_2008 BTO:0006196 https://github.com/biopragmatics/biomappings UMLS:C0549207 ncithesaurus:Vertebra vertebrae PHENOSCAPE:ad A vertebra that is located in the cervical region of the vertebral column. In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery. EMAPA:17674 FMA:9915 GAID:235 MA:0000311 MESH:D002574 NCIT:C12693 SCTID:181820005 Wikipedia:Cervical_vertebrae XAO:0003076 galen:CervicalVertebra cervical vertebrae uberon vertebrae cervicales UBERON:0002413 cervical vertebra http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg true A vertebra that is located in the cervical region of the vertebral column. http://orcid.org/0000-0002-6601-2165 cervical vertebrae vertebrae cervicales Wikipedia:Cervical_vertebrae An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin AEO:0000109 BILA:0000117 BTO:0001348 EFO:0000963 EHDAA:9198 GAID:1245 MAT:0000094 MESH:D013623 MIAA:0000094 WBbt:0005741 Wikipedia:Tail caudal subdivision uberon UBERON:0002415 tail An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. AEO:0000109 Wikipedia:Tail caudal subdivision https://orcid.org/0000-0002-6601-2165 Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] UBERON:0007029 AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 EFO:0000807 EHDAA2:0000836 EHDAA2_RETIRED:0003154 EHDAA:6520 EMAPA:17524 EV:0100151 FBbt:00004969 FMA:72979 HAO:0000421 MA:0000014 MAT:0000033 MESH:D034582 MIAA:0000033 NCIT:C12907 SCTID:361692004 TADS:0000108 UMLS:C0037267 VHOG:0000403 Wikipedia:Integumentary_system XAO:0000176 galen:Surface integumentary system uberon body surface dermal system external covering of organism integumentum commune organism surface surface UBERON:0002416 integumental system Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. CARO:0002001 http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/29 (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] 2012-09-17 VHOG:0000403 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) http://bgee.unil.ch/ FBbt:00004969 UMLS:C0037267 ncithesaurus:Integumentary_System integumentary system FMA:72979 dermal system MIAA:0000033 integumentum commune Wikipedia:Integumentary_system organism surface EHDAA2:0003154 surface BILA:0000118 The abdominal segment of the torso. EMAPA:35104 FMA:259211 MA:0000021 SCTID:362875007 Wikipedia:Lumbar uberon abdomen/pelvis/perineum lower body lower trunk lumbar region UBERON:0002417 abdominal segment of trunk FMA The abdominal segment of the torso. Wikipedia:Lumbar abdomen/pelvis/perineum MA:0000021 lower body MA:0000021 lower trunk FMA:259211 lumbar region https://orcid.org/0000-0002-6601-2165 Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] AAO:0000060 AEO:0000087 BTO:0000206 EFO:0000949 EHDAA2:0003087 EMAPA:32730 EV:0100141 FMA:37377 GAID:99 MA:0000104 MAT:0000189 MESH:D002356 MIAA:0000189 NCIT:C12373 NCIT:C32268 SCTID:309312004 TAO:0001501 UMLS:C0007301 VHOG:0001207 VSAO:0000040 Wikipedia:Cartilage XAO:0000170 ZFA:0005622 galen:Cartilage cartilage tissue cartilaginous tissue chondrogenic tissue uberon cartilage cartilages portion of cartilage tissue UBERON:0002418 Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W] cartilage tissue http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg https://github.com/obophenotype/uberon/issues/117 Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000040 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/37 https://sourceforge.net/p/obo/vertebrate-skeletal-anatomy-vsao-term-requests/5 A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] 2012-06-20 AAO:0000060 AAO AAO:LAP Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] 2012-08-14 TAO:0001501 TAO ZFIN:curator Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] 2012-08-14 VSAO:0000040 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000060 AAO Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] 2012-09-17 VHOG:0001207 VHOG DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012) http://bgee.unil.ch/ UMLS:C0007301 ncithesaurus:Cartilage cartilage tissue FMA:37377 chondrogenic tissue VSAO:0000040 cartilages VHOG:0001207 portion of cartilage tissue FMA:37377 A gland that is part of a skin of body [Automatically generated definition]. check FMA, use plural for now as general class not there EMAPA:35774 FMA:71878 MA:0000146 SCTID:110485007 glandulae cutis uberon set of skin glands skin glands skin glands set UBERON:0002419 skin gland A gland that is part of a skin of body [Automatically generated definition]. OBOL:automatic glandulae cutis FMA:71878 FMA:TA set of skin glands FMA:71878 skin glands skin glands set The part of the digestive system that contains the liver and the biliary system. System responsible for the production and movement of bile[ZFIN:curator]. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008] AAO:0011056 CALOHA:TS-1308 EFO:0000800 EHDAA2:0000998 EHDAA:2189 EMAPA:16840 EV:0100088 MA:0000324 MAT:0000024 MIAA:0000024 NCIT:C43612 TAO:0000036 UMLS:C1711359 VHOG:0000294 Wikipedia:Hepatobiliary_system XAO:0000132 ZFA:0000036 hepaticobiliary system liver and biliary system uberon liver/biliary system UBERON:0002423 hepatobiliary system The part of the digestive system that contains the liver and the biliary system. http://orcid.org/0000-0002-6601-2165 System responsible for the production and movement of bile[ZFIN:curator]. ZFIN:curator UMLS:C1711359 ncithesaurus:Hepatobiliary_System hepaticobiliary system GO:0061008 An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues. consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme AAO:0010357 BTO:0001775 CALOHA:TS-0715 EHDAA2:0001325 EHDAA:2187 EMAPA:16839 EMAPA:26942 FMA:265152 MA:0000344 NCIT:C49595 TAO:0000816 UMLS:C1709332 VHOG:0000187 XAO:0003201 ZFA:0000816 epithelium of mucosa of mouth epithelium of oral mucosa uberon UBERON:0002424 oral epithelium AAO-modified An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues. https://orcid.org/0000-0002-6601-2165 The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. ZFA:0000816 the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme PMID:16488870 UMLS:C1709332 ncithesaurus:Oral_Cavity_Epithelium epithelium of mucosa of mouth FMA:265152 epithelium of oral mucosa FMA:265152 Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. EMAPA:16589 EMAPA:19032 FMA:84882 MA:0000484 SCTID:243955001 VHOG:0000538 Wikipedia:Visceral_pericardium lamina visceralis pericardii serosi serous visceral pericardium visceral lamina of serous pericardium visceral layer of serous pericardium visceral pericardium uberon epicardium pericardium visceral mesothelium UBERON:0002425 visceral serous pericardium cjm FMA Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. Wikipedia:Visceral_pericardium lamina visceralis pericardii serosi Wikipedia:Epicardium visceral pericardium VHOG:0000538 epicardium MA:0000484 pericardium visceral mesothelium EMAPA:16589 A blood vessel that is part of a choroid [Automatically generated definition]. EMAPA:17828 FMA:76550 MA:0001237 blood vessel of choroid blood vessel of choroid coat blood vessel of choroidea blood vessel of posterior uvea choroid blood vessel choroid blood vessels choroid blood vessels set choroid coat blood vessel choroidea blood vessel posterior uvea blood vessel vasa sanguinea choroideae uberon set of choroid blood vessels UBERON:0002443 cannot find singular in FMA, using Set class choroidal blood vessel A blood vessel that is part of a choroid [Automatically generated definition]. OBOL:automatic blood vessel of choroid OBOL:automatic blood vessel of choroid coat OBOL:automatic blood vessel of choroidea OBOL:automatic blood vessel of posterior uvea OBOL:automatic choroid blood vessel OBOL:automatic choroid coat blood vessel OBOL:automatic choroidea blood vessel OBOL:automatic posterior uvea blood vessel OBOL:automatic vasa sanguinea choroideae FMA:76550 FMA:TA set of choroid blood vessels FMA:76550 The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries. Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061]. Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG] UBERON:0006001 EHDAA2:0000882 EHDAA:4340 EMAPA:17616 MA:0001985 SCTID:360401001 TAO:0001061 VHOG:0000225 XAO:0004165 ZFA:0001061 intersegmental artery uberon intersegmental arteries UBERON:0002457 intersomitic artery The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries. MP:0010662 Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061]. ZFA:0001061 Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG] 2012-09-17 VHOG:0000225 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612 http://bgee.unil.ch/ intersegmental artery ZFA:0001061 intersegmental arteries ZFA:0001061 Arteries that supply the spinal cord. EHDAA2:0001890 EHDAA:4355 EMAPA:18241 MA:0002043 NCIT:C33587 SCTID:244228006 TAO:0000682 UMLS:C0447043 Wikipedia:Spinal_artery ZFA:0000682 spinal arteries uberon UBERON:0002458 spinal artery Arteries that supply the spinal cord. Wikipedia:Spinal_artery https://orcid.org/0000-0002-6601-2165 UMLS:C0447043 ncithesaurus:Spinal_Artery spinal arteries ZFA:0000682 Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. BTO:0000644 FMA:62974 GAID:1162 MA:0002515 MESH:D007419 NCIT:C32875 UMLS:C0021849 Wikipedia:Succus_entericus intestinal secretion succus entericus uberon intestinal juice UBERON:0002466 intestine secretion Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. Wikipedia:Succus_entericus UMLS:C0021849 ncithesaurus:Intestinal_Secretion intestinal secretion FMA:62974 succus entericus Wikipedia:Succus_entericus intestinal juice BTO:0000644 A mucosa that is part of a esophagus [Automatically generated definition]. UBERON:0003345 BTO:0002859 EMAPA:26981 FMA:62996 MA:0002680 MESH:D000071041 NCIT:C32538 SCTID:362127004 UMLS:C0227176 esophageal mucosa esophageal mucous membrane esophagus mucosa esophagus mucous membrane lamina muscularis mucosae oesophageae mucosa of esophagus mucosa of oesophagus mucous membrane of esophagus mucous membrane of oesophagus oesophageal mucosa oesophagus mucosa oesophagus mucous membrane tunica mucosa esophagi tunica mucosa oesophageae tunica mucosa oesophagi uberon muscularis mucosae of oesophagus tunica mucosa oesophagi UBERON:0002469 esophagus mucosa A mucosa that is part of a esophagus [Automatically generated definition]. OBOL:automatic MESH:D000071041 https://github.com/biopragmatics/biomappings UMLS:C0227176 ncithesaurus:Esophageal_Mucosa esophagus mucosa FMA:62996 esophagus mucous membrane OBOL:automatic lamina muscularis mucosae oesophageae FMA:62996 FMA:TA mucosa of esophagus OBOL:automatic mucosa of oesophagus OBOL:automatic mucous membrane of oesophagus FMA:62996 oesophageal mucosa FMA:62996 oesophagus mucous membrane OBOL:automatic tunica mucosa oesophageae FMA:62996 FMA:TA muscularis mucosae of oesophagus FMA:62996 tunica mucosa oesophagi BTO:0002859 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 MA:0002780 MESH:D001842 NCIT:C13076 UMLS:C0391978 VSAO:0000047 Wikipedia:Bone_tissue XAO:0004040 ZFA:0005621 galen:BoneTissue calcium tissue osseous tissue osteogenic tissue mineralized bone tissue uberon bone portion of bone tissue UBERON:0002481 bone tissue VSAO https://github.com/obophenotype/uberon/issues/117 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000047 http://dx.plos.org/10.1371/journal.pone.0051070 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] 2012-08-14 VSAO:0000047 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 UMLS:C0391978 ncithesaurus:Bone_Tissue osteogenic tissue VSAO:curator mineralized bone tissue XAO:0004040 bone MESH:A02.835.232 portion of bone tissue FMA:224804 An epithelium that is part of a iris [Automatically generated definition]. EMAPA:35447 FMA:58517 MA:0002826 epithelial tissue of iris epithelium of iris epithelium pigmentosum (iris) epithelium pigmentosum iridis iris epithelial tissue iris epithelium pigmented epithelium of iris uberon iris pigmented epithelium UBERON:0002506 iris epithelium FMA MA MP An epithelium that is part of a iris [Automatically generated definition]. OBOL:automatic epithelial tissue of iris OBOL:automatic epithelium of iris OBOL:automatic epithelium pigmentosum (iris) FMA:58517 epithelium pigmentosum iridis FMA:58517 FMA:TA iris epithelial tissue OBOL:automatic iris epithelium FMA:58517 pigmented epithelium of iris FMA:58517 iris pigmented epithelium MA:0002826 The supporting bundles of muscular fibers lining the walls of the ventricles of the heart. The purpose of the trabeculae carneae is most likely to prevent suction that would occur with a flat surfaced membrane and thus impair the heart's ability to pump efficiently. The trabeculae carneae also serve a similar function to papillary muscles in that their contraction pulls on the chordae tendineae, preventing inversion of the mitral (bicuspid) and tricuspid valves, that is, their bulging towards the atrial chambers, which would lead to subsequent leakage of the blood into the atria. So by the action of papillary muscles on the atrioventricular valves, backflow of the blood from the ventricles into the atria is prevented Note that WP states they are ventricular, but MP has classes for atrial ventricular carnea. EMAPA:18626 FMA:7269 MA:0002831 SCTID:118755002 Wikipedia:Trabeculae_carneae ventricle trabecula carnea uberon cardiac trabecula columnae carneae heart trabecula trabecula of heart trabeculae carneae trabeculae carneae cordis ventricular trabecula UBERON:0002511 trabecula carnea WP The supporting bundles of muscular fibers lining the walls of the ventricles of the heart. MGI:monikat MP:0004067 The purpose of the trabeculae carneae is most likely to prevent suction that would occur with a flat surfaced membrane and thus impair the heart's ability to pump efficiently. The trabeculae carneae also serve a similar function to papillary muscles in that their contraction pulls on the chordae tendineae, preventing inversion of the mitral (bicuspid) and tricuspid valves, that is, their bulging towards the atrial chambers, which would lead to subsequent leakage of the blood into the atria. So by the action of papillary muscles on the atrioventricular valves, backflow of the blood from the ventricles into the atria is prevented WP Note that WP states they are ventricular, but MP has classes for atrial ventricular carnea. MP ventricle trabecula carnea MA:0002831 cardiac trabecula GO:0060347 columnae carneae Wikipedia:Trabeculae_carneae heart trabecula GO:0060347 trabeculae carneae trabeculae carneae cordis Wikipedia:Trabeculae_carneae ventricular trabecula MA:0002831 Replacement bone that forms within cartilage. placement in this class to be inferred Replacement bone that forms within cartilage.[VSAO] some structures, e.g. in ZFA are both intramembrane and endochondral AAO:0010776 AEO:0000083 BTO:0002157 EHDAA2:0003083 FMA:24321 TAO:0001591 VSAO:0000145 XAO:0004018 ZFA:0001591 ossified chondrogenic bone uberon cartilaginous bone endochondral bones UBERON:0002513 endochondral bone https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg VSAO VSAO Replacement bone that forms within cartilage. GO:0001958 GO_REF:0000034 VSAO:0000145 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/54 Replacement bone that forms within cartilage.[VSAO] 2012-08-14 VSAO:0000145 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 some structures, e.g. in ZFA are both intramembrane and endochondral ZFA ossified chondrogenic bone VSAO:0000145 cartilaginous bone BTO:0002157 endochondral bones ZFA:0001591 Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] EMAPA:36615 TAO:0001644 Wikipedia:Intramembranous_ossification ZFA:0001635 uberon intramembranous bones membrane bone UBERON:0002514 intramembranous bone VSAO Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. GO:0001957 Wikipedia:Intramembranous_ossification https://github.com/obophenotype/uberon/issues/267 Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] 2012-08-14 TAO:0001644 TAO TAO:wd [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] 2012-09-06 TAO:0001644 TAO Curator intramembranous bones ZFA:0001635 membrane bone AEO:0000085 The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof. basicranial FMA:52801 MA:0002840 MESH:D019291 MFMO:0000044 NCIT:C12493 SCTID:181890004 UMLS:C0149543 Wikipedia:Base_of_skull base of cranium base of skull basis cranii cranial base uberon UBERON:0002517 The skull base is formed from a series of cartilages either side of, and rostral to, the notochord, whose tip lies just caudal to the pituitary gland. It is closely associated with the sensory capsules, which partially or completely sur- round the olfactory epithelium, the eye, and the inner ear[PMID:11523816] basicranium http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof. Wikipedia:Base_of_skull UMLS:C0149543 ncithesaurus:Base_of_the_Skull base of skull FMA:52801 basis cranii FMA:52801 FMA:TA Wikipedia:Base_of_skull cranial base FMA:52801 MA:0002840 Connective tissue composed of elastic fibers. FMA:20113 GAID:926 MA:0002853 MESH:D004547 NCIT:C32495 SCTID:27197004 Wikipedia:Elastic_fiber elastic connective tissue textus connectivus elasticus elastic fiber uberon UBERON:0002521 elastic tissue http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png Connective tissue composed of elastic fibers. http://orcid.org/0000-0002-6601-2165 textus connectivus elasticus The middle layer of an artery or vein. [WP,unvetted]. BTO:0002011 EMAPA:36298 FMA:55590 GAID:170 MA:0002855 MESH:D017540 NCIT:C33821 SCTID:61695000 UMLS:C0162867 Wikipedia:Tunica_media uberon tunica media vasorum UBERON:0002522 May be composed of smooth muscle and elastic tissue tunica media https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg MA cjm cjm The middle layer of an artery or vein. [WP,unvetted]. Wikipedia:Tunica_media UMLS:C0162867 ncithesaurus:Tunica_Media tunica media vasorum BTO:0002011 Wikipedia:Tunica_media The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] BTO:0002012 EMAPA:36297 FMA:55589 GAID:523 MA:0002861 MESH:D017539 NCIT:C33820 SCTID:8361002 SCTID:87483006 UMLS:C0162864 Wikipedia:Tunica_intima uberon Bichat's tunic intima tunica intima vasorum UBERON:0002523 tunica intima https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg FMA check for exceptions, e.g. capillaries ISBN:0073040584 The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. ISBN:0073040584 NCIT:C33820 Wikipedia:Tunica_intima The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] Wikipedia Wikipedia:Tunica_intima UMLS:C0162864 ncithesaurus:Tunica_Intima Bichat's tunic BTO:0002012 intima BTO:0002012 tunica intima vasorum BTO:0002012 An organ that functions as a secretory or excretory organ. glandular AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 NCIT:C13319 SCTID:134358001 UMLS:C1285092 Wikipedia:Gland WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png An organ that functions as a secretory or excretory organ. MGI:csmith MP:0002163 FBbt:00100317 UMLS:C1285092 ncithesaurus:Gland glandular organ http://orcid.org/0000-0002-6601-2165 Druese BTO:0000522 glandula BTO:0000522 Wikipedia:Gland In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 MIAA:0000067 VHOG:0000243 Wikipedia:Epiblast epiblast uberon blastocyst ectoblast epiblastus primitive ectoderm UBERON:0002532 epiblast (generic) http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. Wikipedia:Epiblast ZFIN:curator In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] 2012-09-17 VHOG:0000243 VHOG DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) http://bgee.unil.ch/ epiblast VHOG:0000243 ectoblast MP:0003886 epiblastus Wikipedia:Epiblast primitive ectoderm VHOG:0000243 The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] AAO:0011104 BTO:0001445 EFO:0002748 EHDAA2:0001976 EHDAA:1595 EMAPA:16580 MAT:0000070 MIAA:0000070 TAO:0000077 VHOG:0000201 XAO:0000107 ZFA:0000077 tail bud tailbud uberon end bud tail bud mesenchyme UBERON:0002533 post-anal tail bud The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. BTO:0001445 Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] 2012-06-20 AAO:0011104 AAO ISBN:0815318960 OMD:tail+bud (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] 2012-09-17 VHOG:0000201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ tail bud ZFA:0000077 end bud BTO:0001445 tail bud mesenchyme ZFA:0000077 Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians. gill Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt]. this term should be ceded to the arthropod anatomy ontology BTO:0001237 EFO:0000939 FBbt:00007152 HAO:0000933 MAT:0000163 MIAA:0000163 TGMA:0000540 Wikipedia:Sensillum sensillum uberon UBERON:0002536 arthropod sensillum Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt]. FBbt:00007152 Wikipedia:Sensillum FBbt:00007152 sensillum FBbt:00007152 HAO:0000933 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering AAO:0010359 BTO:0001785 EFO:0000959 EHDAA:571 EMAPA:16117 FMA:293015 GAID:1292 MAT:0000242 MESH:D001934 MIAA:0000242 NCIT:C34249 SCTID:308766004 TAO:0001306 UMLS:C0080322 VHOG:0000155 Wikipedia:Pharyngeal_arch XAO:0000096 ZFA:0001306 pharyngeal arches branchial arch uberon arcus pharyngei visceral arch UBERON:0002539 pharyngeal arch http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png EHDAA2 PMID:16313389 http://tolweb.org/Chordata/2499 PMID:16313389 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. PMID:16313389 ZFA:yb http://orcid.org/0000-0002-6601-2165 One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010359 AAO NLM:branchial+arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] 2012-09-17 VHOG:0000155 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ UMLS:C0080322 ncithesaurus:Pharyngeal_Arch pharyngeal arches branchial arch BTO:0001785 MP:0002884 arcus pharyngei Wikipedia:Pharyngeal_arch Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass ectodermal placode placode AAO:0010466 EFO:0001650 FMA:293966 MAT:0000369 MIAA:0000369 XAO:0000305 ectodermal cranial placode uberon cranial placodes UBERON:0002546 cranial placode cjm PMID:11523831 PMID:22512454 Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. http://www.ncbi.nlm.nih.gov/books/NBK53175/ https://github.com/obophenotype/uberon/issues/135 https://github.com/seger/aao/issues/4 https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/ Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons PMID:11523831 ectodermal placode FMA:293966 PMID:22512454 placode Wikipedia:Placode ectodermal cranial placode UBERON:cjm cranial placodes XAO:0000305 A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. TODO discriminate between stages and organisms Whole organism that is premetamorphic or a very immature individual.[TAO] larval AEO:0000126 BTO:0000707 FBbt:00001727 HAO:0000459 MESH:D007814 TAO:0002048 Wikipedia:Larva larval organism ammocoete bipinnaria caterpillar glochidium grub leptocephalus maggot naiad nymph planula tadpole trochophore veliger wriggler zoea uberon UBERON:0002548 larva A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. Wikipedia:Larva Whole organism that is premetamorphic or a very immature individual.[TAO] 2012-08-14 TAO:0002048 TAO TAO:wd FBbt:00001727 MESH:D007814 https://github.com/biopragmatics/biomappings larval organism TAO:0002048 ammocoete Wikipedia:Larva bipinnaria Wikipedia:Larva caterpillar Wikipedia:Larva glochidium Wikipedia:Larva grub Wikipedia:Larva leptocephalus Wikipedia:Larva maggot Wikipedia:Larva naiad Wikipedia:Larva nymph Wikipedia:Larva planula Wikipedia:Larva tadpole Wikipedia:Larva trochophore Wikipedia:Larva veliger Wikipedia:Larva wriggler Wikipedia:Larva zoea Wikipedia:Larva Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. cavity BIRNLEX:1011 EMAPA:37442 FMA:67552 MA:0002447 NCIT:C34007 galen:Cavity uberon UBERON:0002553 anatomical cavity Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. FMA:67552 EMAPA:37442 MA:th BIRNLEX:1019 FMA:12237 SCTID:362606005 cavity of organ uberon UBERON:0002558 organ cavity cavity of organ FMA:12237 The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube. BIRNLEX:1029 FMA:75007 cavity of neuraxis cavity of ventricular system of neuraxis neuraxis cavity neuraxis lumen uberon UBERON:0002561 lumen of central nervous system The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube. https://orcid.org/0000-0002-6601-2165 DOI:10.1186/s12983-014-0089-2 cavity of neuraxis FMA:75007 cavity of ventricular system of neuraxis FMA:75007 neuraxis cavity FMA:75007 Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 FMA:55676 NCIT:C13031 SCTID:384763002 UMLS:C0445620 anatomical structure of brain biological structure of brain brain anatomical structure brain biological structure brain part neuraxis segment neuroanatomical region segment of brain uberon UBERON:0002616 regional part of brain Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 UMLS:C0445620 ncithesaurus:Brain_Part anatomical structure of brain OBOL:automatic biological structure of brain OBOL:automatic brain anatomical structure OBOL:automatic brain biological structure OBOL:automatic neuraxis segment FMA:55676 segment of brain BIRNLEX:1167 A spinal cord segment that adjacent_to a cervical region. BIRNLEX:1499 FMA:71166 MA:0003081 MESH:D066193 NCIT:C12892 SCTID:180960003 UMLS:C0581619 UMLS:C1278837 neuronames:1654 cervical segment of spinal cord cervical segments of spinal cord [1-8] cervical spinal cord pars cervicalis medullae spinalis segmenta cervicalia medullae spinalis [1-8 uberon UBERON:0002726 cervical spinal cord A spinal cord segment that adjacent_to a cervical region. OBOL:automatic MESH:D066193 https://github.com/biopragmatics/biomappings UMLS:C0581619 BIRNLEX:1499 ncithesaurus:Cervical_Spinal_Cord UMLS:C1278837 BIRNLEX:1499 cervical segment of spinal cord FMA:71166 cervical segments of spinal cord [1-8] FMA:71166 cervical spinal cord FMA:71166 pars cervicalis medullae spinalis FMA:71166 FMA:TA segmenta cervicalia medullae spinalis [1-8 FMA:71166 FMA:TA A nucleus of brain that is part of a trigeminal nuclear complex. massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. BM:V BTO:0001074 CALOHA:TS-2077 EMAPA:35883 EV:0100271 FMA:71247 GAID:604 MA:0001028 MESH:D014278 NCIT:C12807 SCTID:280164007 UMLS:C0040999 VHOG:0001353 http://uri.neuinfo.org/nif/nifstd/nifext_11 nucleus of trigeminal nuclear complex trigeminal V nucleus trigeminal nuclear complex nucleus trigeminal nucleus uberon nucleus mesencephalicus nervi trigemini nucleus mesencephalicus trigeminalis nucleus tractus mesencephali nervi trigeminalis UBERON:0002925 trigeminal nucleus A nucleus of brain that is part of a trigeminal nuclear complex. OBOL:automatic massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. GO https://github.com/obophenotype/mouse-anatomy-ontology/issues/58 UMLS:C0040999 ncithesaurus:Trigeminal_Nucleus nucleus of trigeminal nuclear complex FMA:71247 trigeminal V nucleus MA:0001028 trigeminal nuclear complex nucleus FMA:71247 trigeminal nucleus FMA:71248 nucleus mesencephalicus nervi trigemini BTO:0001074 nucleus mesencephalicus trigeminalis BTO:0001074 nucleus tractus mesencephali nervi trigeminalis BTO:0001074 Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum] BAMS:PTg BIRNLEX:923 DHBA:12416 FMA:71108 HBA:9135 MESH:D065821 SCTID:362401009 UMLS:C0228426 Wikipedia:Pontine_tegmentum neuronames:557 dorsal pons dorsal portion of pons tegmental portion of pons tegmentum of pons tegmentum pontis uberon pars dorsalis pontis pars posterior pontis tegmentum pontis UBERON:0003023 pontine tegmentum https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). BIRNLEX:923 MESH:D065821 https://github.com/biopragmatics/biomappings UMLS:C0228426 BIRNLEX:923 neuronames:557 BIRNLEX:923 dorsal portion of pons FMA:71108 tegmental portion of pons FMA:71108 tegmentum of pons FMA:71108 tegmentum pontis FMA:71108 FMA:TA pars dorsalis pontis NeuroNames:557 pars posterior pontis NeuroNames:557 tegmentum pontis Wikipedia:Pontine_tegmentum A wall, dividing a cavity or structure into smaller ones[WP]. septal AAO:0011127 FMA:86461 Wikipedia:Septum septa uberon UBERON:0003037 general anatomical term in FMA septum A wall, dividing a cavity or structure into smaller ones[WP]. Wikipedia:Septum septa The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. BIRNLEX:966 FMA:71167 MA:0003082 NCIT:C12894 SCTID:278750009 UMLS:C0581620 Wikipedia:Thoracic_spinal_cord neuronames:1718 pars thoracica medullae spinalis segmenta thoracica medullae spinalis [1-12] thoracic region of spinal cord thoracic segment of spinal cord thoracic segments of spinal cord [1-12] thoracic spinal cord uberon UBERON:0003038 thoracic spinal cord http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. Wikipedia:Thoracic_spinal_cord UMLS:C0581620 BIRNLEX:966 ncithesaurus:Thoracic_Spinal_Cord pars thoracica medullae spinalis FMA:71167 FMA:TA segmenta thoracica medullae spinalis [1-12] FMA:71167 FMA:TA thoracic region of spinal cord FMA:71167 thoracic segment of spinal cord FMA:71167 thoracic segments of spinal cord [1-12] FMA:71167 thoracic spinal cord FMA:71167 The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] AAO:0011064 DMBA:16810 EHDAA2:0004395 EHDAA:5789 EMAPA:32857 NCIT:C93172 TAO:0000042 VHOG:0000649 XAO:0000016 ZFA:0000042 neuronames:2076 MHB mid-hindbrain boundary mid-hindbrain junction midbrain hindbrain boundary uberon isthmic organizer territory isthmo-cerebellar region isthmus isthmus/MHB UBERON:0003052 midbrain-hindbrain boundary ZFA https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/ ZFA ZFA The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. GO:0021555 Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000649 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) http://bgee.unil.ch/ isthmic organizer territory XAO:0000016 isthmo-cerebellar region VHOG:0000649 isthmus/MHB Geisha:syn NCBITaxon:8782 A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP] In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html) BTO:0003377 EHDAA2:0001846 EHDAA:6538 FMA:295662 NCIT:C34247 TAO:0001185 UMLS:C1518973 VHOG:0001680 XAO:0000029 ZFA:0001185 skin periderm uberon EVL epidermis epithelial layer epidermis outer layer epitrichium periderm UBERON:0003055 periderm EHDAA2 EHDAA2 ZFA A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. ISBN:9780878932504 The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001185 TAO ZFIN:curator relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] 2012-08-14 TAO:0001185 TAO BTO:0003377 https://github.com/biopragmatics/biomappings UMLS:C1518973 ncithesaurus:Periderm skin periderm EHDAA2:0001846 EVL ZFA:0001185 epitrichium MP:0013530 The portion of neural plate anterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 VHOG:0001200 XAO:0000045 ZFA:0007016 uberon anterior neural plate UBERON:0003056 pre-chordal neural plate The portion of neural plate anterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001200 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The portion of neural plate posterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 VHOG:0001201 XAO:0000046 ZFA:0007017 uberon posterior neural plate UBERON:0003057 chordal neural plate The portion of neural plate posterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 EMAPA:16752 TAO:0000279 VHOG:0000559 XAO:0000057 ZFA:0000279 segmental plate unsegmented paraxial mesoderm uberon PSM presumptive somite mesoderm somitogenic mesoderm somitomeric mesoderm unsegmented mesenchyme UBERON:0003059 presomitic mesoderm Bgee:AN Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000279 TAO ZFIN:curator It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] 2012-09-17 VHOG:0000559 VHOG DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) http://bgee.unil.ch/ unsegmented paraxial mesoderm https://orcid.org/0000-0002-6601-2165 somitomeric mesoderm GO:0002075 unsegmented mesenchyme VHOG:0000559 Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 EHDAA:207 NCIT:C34113 TAO:0000094 TE:E5.11.2.0.0.0.4 UMLS:C1511224 VHOG:0000085 Wikipedia:Blood_island_of_umbilical_vesicle XAO:0000067 ZFA:0000094 blood islands uberon VBI caudal hematopoietic tissue posterior ICM posterior blood island ventral blood island UBERON:0003061 blood island Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000094 TAO ZFIN:curator Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] 2012-06-20 AAO:0011006 AAO AAO:EJS relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] 2012-08-14 TAO:0000094 TAO Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000085 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) http://bgee.unil.ch/ EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac EHDAA2 UMLS:C1511224 ncithesaurus:Blood_Island blood islands A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue. TODO - check; developmental relationship to anterior hypoblast in ZFA? Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] UBERON:0004881 head mesenchyme head mesoderm AAO:0011085 EHDAA2:0001493 EHDAA:181 FMA:295532 TAO:0000060 VHOG:0000086 Wikipedia:Prechordal_plate XAO:0000079 ZFA:0000060 uberon UBERON:0003063 prechordal plate ZFA PMID:16313393 A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue. ISBN:0838580343 MP:0004387 Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000060 TAO ZFIN:curator Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] 2012-09-17 VHOG:0000086 VHOG http://bgee.unil.ch/ There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] 2012-09-17 VHOG:0000086 VHOG DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008) http://bgee.unil.ch/ head mesenchyme XAO:0000079 head mesoderm XAO:0000079 The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). AAO:0010575 EMAPA:16056 EMAPA:16178 FMA:293147 NCIT:C34193 SCTID:361476001 TAO:0001206 UMLS:C1284010 VHOG:0000087 Wikipedia:Intermediate_mesoderm XAO:0000085 ZFA:0001206 uberon IM intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium UBERON:0003064 intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png AAO EMAPA XAO The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. GOC:curators Wikipedia:Intermediate_mesoderm Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] 2012-06-20 AAO:0010575 AAO AAO:EJS (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] 2012-09-17 VHOG:0000087 VHOG Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43 http://bgee.unil.ch/ all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). ZFA UMLS:C1284010 ncithesaurus:Intermediate_Mesoderm intermediate mesenchyme https://github.com/obophenotype/uberon/wiki/The-neural-crest intermediate plate EMAPA:16178 intermediate plate mesoderm https://orcid.org/0000-0002-6601-2165 mesenchyma intermedium Wikipedia:Intermediate_mesoderm Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] TAO:0001310 VHOG:0000103 XAO:0000187 ZFA:0001310 dorsolateral placodes uberon UBERON:0003067 The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode dorsolateral placode NCBIBook:NBK53175 Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. ZFIN:curator In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000103 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ dorsolateral placodes ZFA:0001310 The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 VHOG:0000107 Wikipedia:Chordamesoderm XAO:0000205 ZFA:0001204 uberon chordamesoderm UBERON:0003068 axial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. GO:0048318 Wikipedia:Chordamesoderm The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000107 VHOG http://bgee.unil.ch/ chordamesoderm Wikipedia:Chordamesoderm A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...' EFO:0003433 EHDAA2:0004209 TAO:0000162 VHOG:0000109 XAO:0000225 ZFA:0000162 trigeminal V placode trigeminal placode uberon profundus V placode profundus placode trigeminal placodes UBERON:0003070 trigeminal placode complex ISBN:0471888893 A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. PMID:22512454 http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/693 The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] XAO The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000162 TAO ZFIN:curator The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000109 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ trigeminal placode EHDAA2:0004209 VHOG:0000109 XAO:0000225 ZFA:0000162 profundus V placode ISBN:0471888893 profundus placode ISBN:0471888893 trigeminal placodes ZFA:0000162 Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. UBERON:0005060 AAO:0011038 EFO:0003541 EHDAA2:0004431 TAO:0000570 XAO:0000227 XAO:0004090 ZFA:0000570 eye placode occular primordium ocular primordium optic placode optic placode of camera-type eye optic primordium uberon eye anlage eye field optic field optic placodes UBERON:0003071 eye primordium EHDAA2 PMID:16496288 XAO Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. GO:0046619 ZFA:0000570 TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. GO eye placode OBOL:automatic optic placode GO:0046619 optic placode of camera-type eye GO:0046619 https://orcid.org/0000-0002-6601-2165 eye anlage XAO:0000227 optic placodes Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] BTO:0005351 EHDAA2:0001303 EHDAA:2912 EMAPA:16674 NCIT:C34233 SCTID:308789007 TAO:0001202 UMLS:C0231109 VHOG:0000167 ZFA:0001202 uberon eye cup eyecup ocular cup ophtalmic cup UBERON:0003072 optic cup ZFA ZFA Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. MP:0004269 Wikipedia:Optic_cup_(embryology) ZFA:0001202 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] 2012-09-17 VHOG:0000167 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C0231109 ncithesaurus:Optic_Cup eyecup BTO:0005351 ocular cup VHOG:0000167 ophtalmic cup BTO:0005351 A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) AAO:0011055 EFO:0003494 EHDAA2:0000982 EHDAA:2908 EMAPA:16672 FMA:296767 NCIT:C34202 TAO:0000122 UMLS:C1517770 VHOG:0000166 Wikipedia:Lens_placode XAO:0000240 ZFA:0000122 uberon lens placodes placoda lentis UBERON:0003073 lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png NCBIBook:NBK53175 ZFA A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. Wikipedia:Lens_placode ZFIN:curator Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000122 TAO ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000166 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) NCBIBook:NBK53175 UMLS:C1517770 ncithesaurus:Lens_Placodes lens placodes ZFA:0000122 placoda lentis Wikipedia:Lens_placode A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 DMBA:15565 EHDAA:346 EHDAA:902 EMAPA:35593 FMA:293879 MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 UMLS:C0920623 VHOG:0000068 Wikipedia:Neural_plate XAO:0000249 ZFA:0000132 neuronames:1362 uberon lamina neuralis presumptive central nervous system UBERON:0003075 neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png GOTAX:0000352 Wikipedia Bgee:AN A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. ISBN:0815318960 OMD:neural+plate Wikipedia:Neural_plate ZFIN:curator The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000132 TAO ZFIN:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000068 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ MESH:D054258 https://github.com/biopragmatics/biomappings UMLS:C0920623 ncithesaurus:Neural_Plate lamina neuralis Wikipedia:Neural_plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011082 TAO:0007037 VHOG:0001383 XAO:0000250 ZFA:0007037 uberon UBERON:0003076 posterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001383 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 EMAPA:16751 FMA:293145 NCIT:C34244 SCTID:361475002 TAO:0000255 UMLS:C1284009 VHOG:0000114 Wikipedia:Paraxial_mesoderm XAO:0000259 ZFA:0000255 paraxial mesenchyme somitic mesoderm uberon mesoderma paraxiale UBERON:0003077 paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 Bgee:AN The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. GO:0048339 https://github.com/obophenotype/uberon/issues/30 Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] 2012-06-20 AAO:0010568 AAO AAO:EJS Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] 2012-09-17 VHOG:0000114 VHOG DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) http://bgee.unil.ch/ note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) ZFA UMLS:C1284009 ncithesaurus:Paraxial_Mesoderm paraxial mesenchyme ZFA:0000255 https://github.com/obophenotype/uberon/issues/30 https://github.com/obophenotype/uberon/wiki/The-neural-crest somitic mesoderm ISBN:9780878932504 mesoderma paraxiale Wikipedia:Paraxial_mesoderm Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group AAO:0011036 EFO:0003455 FMA:293968 TAO:0001294 VHOG:0000117 XAO:0000284 ZFA:0001294 epibranchial placodes uberon ventrolateral placode UBERON:0003078 epibranchial placode NCBIBook:NBK53175 ZFA ZFA EHDAA2-abduced Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. VHOG:0000117 Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] 2012-09-17 VHOG:0000117 VHOG http://bgee.unil.ch/ These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000117 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively NCBIBook:NBK53175 in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group XAO epibranchial placodes ZFA:0001294 ventrolateral placode ISBN:0471888893 TODO - add grouping class for the anterior end of the neural tube at all stages (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011012 TAO:0007038 VHOG:0001384 XAO:0000307 ZFA:0007038 uberon UBERON:0003080 anterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001384 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 EMAPA:16179 FMA:293149 NCIT:C34199 SCTID:361477005 TAO:0000121 UMLS:C1517749 VHOG:0000118 Wikipedia:Lateral_plate_mesoderm XAO:0000311 ZFA:0000121 LPM lateral mesoderm uberon lateral plate lateral plate mesenchyme mesoderma laminae lateralis UBERON:0003081 lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 EHDAA2 VHOG Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. MP:0010117 Wikipedia:Lateral_plate_mesoderm Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] 2012-06-20 AAO:0010574 AAO AAO:EJS The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000118 VHOG http://bgee.unil.ch/ A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] 2012-09-17 VHOG:0000118 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ subclass of mesoderm in ZFA. ZFA UMLS:C1517749 ncithesaurus:Lateral_Mesoderm LPM ZFA:0000121 lateral mesoderm GO:0048368 lateral plate mesenchyme EHDAA2:0000919 mesoderma laminae lateralis Wikipedia:Lateral_plate_mesoderm A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] AAO:0011067 AEO:0001018 BTO:0000742 EHDAA2_RETIRED:0003431 EHDAA:1721 EHDAA:1727 EHDAA:1733 EHDAA:1739 EMAPA:32841 FMA:295658 NCIT:C34214 SCTID:344535001 TAO:0001056 UMLS:C1513802 VHOG:0001244 Wikipedia:Myotome XAO:0000315 ZFA:0001056 myomeres uberon muscle plate myomere myotome region myotomes myotomus UBERON:0003082 myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AEO:0001018 Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001056 TAO ZFIN:curator In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] 2012-09-17 VHOG:0001244 VHOG DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003) http://bgee.unil.ch/ UMLS:C1513802 ncithesaurus:Myotome_Region myomeres TAO:0001056 myotomus Wikipedia:Myotome Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010582 EFO:0003605 EHDAA2:0001901 TAO:0001024 VHOG:0000062 Wikipedia:Trunk_neural_crest XAO:0000319 ZFA:0001024 TNC uberon trunk crest UBERON:0003083 trunk neural crest ZFA Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. ISBN:0815318960 Wikipedia:Trunk_neural_crest Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] 2012-06-20 AAO:0010582 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000062 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ TNC XAO:0000319 Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 TAO:0000028 UMLS:C1514450 XAO:0000336 ZFA:0000028 uberon cardiac field fused heart primordium UBERON:0003084 heart primordium Obol ZFA ZFA XAO Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] 2012-08-14 TAO:0000028 TAO ZFIN:curator The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] 2012-06-20 AAO:0011044 AAO XAO:curator relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] 2012-08-14 TAO:0000028 TAO UMLS:C1514450 ncithesaurus:Primordium_of_the_Heart cardiac field ZFA:0000028 Extension of the dorsal aorta in the tail. Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO] The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO] AAO:0011023 EFO:0003472 TAO:0000011 VHOG:0000123 Wikipedia:Caudal_artery XAO:0000364 ZFA:0000011 uberon CA UBERON:0003086 caudal artery Extension of the dorsal aorta in the tail. Wikipedia:Caudal_artery ZFIN:curator Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000011 TAO ZFIN:curator The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO] 2012-06-20 AAO:0011023 AAO ISBN:0-226-55763-4 Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] part_of somite in XAO AAO:0010571 AEO:0000212 BTO:0006255 EHDAA2:0003439 EMAPA:31159 FMA:295652 NCIT:C34287 TAO:0001080 UMLS:C0183176 VHOG:0000680 Wikipedia:Sclerotome XAO:0000397 ZFA:0001080 sclerotomes uberon sclerotomus UBERON:0003089 sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png EHDAA2 EHDAA2 VHOG:0000680 ZFA Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Wikipedia:Sclerotome XB:curator https://github.com/obophenotype/uberon/issues/316 Skeletogenic portion of somites.[AAO] 2012-06-20 AAO:0010571 AAO AAO:EJS The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] 2012-09-17 VHOG:0000680 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ part_of somite in XAO XAO BTO:0006255 https://github.com/biopragmatics/biomappings UMLS:C0183176 ncithesaurus:Sclerotome sclerotomes TAO:0001080 sclerotomus Wikipedia:Sclerotome Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] Neural crest that is part of the head.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010580 EFO:0003645 EHDAA2:0004420 EMAPA:16091 TAO:0001194 VHOG:0000063 Wikipedia:Cranial_neural_crest XAO:0001001 ZFA:0001194 CNC cephalic neural crest cranial NCC population head NCC population uberon crista neuralis cranialis head crest head neural crest UBERON:0003099 cranial neural crest Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. MGI:anna Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] 2012-06-20 AAO:0010580 AAO AAO:EJS Neural crest that is part of the head.[TAO] 2012-08-14 TAO:0001194 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000063 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ CNC XAO:0001001 cephalic neural crest EMAPA:16091 crista neuralis cranialis Wikipedia:Cranial_neural_crest Gonochoristic organism that can produce female gametes. AAO:0010030 BILA:0000028 CARO:0000028 FBbt:00007011 FMA:67812 HAO:0000028 SCTID:362608006 TAO:0000303 TGMA:0001839 XAO:0003005 ZFA:0000303 female human body uberon female UBERON:0003100 female organism Gonochoristic organism that can produce female gametes. CARO:0000028 FBbt:00007011 female human body FMA:67812 female TAO:0000303 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. consider obsoleting. See issue/1305 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] AAO:0010337 AEO_RETIRED:0000010 EHDAA2_RETIRED:0003010 TAO:0000292 VSAO:0000001 Wikipedia:Surface_structure XAO:0003028 ZFA:0000292 galen:SurfaceRegion anatomical surface feature uberon surface feature surface region surface structures UBERON:0003102 surface structure Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/24 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] 2012-08-14 TAO:0000292 TAO ZFIN:curator anatomical surface feature EHDAA2:0003010 surface structures ZFA:0000292 Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 VHOG:0001723 XAO:0003041 ZFA:0000496 uberon organ UBERON:0003103 compound organ Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. CARO:0000024 Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 CALOHA:TS-0620 EHDAA2:0003145 EV:0100007 NCIT:C13301 TAO:0000393 UMLS:C0162415 VHOG:0000170 Wikipedia:Mesenchyme XAO:0003046 ZFA:0000393 mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue uberon mesenchyma UBERON:0003104 mesenchyme http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000393 TAO ZFIN:curator Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] 2012-06-20 AAO:0010427 AAO AAO:EJS UMLS:C0162415 ncithesaurus:Mesenchyme mesenchyma Wikipedia:Mesenchyme Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ. Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO] Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO] AAO:0010206 EFO:0003525 NCIT:C98765 TAO:0000351 XAO:0003172 ZFA:0000351 uberon ethmoid region UBERON:0003112 olfactory region Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ. TAO:0000351 Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO] 2012-08-14 TAO:0000351 TAO TAO:MAH Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO] 2012-06-20 AAO:0010206 AAO AAO:EJS ethmoid region ZFA:0000351 Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] AAO:0010154 TAO:0000863 VHOG:0001665 Wikipedia:Skull_roof XAO:0003169 ZFA:0000863 dendrocranium exocranium dermal skull roof dermatocranial cover roof of skull skull roof uberon dermal bone cranium dermal part of skull dermal skull bones roofing bones of the skull skull exoskeleton UBERON:0003113 dermatocranium Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. Wikipedia:Skull_roof ZFA:0000863 ISBN:0073040584 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] 2012-08-14 TAO:0000863 TAO ZFIN:curator Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] 2012-06-20 AAO:0010154 AAO AAO:BJB dendrocranium TAO:0000863 exocranium UBERONREF:0000007 dermal skull roof PMID:11523816 Wikipedia:Skull_roof roof of skull Wikipedia:Skull_roof skull roof PMID:11523816 Wikipedia:Skull_roof dermal bone cranium ZFA:0000863 roofing bones of the skull Wikipedia:Skull_roof Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus. The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, called branchial arch 2 and df VP4 4 AAO:0010366 EHDAA2:0000086 EHDAA:1663 EMAPA:16760 FMA:293035 SCTID:308770007 TAO:0001599 VHOG:0000299 XAO:0000449 ZFA:0001607 4th branchial arch 4th pharyngeal arch 4th visceral arch fourth pharyngeal arch gill arch 2 second gill arch visceral arch 4 uberon 4th arch branchial arch 2 fourth visceral arch second branchial arch UBERON:0003115 pharyngeal arch 4 Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus. MP:0006340 The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] 2012-06-20 AAO:0010366 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000299 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ in XAO, called branchial arch 2 and df VP4 XAO 4th branchial arch gill arch 2 ZFA:0001607 second gill arch ZFA:0001607 4th arch EHDAA2:0000086 branchial arch 2 AAO:0010366 ZFA:0001607 fourth visceral arch VHOG:0000299 second branchial arch ZFA:0001607 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles. The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 6 UBERON:0004349 AAO:0010368 EHDAA2:0004075 EMAPA:32766 FMA:293047 SCTID:308772004 TAO:0001601 VHOG:0001205 XAO:0000453 ZFA:0001609 6th arch gill arch 4 sixth branchial arch visceral arch 6 uberon 6th pharyngeal arch 6th visceral arch branchial arch 4 fourth branchial arch sixth pharyngeal arch sixth visceral arch UBERON:0003117 pharyngeal arch 6 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles. MP:0006347 The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] 2012-06-20 AAO:0010368 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0001205 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ 6th arch EHDAA2:0004075 gill arch 4 ZFA:0001609 visceral arch 6 ZFA:0001609 6th pharyngeal arch VHOG:0001205 6th visceral arch VHOG:0001205 branchial arch 4 AAO:0010368 ZFA:0001609 fourth branchial arch sixth pharyngeal arch VHOG:0001205 sixth visceral arch XAO:0000453 The vessels formed within the first pair of branchial arches in embryogenesis. Disappears early in development in tetrapods ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas UBERON:0004371 AAO:0010415 EHDAA2:0000007 EMAPA:16202 EMAPA:16685 SCTID:308774003 TAO:0005005 VHOG:0000149 XAO:0000342 ZFA:0005005 1st arch artery AA1 aortic arch 1 first aortic arch first branchial arch artery mandibular aortic arch uberon 1st aortic arch artery 1st branchial arch artery 1st pharyngeal arch artery first arch artery UBERON:0003118 pharyngeal arch artery 1 The vessels formed within the first pair of branchial arches in embryogenesis. MP:0010355 ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas ZFA 1st arch artery EMAPA:16685 AA1 ZFA:0005005 aortic arch 1 ZFA:0005005 first aortic arch XAO:0000342 mandibular aortic arch ZFA:0005005 1st aortic arch artery EMAPA:16685 1st branchial arch artery EMAPA:16685 1st pharyngeal arch artery EMAPA:16685 first arch artery EMAPA:16685 The vessels formed within the fourth pair of branchial arches in embryogenesis. Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta UBERON:0004350 AAO:0010420 EHDAA2:0000087 EMAPA:17004 SCTID:308777005 TAO:0005008 Wikipedia:Aortic_arches#Arch_4 XAO:0000355 ZFA:0005008 4th arch artery AA4 aortic arch 4 fourth aortic arch fourth branchial arch artery uberon 4th aortic arch artery 4th branchial arch artery 4th pharyngeal arch artery systemic arch UBERON:0003121 proximal right subclavian pharyngeal arch artery 4 The vessels formed within the fourth pair of branchial arches in embryogenesis. MP:0006354 Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005008 TAO ZFIN:curator The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] 2012-06-20 AAO:0010420 AAO ISBN:0-02-377110-0 The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. Wikipedia:Aortic_arches#Arch_4 4th arch artery EHDAA2:0000087 AA4 ZFA:0005008 aortic arch 4 ZFA:0005008 fourth aortic arch XAO:0000355 4th aortic arch artery EMAPA:17004 4th branchial arch artery EMAPA:17004 4th pharyngeal arch artery EMAPA:17004 systemic arch ISBN:0073040584 XAO:0000355 The vessels formed within the sixth pair of branchial arches in embryogenesis. The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries UBERON:0004351 AAO:0010422 EHDAA2:0000102 EMAPA:17005 SCTID:308779008 TAO:0005016 VHOG:0000144 Wikipedia:Aortic_arches#Arch_6 XAO:0000353 ZFA:0005016 6th arch artery AA6 aortic arch 6 sixth aortic arch sixth branchial arch artery uberon 6th aortic arch artery 6th branchial arch artery 6th pharyngeal arch artery pulmonary arch UBERON:0003123 pharyngeal arch artery 6 The vessels formed within the sixth pair of branchial arches in embryogenesis. MP:0006355 The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005016 TAO ZFIN:curator The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] 2012-06-20 AAO:0010422 AAO ISBN:0-02-377110-0 The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. Wikipedia:Aortic_arches#Arch_6 the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries http://emedicine.medscape.com/article/899609-overview 6th arch artery EMAPA:17005 AA6 ZFA:0005016 aortic arch 6 ZFA:0005016 sixth aortic arch XAO:0000353 6th aortic arch artery EMAPA:17005 6th branchial arch artery EMAPA:17005 6th pharyngeal arch artery EMAPA:17005 pulmonary arch ISBN:0073040584 Upper portion of the skull that excludes the mandible (when present in the organism). cranial the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton BTO:0001328 EFO:0000831 EHDAA:6029 EMAPA:17680 FMA:71325 MA:0000316 MAT:0000340 MESH:D012886 MIAA:0000340 SCTID:181889008 VHOG:0000334 Wikipedia:Cranium_(anatomy) bones of cranium ossa cranii set of bones of cranium skull minus mandible upper part of skull uberon calvarium epicranial plate skeletal system of head UBERON:0003128 cranium FMA-inferred Upper portion of the skull that excludes the mandible (when present in the organism). Wikipedia:Cranium_(anatomy) http://orcid.org/0000-0002-6601-2165 the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium FMA The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton WP MESH:D012886 https://github.com/biopragmatics/biomappings bones of cranium FMA:71325 ossa cranii FMA:71325 FMA:TA set of bones of cranium FMA:71325 calvarium BTO:0001328 Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates BTO:0001295 CALOHA:TS-2344 EHDAA2:0000325 EMAPA:17680 FMA:46565 GAID:82 MESH:D012886 NCIT:C12789 SCTID:110530005 UMLS:C0037303 Wikipedia:Skull WikipediaCategory:Skull galen:Skull uberon cranial skeleton skeletal system of head UBERON:0003129 skull FMA Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. PMID:11523816 Wikipedia:Skull http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376 in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. FMA A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates WP UMLS:C0037303 ncithesaurus:Skull An organ involved in reproduction. GO uses genitalia for the singular organ EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 NCIT:C25177 SCTID:128181006 TGMA:0000591 UMLS:C0017420 WBbt:0008422 genital organ reproductive system organ sex organ uberon genitalia UBERON:0003133 reproductive organ An organ involved in reproduction. UBERON:xp GO uses genitalia for the singular organ GO EMAPA:37731 MA:th UMLS:C0017420 ncithesaurus:Genitalia genitalia A female organ involved in reproduction. EMAPA:28540 MA:0000544 female organism reproductive organ female organism reproductive structure female organism reproductive system organ female organism sex organ female reproductive gland/organ female reproductive system organ female sex organ reproductive organ of female organism reproductive structure of female organism reproductive system organ of female organism sex organ of female organism uberon UBERON:0003134 female reproductive organ A female organ involved in reproduction. UBERON:xp female organism reproductive organ OBOL:automatic female organism reproductive structure OBOL:automatic female organism reproductive system organ OBOL:automatic female organism sex organ OBOL:automatic female reproductive gland/organ MA:0000544 reproductive organ of female organism OBOL:automatic reproductive structure of female organism OBOL:automatic reproductive system organ of female organism OBOL:automatic sex organ of female organism OBOL:automatic Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. uberon UBERON:0003218 ovary septum Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. GO:0080126 An epithelium that is part of a upper jaw [Automatically generated definition]. EHDAA2:0002119 EHDAA:8027 EMAPA:17943 EMAPA:18971 epithelial tissue of palatoquadrate arch epithelial tissue of upper jaw epithelium of palatoquadrate arch palatoquadrate arch epithelial tissue palatoquadrate arch epithelium upper jaw epithelial tissue upper jaw epithelium uberon UBERON:0003235 epithelium of upper jaw An epithelium that is part of a upper jaw [Automatically generated definition]. OBOL:automatic epithelial tissue of palatoquadrate arch OBOL:automatic epithelial tissue of upper jaw OBOL:automatic epithelium of palatoquadrate arch OBOL:automatic palatoquadrate arch epithelial tissue OBOL:automatic palatoquadrate arch epithelium OBOL:automatic upper jaw epithelial tissue OBOL:automatic upper jaw epithelium OBOL:automatic An epithelium that is part of a lower jaw [Automatically generated definition]. EHDAA2:0001019 EHDAA:7999 EMAPA:35516 VHOG:0000802 epithelial tissue of lower jaw epithelial tissue of ventral mandibular arch epithelium of ventral mandibular arch lower jaw epithelial tissue lower jaw epithelium ventral mandibular arch epithelial tissue ventral mandibular arch epithelium uberon UBERON:0003236 epithelium of lower jaw An epithelium that is part of a lower jaw [Automatically generated definition]. OBOL:automatic epithelial tissue of lower jaw OBOL:automatic epithelial tissue of ventral mandibular arch OBOL:automatic epithelium of ventral mandibular arch OBOL:automatic lower jaw epithelial tissue OBOL:automatic lower jaw epithelium OBOL:automatic ventral mandibular arch epithelial tissue OBOL:automatic ventral mandibular arch epithelium OBOL:automatic The portion of the yolk sac that is derived from endoderm and lines the yolk sac. EHDAA2:0002215 EHDAA:166 EMAPA:16086 VHOG:0000626 uberon UBERON:0003257 yolk sac endoderm EHDAA2 The portion of the yolk sac that is derived from endoderm and lines the yolk sac. UBERON:cjm An endoderm that is part of a foregut [Automatically generated definition]. TODO - check EHDAA2:0004568 EHDAA:524 foregut endoderm uberon UBERON:0003258 endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut endoderm OBOL:automatic An endoderm that is part of a midgut [Automatically generated definition]. TODO - check EHDAA:987 EMAPA:16257 RETIRED_EHDAA2:0001194 VHOG:0001080 midgut endoderm uberon UBERON:0003259 endoderm of midgut An endoderm that is part of a midgut [Automatically generated definition]. OBOL:automatic midgut endoderm OBOL:automatic An endoderm that is part of a hindgut [Automatically generated definition]. TODO - check EHDAA:979 RETIRED_EHDAA2:0000781 hindgut endoderm uberon UBERON:0003260 endoderm of hindgut An endoderm that is part of a hindgut [Automatically generated definition]. OBOL:automatic hindgut endoderm OBOL:automatic A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. EHDAA2:0000486 EHDAA:2923 EMAPA:17844 eye skeletal muscle eye skeletal muscle tissue skeletal muscle tissue of eye uberon eye skeletal muscle group UBERON:0003269 skeletal muscle tissue of eye A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. OBOL:automatic eye skeletal muscle OBOL:automatic eye skeletal muscle tissue OBOL:automatic skeletal muscle tissue of eye OBOL:automatic eye skeletal muscle group EHDAA2:0000486 A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones. The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 upper jaw AAO:0000622 EHDAA2:0002128 EHDAA:8041 EMAPA:17927 FMA:54397 MA:0001908 VHOG:0000429 XAO:0003087 upper jaw skeleton uberon UBERON:0003277 skeleton of upper jaw A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones. http://orcid.org/0000-0002-6601-2165 The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] 2012-09-17 VHOG:0000429 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101 http://bgee.unil.ch/ EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 EMAPA upper jaw MA:0001908 A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 lower jaw mandible AAO:0000274 EHDAA2:0004606 EHDAA:8005 EMAPA:17906 EMAPA:17910 FMA:54398 MA:0001906 TAO:0001273 VHOG:0000428 XAO:0003084 ZFA:0001273 lower jaw skeleton uberon mandibles mandibular series UBERON:0003278 skeleton of lower jaw EHDAA2 VHOG-modified A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. http://orcid.org/0000-0002-6601-2165 The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] 2012-08-14 TAO:0001273 TAO ZFIN:curator The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] 2012-09-17 VHOG:0000428 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101 http://bgee.unil.ch/ Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 FMA lower jaw MA:0001906 ZFA:0001273 mandible ZFA:0001273 lower jaw skeleton AAO:0000274 mandibles TAO:0001273 mandibular series ZFA:0001273 The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. TODO - check primitive vs developed The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG] EHDAA2:0001922 EHDAA:2999 EMAPA:17024 MA:0001617 SCTID:261623000 VHOG:0000358 mesentery of ventriculus mesogaster mesogastium mesogastrium stomach mesentery ventriculus mesentery uberon UBERON:0003281 mesentery of stomach MA MA The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. http://medical-dictionary.thefreedictionary.com/mesogastrium The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG] 2012-09-17 VHOG:0000358 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/mesogastrium mesentery of ventriculus OBOL:automatic mesogaster http://medical-dictionary.thefreedictionary.com/mesogastrium mesogastium MA:0001617 mesogastrium http://www.vivo.colostate.edu/hbooks/pathphys/misc_topics/peritoneum.html stomach mesentery Obol:obol ventriculus mesentery OBOL:automatic A mesentery that surrounds the heart. EHDAA:432 EMAPA:16212 RETIRED_EHDAA2:0000739 VHOG:0000353 heart mesentery uberon cardiac mesentery mesocardium UBERON:0003282 mesentery of heart A mesentery that surrounds the heart. MA:th heart mesentery OBOL:automatic cardiac mesentery EMAPA:16212 mesocardium MA:0000098 A mesentery that is part of a esophagus [Automatically generated definition]. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0001288 EHDAA:2943 EMAPA:16836 MA:0001569 VHOG:0000415 esophagus mesentery gullet mesentery mesentery of esophagus mesentery of gullet meso-esophagus oesophagus mesentery uberon UBERON:0003283 mesentery of oesophagus A mesentery that is part of a esophagus [Automatically generated definition]. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000415 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ esophagus mesentery MA:0001569 gullet mesentery OBOL:automatic mesentery of esophagus OBOL:automatic mesentery of gullet OBOL:automatic oesophagus mesentery VHOG:0000415 A mesentery that is part of a midgut [Automatically generated definition]. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0001202 EHDAA:3031 EMAPA:16721 EMAPA:17039 EMAPA:17197 VHOG:0000413 midgut mesentery uberon UBERON:0003284 mesentery of midgut A mesentery that is part of a midgut [Automatically generated definition]. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000413 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ midgut mesentery OBOL:automatic A gland that is part of a foregut [Automatically generated definition]. EHDAA2:0000567 EHDAA:950 EMAPA:16557 VHOG:0000650 foregut gland uberon UBERON:0003294 gland of foregut A gland that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut gland OBOL:automatic Racemose mucous glands beneath the mucous membrane of the pharynx. BTO:0004849 EHDAA2:0001461 EHDAA:2967 FMA:55075 pharynx gland uberon glandulae pharyngeae UBERON:0003295 pharyngeal gland BTO Racemose mucous glands beneath the mucous membrane of the pharynx. http://www.biology-online.org/dictionary/ pharynx gland EHDAA2:0001461 glandulae pharyngeae BTO:0004849 A gland that is part of a integumental system [Automatically generated definition]. EHDAA2:0000837 EHDAA:6522 EMAPA:17758 MA:0000144 VHOG:0000654 integumental gland integumental system gland integumentary gland uberon UBERON:0003297 gland of integumental system A gland that is part of a integumental system [Automatically generated definition]. OBOL:automatic integumental gland http://orcid.org/0000-0002-6601-2165 integumental system gland http://orcid.org/0000-0002-6601-2165 integumentary gland http://orcid.org/0000-0002-6601-2165 A blood island that is part of a mesoderm. in EHDAA2, gives rise to blood and dorsal aorta UBERON:0003305 EHDAA2:0003241 EHDAA:170 EMAPA:16115 mesoderm blood islands uberon mesenchyme blood island UBERON:0003304 mesoderm blood island EHDAA2 EHDAA2 A blood island that is part of a mesoderm. OBOL:automatic in EHDAA2, gives rise to blood and dorsal aorta EHDAA2 mesoderm blood islands EHDAA2:0003241 mesenchyme blood island OBOL:automatic Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 EHDAA:2910 EMAPA:16673 VHOG:0001084 mesenchyme of eye uberon UBERON:0003314 eye mesenchyme EHDAA2 Mesenchyme that is part of a developing camera-type eye. OBOL:automatic mesenchyme of eye OBOL:automatic Mesenchyme that is part of a developing ovary [Automatically generated definition]. EHDAA2:0001362 EHDAA:8128 VHOG:0001441 female reproductive system gonad mesenchyme female reproductive system gonada mesenchyme gonad of female reproductive system mesenchyme gonada of female reproductive system mesenchyme mesenchyme of female reproductive system gonad mesenchyme of female reproductive system gonada mesenchyme of gonad of female reproductive system mesenchyme of gonada of female reproductive system ovary mesenchyme uberon UBERON:0003315 mesenchyme of ovary Mesenchyme that is part of a developing ovary [Automatically generated definition]. OBOL:automatic female reproductive system gonad mesenchyme OBOL:automatic female reproductive system gonada mesenchyme OBOL:automatic gonad of female reproductive system mesenchyme OBOL:automatic gonada of female reproductive system mesenchyme OBOL:automatic mesenchyme of female reproductive system gonad OBOL:automatic mesenchyme of female reproductive system gonada OBOL:automatic mesenchyme of gonad of female reproductive system OBOL:automatic mesenchyme of gonada of female reproductive system OBOL:automatic ovary mesenchyme OBOL:automatic The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme. UBERON:0003264 EHDAA2:0002216 EHDAA:168 EHDAA:205 EMAPA:16087 EMAPA:16267 VHOG:0000503 VHOG:0000617 yolk sac mesenchyme uberon UBERON:0003316 mesenchyme of yolk sac The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme. UBERON:cjm yolk sac mesenchyme OBOL:automatic Mesenchyme that is part of a developing upper jaw [Automatically generated definition]. EHDAA2:0002124 EHDAA:8031 EMAPA:17929 VHOG:0001099 mesenchyme of palatoquadrate arch palatoquadrate arch mesenchyme upper jaw mesenchyme uberon UBERON:0003323 mesenchyme of upper jaw EHDAA2 Mesenchyme that is part of a developing upper jaw [Automatically generated definition]. OBOL:automatic mesenchyme of palatoquadrate arch OBOL:automatic palatoquadrate arch mesenchyme OBOL:automatic upper jaw mesenchyme OBOL:automatic Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. EHDAA2:0001024 EHDAA:8003 EMAPA:17916 VHOG:0001069 lower jaw mesenchyme mesenchyme of ventral mandibular arch ventral mandibular arch mesenchyme uberon UBERON:0003324 mesenchyme of lower jaw EHDAA2 Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. OBOL:automatic lower jaw mesenchyme OBOL:automatic mesenchyme of ventral mandibular arch OBOL:automatic ventral mandibular arch mesenchyme OBOL:automatic A submucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27217 EMAPA:27227 EMAPA:27535 FMA:85399 SCTID:7892006 anal canal submucosa anal canal viewed anatomically submucosa anal region submucosa anatomical anal canal submucosa submucosa of anal canal viewed anatomically submucosa of anal region submucosa of anatomical anal canal uberon UBERON:0003329 submucosa of anal canal A submucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic anal canal submucosa OBOL:automatic anal canal viewed anatomically submucosa OBOL:automatic anal region submucosa OBOL:automatic anatomical anal canal submucosa OBOL:automatic submucosa of anal canal viewed anatomically OBOL:automatic submucosa of anal region OBOL:automatic submucosa of anatomical anal canal OBOL:automatic The submucous layer of the wall of the rectum. BTO:0002114 EMAPA:27083 FMA:15034 SCTID:71683001 rectal submucosa rectum submucosa tela submucosa recti uberon UBERON:0003330 submucosa of rectum The submucous layer of the wall of the rectum. BTO:0002114 rectal submucosa FMA:15034 rectum submucosa OBOL:automatic tela submucosa recti BTO:0002114 A submucosa that is part of a colon [Automatically generated definition]. EMAPA:27379 FMA:14985 MA:0003200 SCTID:61647009 colon submucosa colonic submucosa large bowel submucosa submucosa of large bowel uberon UBERON:0003331 submucosa of colon A submucosa that is part of a colon [Automatically generated definition]. OBOL:automatic colon submucosa OBOL:automatic colonic submucosa FMA:14985 large bowel submucosa OBOL:automatic submucosa of large bowel OBOL:automatic A submucosa that is part of a duodenum [Automatically generated definition]. EMAPA:27027 EMAPA:27097 EMAPA:27239 FMA:14943 MA:0003213 SCTID:76519004 doudenal submucosa duodenal submucosa duodenum submucosa uberon UBERON:0003332 submucosa of duodenum A submucosa that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal submucosa FMA:14943 duodenal submucosa FMA:14943 duodenum submucosa OBOL:automatic A serous membrane that is part of a rectum [Automatically generated definition]. EMAPA:27087 FMA:15039 rectal serosa rectum serosa rectum serous membrane serous membrane of rectum visceral peritoneum of rectum uberon UBERON:0003334 serosa of rectum A serous membrane that is part of a rectum [Automatically generated definition]. OBOL:automatic rectal serosa FMA:15039 rectum serosa OBOL:automatic rectum serous membrane OBOL:automatic serous membrane of rectum OBOL:automatic visceral peritoneum of rectum FMA:15039 A serous membrane that is part of a colon [Automatically generated definition]. EMAPA:27387 FMA:14990 MA:0003199 SCTID:90132000 colon serosa colon serous membrane colonic serosa large bowel serosa large bowel serous membrane serosa of large bowel serous membrane of colon serous membrane of large bowel visceral peritoneum of colon uberon UBERON:0003335 serosa of colon A serous membrane that is part of a colon [Automatically generated definition]. OBOL:automatic colon serosa OBOL:automatic colon serous membrane OBOL:automatic colonic serosa FMA:14990 large bowel serosa OBOL:automatic large bowel serous membrane OBOL:automatic serosa of large bowel OBOL:automatic serous membrane of colon OBOL:automatic serous membrane of large bowel OBOL:automatic visceral peritoneum of colon FMA:14990 A serous membrane that is part of a duodenum [Automatically generated definition]. 1st part serosa, 2nd - 4th adventitia EMAPA:27247 FMA:14948 MA:0003212 SCTID:1236009 doudenal serosa duodenal serosa duodenum serosa duodenum serous membrane serous membrane of duodenum visceral peritoneum of duodenum uberon UBERON:0003336 serosa of duodenum A serous membrane that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal serosa FMA:14948 duodenal serosa FMA:14948 duodenum serosa OBOL:automatic duodenum serous membrane OBOL:automatic serous membrane of duodenum OBOL:automatic visceral peritoneum of duodenum FMA:14948 A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS BIRNLEX:2548 BTO:0001123 EMAPA:32814 MA:0001161 peripheral nervous system ganglion uberon UBERON:0003338 ganglion of peripheral nervous system A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). BIRNLEX:2548 we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS MA peripheral nervous system ganglion OBOL:automatic A ganglion that is part of a central nervous system [Automatically generated definition]. this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia EHDAA2:0000227 EMAPA:16658 FMA:83843 central nervous system ganglion ganglion of neuraxis neuraxis ganglion uberon UBERON:0003339 ganglion of central nervous system A ganglion that is part of a central nervous system [Automatically generated definition]. OBOL:automatic this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia FMA central nervous system ganglion OBOL:automatic ganglion of neuraxis OBOL:automatic neuraxis ganglion OBOL:automatic A mucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27531 FMA:74654 NCIT:C60784 SCTID:362170004 UMLS:C0227414 anal canal mucosa anal canal mucosa of organ anal canal mucous membrane anal canal organ mucosa anal canal viewed anatomically mucosa anal canal viewed anatomically mucosa of organ anal canal viewed anatomically mucous membrane anal canal viewed anatomically organ mucosa anal mucosa anal mucous membrane anal region mucosa anal region mucosa of organ anal region mucous membrane anal region organ mucosa anatomical anal canal mucosa anatomical anal canal mucosa of organ anatomical anal canal mucous membrane anatomical anal canal organ mucosa mucosa of anal canal viewed anatomically mucosa of anal region mucosa of anatomical anal canal mucosa of organ of anal canal mucosa of organ of anal canal viewed anatomically mucosa of organ of anal region mucosa of organ of anatomical anal canal mucous membrane of anal canal mucous membrane of anal canal viewed anatomically mucous membrane of anal region mucous membrane of anatomical anal canal organ mucosa of anal canal organ mucosa of anal canal viewed anatomically organ mucosa of anal region organ mucosa of anatomical anal canal uberon UBERON:0003342 mucosa of anal canal A mucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic UMLS:C0227414 ncithesaurus:Anal_Mucosa anal canal mucosa OBOL:automatic anal canal mucosa of organ OBOL:automatic anal canal mucous membrane OBOL:automatic anal canal organ mucosa OBOL:automatic anal canal viewed anatomically mucosa OBOL:automatic anal canal viewed anatomically mucosa of organ OBOL:automatic anal canal viewed anatomically mucous membrane OBOL:automatic anal canal viewed anatomically organ mucosa OBOL:automatic anal mucosa FMA:74654 anal mucous membrane FMA:74654 anal region mucosa OBOL:automatic anal region mucosa of organ OBOL:automatic anal region mucous membrane OBOL:automatic anal region organ mucosa OBOL:automatic anatomical anal canal mucosa OBOL:automatic anatomical anal canal mucosa of organ OBOL:automatic anatomical anal canal mucous membrane OBOL:automatic anatomical anal canal organ mucosa OBOL:automatic mucosa of anal canal viewed anatomically OBOL:automatic mucosa of anal region OBOL:automatic mucosa of anatomical anal canal OBOL:automatic mucosa of organ of anal canal OBOL:automatic mucosa of organ of anal canal viewed anatomically OBOL:automatic mucosa of organ of anal region OBOL:automatic mucosa of organ of anatomical anal canal OBOL:automatic mucous membrane of anal canal OBOL:automatic mucous membrane of anal canal viewed anatomically OBOL:automatic mucous membrane of anal region OBOL:automatic mucous membrane of anatomical anal canal OBOL:automatic organ mucosa of anal canal OBOL:automatic organ mucosa of anal canal viewed anatomically OBOL:automatic organ mucosa of anal region OBOL:automatic organ mucosa of anatomical anal canal OBOL:automatic A mucosa that is part of a oral opening [Automatically generated definition]. EMAPA:26937 SCTID:362083000 mucosa of oral opening mucosa of oral part of face mucosa of organ of oral opening mucosa of organ of oral part of face mucosa of organ of oral region mucosa of organ of subdivision of mouth mucosa of subdivision of mouth mucous membrane of oral opening mucous membrane of oral part of face mucous membrane of oral region mucous membrane of subdivision of mouth oral opening mucosa oral opening mucosa of organ oral opening mucous membrane oral opening organ mucosa oral part of face mucosa oral part of face mucosa of organ oral part of face mucous membrane oral part of face organ mucosa oral region mucosa oral region mucosa of organ oral region mucous membrane oral region organ mucosa organ mucosa of oral opening organ mucosa of oral part of face organ mucosa of oral region organ mucosa of subdivision of mouth subdivision of mouth mucosa subdivision of mouth mucosa of organ subdivision of mouth mucous membrane subdivision of mouth organ mucosa uberon UBERON:0003343 mucosa of oral region A mucosa that is part of a oral opening [Automatically generated definition]. OBOL:automatic mucosa of oral opening OBOL:automatic mucosa of oral part of face OBOL:automatic mucosa of organ of oral opening OBOL:automatic mucosa of organ of oral part of face OBOL:automatic mucosa of organ of oral region OBOL:automatic mucosa of organ of subdivision of mouth OBOL:automatic mucosa of subdivision of mouth OBOL:automatic mucous membrane of oral opening OBOL:automatic mucous membrane of oral part of face OBOL:automatic mucous membrane of oral region OBOL:automatic mucous membrane of subdivision of mouth OBOL:automatic oral opening mucosa OBOL:automatic oral opening mucosa of organ OBOL:automatic oral opening mucous membrane OBOL:automatic oral opening organ mucosa OBOL:automatic oral part of face mucosa OBOL:automatic oral part of face mucosa of organ OBOL:automatic oral part of face mucous membrane OBOL:automatic oral part of face organ mucosa OBOL:automatic oral region mucosa OBOL:automatic oral region mucosa of organ OBOL:automatic oral region mucous membrane OBOL:automatic oral region organ mucosa OBOL:automatic organ mucosa of oral opening OBOL:automatic organ mucosa of oral part of face OBOL:automatic organ mucosa of oral region OBOL:automatic organ mucosa of subdivision of mouth OBOL:automatic subdivision of mouth mucosa OBOL:automatic subdivision of mouth mucosa of organ OBOL:automatic subdivision of mouth mucous membrane OBOL:automatic subdivision of mouth organ mucosa OBOL:automatic A mucosa that is part of a rectum [Automatically generated definition]. CALOHA:TS-2107 EMAPA:27081 FMA:15033 MA:0003218 SCTID:362167003 mucosa of organ of rectum mucous membrane of rectum organ mucosa of rectum rectal mucosa rectal mucous membrane rectum mucosa rectum mucosa of organ rectum mucous membrane rectum organ mucosa uberon UBERON:0003346 mucosa of rectum A mucosa that is part of a rectum [Automatically generated definition]. OBOL:automatic mucosa of organ of rectum OBOL:automatic mucous membrane of rectum OBOL:automatic organ mucosa of rectum OBOL:automatic rectal mucosa FMA:15033 rectal mucous membrane FMA:15033 rectum mucosa OBOL:automatic rectum mucosa of organ OBOL:automatic rectum mucous membrane OBOL:automatic rectum organ mucosa OBOL:automatic A layer of epithelial cells on the surface of the mucosa. BTO:0003752 uberon lamina epithelialis mucosa lamina epithelialis mucosae UBERON:0003350 lies on top of lamina propria epithelium of mucosa A layer of epithelial cells on the surface of the mucosa. BTO:0003752 lamina epithelialis mucosa BTO:0003752 lamina epithelialis mucosae BTO:0003752 An epithelium that is part of a pharynx [Automatically generated definition]. Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] BSA:0000112 BTO:0005240 EMAPA:16708 MA:0002725 RETIRED_EHDAA2:0001460 TAO:0001174 XAO:0003202 ZFA:0001174 epithelial tissue of pharynx epithelium of pharynx pharynx epithelial tissue pharynx epithelium uberon UBERON:0003351 pharyngeal epithelium ZFA ZFA An epithelium that is part of a pharynx [Automatically generated definition]. OBOL:automatic Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001174 TAO ZFIN:curator epithelial tissue of pharynx OBOL:automatic epithelium of pharynx OBOL:automatic pharynx epithelial tissue OBOL:automatic pharynx epithelium OBOL:automatic An epithelium that is part of a midgut. BTO:0005053 EHDAA2:0001195 EMAPA:16569 MA:0003205 epithelial tissue of midgut midgut epithelial tissue midgut epithelium uberon UBERON:0003352 epithelium of midgut BTO An epithelium that is part of a midgut. OBOL:automatic epithelial tissue of midgut OBOL:automatic midgut epithelial tissue OBOL:automatic midgut epithelium BTO:0005053 OBOL:automatic An epithelium that is part of a hindgut [Automatically generated definition]. EHDAA2:0000782 EMAPA:16717 MA:0003206 epithelial tissue of hindgut hindgut epithelial tissue hindgut epithelium uberon UBERON:0003353 epithelium of hindgut An epithelium that is part of a hindgut [Automatically generated definition]. OBOL:automatic epithelial tissue of hindgut OBOL:automatic hindgut epithelial tissue OBOL:automatic hindgut epithelium OBOL:automatic An epithelium that is part of a rectum [Automatically generated definition]. CALOHA:TS-2066 EHDAA2:0001594 EMAPA:17898 FMA:17510 MA:0003219 VHOG:0001037 epithelial tissue of rectum rectal epithelium rectum epithelial tissue rectum epithelium uberon UBERON:0003354 epithelium of rectum An epithelium that is part of a rectum [Automatically generated definition]. OBOL:automatic epithelial tissue of rectum OBOL:automatic rectal epithelium FMA:17510 rectum epithelial tissue OBOL:automatic rectum epithelium OBOL:automatic An epithelium that is part of a right lung [Automatically generated definition]. EMAPA:17663 MA:0003132 epithelial tissue of right lung right lung epithelial tissue right lung epithelium uberon UBERON:0003364 epithelium of right lung An epithelium that is part of a right lung [Automatically generated definition]. OBOL:automatic epithelial tissue of right lung OBOL:automatic right lung epithelial tissue OBOL:automatic right lung epithelium OBOL:automatic An epithelium that is part of a left lung [Automatically generated definition]. EMAPA:17655 MA:0003131 epithelial tissue of left lung left lung epithelial tissue left lung epithelium uberon UBERON:0003365 epithelium of left lung An epithelium that is part of a left lung [Automatically generated definition]. OBOL:automatic epithelial tissue of left lung OBOL:automatic left lung epithelial tissue OBOL:automatic left lung epithelium OBOL:automatic An unilaminar epithelium that surrounds a pelvic appendage bud. UBERON:0005232 EHDAA2:0001034 EMAPA:16780 VHOG:0001048 hindlimb ectoderm hindlimb bud ectoderm hindlimb ectoderm lower limb bud ectoderm pelvic fin bud ectoderm uberon leg ectoderm UBERON:0003371 pelvic appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pelvic appendage bud. OBOL:automatic hindlimb ectoderm VHOG:0001048 hindlimb bud ectoderm EMAPA:16780 hindlimb ectoderm VHOG:0001048 lower limb bud ectoderm EHDAA2:0001034 pelvic fin bud ectoderm leg ectoderm OBOL:automatic An unilaminar epithelium that surrounds a pectoral appendage bud. UBERON:0005231 UBERON:0005663 EHDAA2:0002134 EMAPA:16407 VHOG:0001047 forelimb bud ectoderm forelimb ectoderm pectoral fin bud ectoderm upper limb bud ectoderm wing ectoderm uberon arm ectoderm UBERON:0003372 pectoral appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pectoral appendage bud. OBOL:automatic forelimb bud ectoderm EMAPA:16407 forelimb ectoderm VHOG:0001047 pectoral fin bud ectoderm upper limb bud ectoderm EHDAA2:0002134 wing ectoderm Geisha:syn NCBITaxon:8782 arm ectoderm OBOL:automatic A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. EHDAA2:0004155 EMAPA:17326 FMA:7282 SCTID:362018002 VHOG:0001227 cardiac muscle of cardiac right atrium cardiac muscle of heart right atrium cardiac muscle tissue of heart right atrium cardiac muscle tissue of right atrium cardiac muscle tissue of right atrium of heart myocardium of right atrium right atrium heart muscle right atrium myocardium textus muscularis of myocardium of right atrium textus muscularis of myocardium of right atrium of heart textus muscularis of myocardium of right cardiac atrium uberon UBERON:0003379 cardiac muscle of right atrium A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. OBOL:automatic cardiac muscle of cardiac right atrium OBOL:automatic cardiac muscle of heart right atrium OBOL:automatic cardiac muscle tissue of heart right atrium OBOL:automatic cardiac muscle tissue of right atrium OBOL:automatic cardiac muscle tissue of right atrium of heart OBOL:automatic right atrium heart muscle EHDAA2:0004155 right atrium myocardium VHOG:0001227 textus muscularis of myocardium of right atrium OBOL:automatic textus muscularis of myocardium of right atrium of heart OBOL:automatic textus muscularis of myocardium of right cardiac atrium OBOL:automatic A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. EHDAA2:0004154 EMAPA:17320 FMA:7285 SCTID:189936008 VHOG:0001225 cardiac left atrium cardiac muscle cardiac left atrium cardiac muscle tissue cardiac muscle of cardiac left atrium cardiac muscle of heart left atrium cardiac muscle of left atrium of heart left atrium heart muscle left atrium myocardium myocardium of left atrium textus muscularis of myocardium of cardiac left atrium textus muscularis of myocardium of heart left atrium textus muscularis of myocardium of left atrium textus muscularis of myocardium of left atrium of heart textus muscularis of myocardium of left cardiac atrium uberon UBERON:0003380 cardiac muscle of left atrium A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. OBOL:automatic cardiac left atrium cardiac muscle OBOL:automatic cardiac left atrium cardiac muscle tissue OBOL:automatic cardiac muscle of cardiac left atrium OBOL:automatic cardiac muscle of heart left atrium OBOL:automatic cardiac muscle of left atrium of heart OBOL:automatic left atrium heart muscle EHDAA2:0004154 left atrium myocardium VHOG:0001225 textus muscularis of myocardium of cardiac left atrium OBOL:automatic textus muscularis of myocardium of heart left atrium OBOL:automatic textus muscularis of myocardium of left atrium OBOL:automatic textus muscularis of myocardium of left atrium of heart OBOL:automatic textus muscularis of myocardium of left cardiac atrium OBOL:automatic A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. EMAPA:17342 FMA:83452 VHOG:0001236 cardiac muscle tissue of right ventricle right ventricular cardiac muscle tissue uberon right ventricle cardiac muscle UBERON:0003381 cardiac muscle of right ventricle A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of right ventricle FMA:83452 right ventricular cardiac muscle tissue GO:0003221 right ventricle cardiac muscle VHOG:0001236 A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. EMAPA:17339 FMA:83453 VHOG:0001234 cardiac muscle tissue of left ventricle left ventricular cardiac muscle tissue uberon left ventricle cardiac muscle UBERON:0003382 cardiac muscle of left ventricle A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of left ventricle FMA:83453 left ventricular cardiac muscle tissue GO:0003220 left ventricle cardiac muscle VHOG:0001234 A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. EHDAA2:0004158 EMAPA:17335 FMA:84084 VHOG:0000999 cardiac muscle of interventricular septum cardiac muscle tissue of interventricular septum interventricular septum cardiac muscle interventricular septum heart muscle interventricular septum myocardium uberon interventricular septum muscle UBERON:0003383 cardiac muscle tissue of interventricular septum A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of interventricular septum FMA:84084 interventricular septum cardiac muscle VHOG:0000999 interventricular septum heart muscle EHDAA2:0004158 interventricular septum myocardium VHOG:0000999 interventricular septum muscle http://orcid.org/0000-0002-6601-2165 A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. EMAPA:18963 pharynx skeletal muscle pharynx skeletal muscle tissue skeletal muscle tissue of pharynx uberon UBERON:0003384 skeletal muscle tissue of pharynx A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. OBOL:automatic pharynx skeletal muscle OBOL:automatic pharynx skeletal muscle tissue OBOL:automatic skeletal muscle tissue of pharynx OBOL:automatic Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi. Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle EMAPA:18807 MA:0001268 ocular smooth muscle uberon UBERON:0003386 smooth muscle of eye Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi. MGI:cwg MP:0005247 ocular smooth muscle MA:0001268 A mesothelium that is part of a pericardium [Automatically generated definition]. RETIRED_EHDAA2:0001436 cavity of pericardial sac meso-epithelium cavity of pericardial sac mesothelium meso-epithelium of cavity of pericardial sac meso-epithelium of pericardial cavity mesothelium of cavity of pericardial sac pericardial cavity meso-epithelium pericardial cavity mesothelium uberon UBERON:0003388 mesothelium of pericardial cavity A mesothelium that is part of a pericardium [Automatically generated definition]. OBOL:automatic cavity of pericardial sac meso-epithelium OBOL:automatic cavity of pericardial sac mesothelium OBOL:automatic meso-epithelium of cavity of pericardial sac OBOL:automatic meso-epithelium of pericardial cavity OBOL:automatic mesothelium of cavity of pericardial sac OBOL:automatic pericardial cavity meso-epithelium OBOL:automatic pericardial cavity mesothelium OBOL:automatic A mesothelium that is part of a diaphragm [Automatically generated definition]. EMAPA:18429 diaphragm meso-epithelium diaphragm mesothelium meso-epithelium of diaphragm meso-epithelium of thoracic diaphragm mesothelium of thoracic diaphragm thoracic diaphragm meso-epithelium thoracic diaphragm mesothelium uberon UBERON:0003389 mesothelium of diaphragm A mesothelium that is part of a diaphragm [Automatically generated definition]. OBOL:automatic diaphragm meso-epithelium OBOL:automatic diaphragm mesothelium OBOL:automatic meso-epithelium of diaphragm OBOL:automatic meso-epithelium of thoracic diaphragm OBOL:automatic mesothelium of thoracic diaphragm OBOL:automatic thoracic diaphragm meso-epithelium OBOL:automatic thoracic diaphragm mesothelium OBOL:automatic A mesothelium that is part of a pleural cavity [Automatically generated definition]. BTO:0003155 EHDAA2:0001476 EMAPA:16775 FMA:18148 meso-epithelium of pleural cavity mesothelium of pleura pleural cavity meso-epithelium pleural cavity mesothelium pleural mesothelium uberon pleura UBERON:0003390 mesothelium of pleural cavity A mesothelium that is part of a pleural cavity [Automatically generated definition]. OBOL:automatic meso-epithelium of pleural cavity OBOL:automatic mesothelium of pleura FMA:18148 pleural cavity meso-epithelium OBOL:automatic pleural cavity mesothelium OBOL:automatic pleural mesothelium EMAPA:16775 pleura EMAPA:16775 A mesentery that is part of a urinary system [Automatically generated definition]. EMAPA:17367 MA:0003233 excretory system mesentery mesentery of excretory system mesentery of renal system mesentery of systema urinaria renal system mesentery systema urinaria mesentery urinary system mesentery uberon UBERON:0003393 mesentery of urinary system A mesentery that is part of a urinary system [Automatically generated definition]. OBOL:automatic excretory system mesentery OBOL:automatic mesentery of excretory system OBOL:automatic mesentery of renal system OBOL:automatic mesentery of systema urinaria OBOL:automatic renal system mesentery OBOL:automatic systema urinaria mesentery OBOL:automatic urinary system mesentery OBOL:automatic A mesentery that is part of a hindgut [Automatically generated definition]. EMAPA:16718 hindgut mesentery uberon UBERON:0003394 mesentery of hindgut A mesentery that is part of a hindgut [Automatically generated definition]. OBOL:automatic hindgut mesentery OBOL:automatic A mesentery that is part of a rectum [Automatically generated definition]. EMAPA:18664 rectum mesentery uberon UBERON:0003395 mesentery of rectum A mesentery that is part of a rectum [Automatically generated definition]. OBOL:automatic rectum mesentery OBOL:automatic A mesentery that is part of a colon [Automatically generated definition]. EMAPA:18942 FMA:14645 SCTID:245457004 colon mesentery large bowel mesentery large intestinal mesentery mesentery of large bowel mesentery of large intestine mesocolon uberon UBERON:0003396 mesentery of colon FMA A mesentery that is part of a colon [Automatically generated definition]. OBOL:automatic colon mesentery OBOL:automatic large bowel mesentery OBOL:automatic large intestinal mesentery FMA:14645 mesentery of large bowel OBOL:automatic mesentery of large intestine FMA:14645 mesocolon https://github.com/obophenotype/uberon/issues/1473 A mesentery that is part of a duodenum [Automatically generated definition]. EMAPA:19081 duodenum mesentery uberon UBERON:0003397 mesentery of duodenum A mesentery that is part of a duodenum [Automatically generated definition]. OBOL:automatic duodenum mesentery OBOL:automatic A cartilage element that is part of a respiratory system [Automatically generated definition]. EMAPA:18694 MA:0001818 apparatus respiratorius cartilage cartilage of apparatus respiratorius respiratory system cartilage uberon UBERON:0003406 cartilage of respiratory system A cartilage element that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius cartilage OBOL:automatic cartilage of apparatus respiratorius OBOL:automatic respiratory system cartilage OBOL:automatic A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon UBERON:0003408 gland of digestive tract A gland that is part of a digestive tract [Automatically generated definition]. OBOL:automatic digestive tract gland OBOL:automatic gland of digestive tract OBOL:automatic gland of lower gastrointestinal tract OBOL:automatic gut gland MA:0003202 lower gastrointestinal tract gland OBOL:automatic Mesenchyme that is part of a pelvic appendage bud. Mesoderm part of pelvic fin bud.[TAO] EHDAA2:0001035 EMAPA:16781 TAO:0001386 ZFA:0001386 leg mesenchyme lower limb bud mesenchyme hindlimb bud mesenchyme mesoderm pelvic fin bud pelvic fin bud mesenchyme uberon UBERON:0003412 pelvic appendage bud mesenchyme Mesenchyme that is part of a pelvic appendage bud. OBOL:automatic Mesoderm part of pelvic fin bud.[TAO] 2012-08-14 TAO:0001386 TAO ZFIN:curator leg mesenchyme OBOL:automatic lower limb bud mesenchyme EHDAA2:0001035 hindlimb bud mesenchyme EMAPA:16781 mesoderm pelvic fin bud ZFA:0001386 pelvic fin bud mesenchyme Mesenchyme that is part of a pectoral appendage bud. Mesoderm that is part of the pectoral fin bud.[TAO] UBERON:0005703 EHDAA2:0002135 EHDAA:1703 EMAPA:16408 TAO:0000789 ZFA:0000789 arm mesenchyme forelimb bud mesenchyme mesoderm pectoral fin bud pectoral fin bud mesenchyme upper limb bud mesenchyme wing mesenchyme uberon UBERON:0003413 pectoral appendage bud mesenchyme Mesenchyme that is part of a pectoral appendage bud. OBOL:automatic Mesoderm that is part of the pectoral fin bud.[TAO] 2012-08-14 TAO:0000789 TAO ZFIN:curator arm mesenchyme OBOL:automatic forelimb bud mesenchyme EMAPA:16408 mesoderm pectoral fin bud ZFA:0000789 pectoral fin bud mesenchyme upper limb bud mesenchyme EHDAA2:0002135 wing mesenchyme OBOL:automatic An adipose tissue that is part of a dermis [Automatically generated definition]. MA:0000798 adipose tissue of dermis dermis fat tissue dermis fatty tissue fat tissue of dermis fatty tissue of dermis uberon UBERON:0003426 dermis adipose tissue An adipose tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic adipose tissue of dermis OBOL:automatic dermis fat tissue OBOL:automatic dermis fatty tissue OBOL:automatic fat tissue of dermis OBOL:automatic fatty tissue of dermis OBOL:automatic A nerve that is part of an abdomen [Automatically generated definition]. MA:0000521 nerve of abdomen uberon UBERON:0003429 abdomen nerve A nerve that is part of an abdomen [Automatically generated definition]. OBOL:automatic nerve of abdomen OBOL:automatic A nerve that is part of a neck [Automatically generated definition]. EMAPA:37263 MA:0000588 neck (volume) nerve nerve of neck nerve of neck (volume) uberon UBERON:0003430 neck nerve A nerve that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37263 MA:th neck (volume) nerve OBOL:automatic nerve of neck OBOL:automatic nerve of neck (volume) OBOL:automatic Any nerve that innervates the iris. added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea EMAPA:35449 MA:0001291 nerve of iris ciliary nerve uberon UBERON:0003438 iris nerve Any nerve that innervates the iris. UBERON:cjm nerve of iris OBOL:automatic A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). EMAPA:37264 MA:0000515 nerve of torso nerve of trunk torso nerve uberon trunk nerve UBERON:0003439 nerve of trunk region A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). http://orcid.org/0000-0002-6601-2165 EMAPA:37264 MA:th nerve of torso OBOL:automatic nerve of trunk OBOL:automatic torso nerve OBOL:automatic trunk nerve MA:0000515 A nerve that is located in a thoracic cavity [Automatically generated definition]. consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve EMAPA:37267 MA:0000556 cavity of chest nerve cavity of thorax nerve chest cavity nerve nerve of cavity of chest nerve of cavity of thorax nerve of chest cavity nerve of pectoral cavity nerve of thoracic cavity pectoral cavity nerve uberon UBERON:0003443 thoracic cavity nerve A nerve that is located in a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37267 MA:th cavity of chest nerve OBOL:automatic cavity of thorax nerve OBOL:automatic chest cavity nerve OBOL:automatic nerve of cavity of chest OBOL:automatic nerve of cavity of thorax OBOL:automatic nerve of chest cavity OBOL:automatic nerve of pectoral cavity OBOL:automatic nerve of thoracic cavity OBOL:automatic pectoral cavity nerve OBOL:automatic A nerve that is part of a pelvis [Automatically generated definition]. EMAPA:37269 MA:0000542 nerve of pelvis uberon UBERON:0003444 pelvis nerve A nerve that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37269 MA:th nerve of pelvis OBOL:automatic A portion of cardiac muscle tissue that is part of a trabecula carnea [Automatically generated definition]. EMAPA:36573 FMA:84428 MA:0002833 cardiac muscle muscle tissue of trabecula carnea cardiac muscle of trabecula carnea cardiac muscle textus muscularis of trabecula carnea cardiac muscle tissue of trabecula carnea heart muscle muscle tissue of trabecula carnea heart muscle textus muscularis of trabecula carnea heart myocardium muscle tissue of trabecula carnea heart myocardium textus muscularis of trabecula carnea muscle of heart muscle tissue of trabecula carnea muscle of heart textus muscularis of trabecula carnea muscle tissue of cardiac muscle of trabecula carnea muscle tissue of heart muscle of trabecula carnea muscle tissue of heart myocardium of trabecula carnea muscle tissue of muscle of heart of trabecula carnea muscle tissue of myocardium of trabecula carnea myocardium muscle tissue of trabecula carnea myocardium textus muscularis of trabecula carnea textus muscularis of cardiac muscle of trabecula carnea textus muscularis of heart muscle of trabecula carnea textus muscularis of heart myocardium of trabecula carnea textus muscularis of muscle of heart of trabecula carnea textus muscularis of myocardium of trabecula carnea trabecula carnea cardiac muscle trabecula carnea cardiac muscle muscle tissue trabecula carnea cardiac muscle textus muscularis trabecula carnea heart muscle muscle tissue trabecula carnea heart muscle textus muscularis trabecula carnea heart myocardium muscle tissue trabecula carnea heart myocardium textus muscularis trabecula carnea muscle of heart muscle tissue trabecula carnea muscle of heart textus muscularis trabecula carnea muscle tissue of cardiac muscle trabecula carnea muscle tissue of heart muscle trabecula carnea muscle tissue of heart myocardium trabecula carnea muscle tissue of muscle of heart trabecula carnea muscle tissue of myocardium trabecula carnea myocardium muscle tissue trabecula carnea myocardium textus muscularis trabecula carnea textus muscularis of cardiac muscle trabecula carnea textus muscularis of heart muscle trabecula carnea textus muscularis of heart myocardium trabecula carnea textus muscularis of muscle of heart trabecula carnea textus muscularis of myocardium uberon UBERON:0003452 trabecula carnea cardiac muscle tissue A portion of cardiac muscle tissue that is part of a trabecula carnea [Automatically generated definition]. OBOL:automatic cardiac muscle muscle tissue of trabecula carnea OBOL:automatic cardiac muscle of trabecula carnea OBOL:automatic cardiac muscle textus muscularis of trabecula carnea OBOL:automatic cardiac muscle tissue of trabecula carnea OBOL:automatic heart muscle muscle tissue of trabecula carnea OBOL:automatic heart muscle textus muscularis of trabecula carnea OBOL:automatic heart myocardium muscle tissue of trabecula carnea OBOL:automatic heart myocardium textus muscularis of trabecula carnea OBOL:automatic muscle of heart muscle tissue of trabecula carnea OBOL:automatic muscle of heart textus muscularis of trabecula carnea OBOL:automatic muscle tissue of cardiac muscle of trabecula carnea OBOL:automatic muscle tissue of heart muscle of trabecula carnea OBOL:automatic muscle tissue of heart myocardium of trabecula carnea OBOL:automatic muscle tissue of muscle of heart of trabecula carnea OBOL:automatic muscle tissue of myocardium of trabecula carnea OBOL:automatic myocardium muscle tissue of trabecula carnea OBOL:automatic myocardium textus muscularis of trabecula carnea OBOL:automatic textus muscularis of cardiac muscle of trabecula carnea OBOL:automatic textus muscularis of heart muscle of trabecula carnea OBOL:automatic textus muscularis of heart myocardium of trabecula carnea OBOL:automatic textus muscularis of muscle of heart of trabecula carnea OBOL:automatic textus muscularis of myocardium of trabecula carnea OBOL:automatic trabecula carnea cardiac muscle OBOL:automatic trabecula carnea cardiac muscle muscle tissue OBOL:automatic trabecula carnea cardiac muscle textus muscularis OBOL:automatic trabecula carnea heart muscle muscle tissue OBOL:automatic trabecula carnea heart muscle textus muscularis OBOL:automatic trabecula carnea heart myocardium muscle tissue OBOL:automatic trabecula carnea heart myocardium textus muscularis OBOL:automatic trabecula carnea muscle of heart muscle tissue OBOL:automatic trabecula carnea muscle of heart textus muscularis OBOL:automatic trabecula carnea muscle tissue of cardiac muscle OBOL:automatic trabecula carnea muscle tissue of heart muscle OBOL:automatic trabecula carnea muscle tissue of heart myocardium OBOL:automatic trabecula carnea muscle tissue of muscle of heart OBOL:automatic trabecula carnea muscle tissue of myocardium OBOL:automatic trabecula carnea myocardium muscle tissue OBOL:automatic trabecula carnea myocardium textus muscularis OBOL:automatic trabecula carnea textus muscularis of cardiac muscle OBOL:automatic trabecula carnea textus muscularis of heart muscle OBOL:automatic trabecula carnea textus muscularis of heart myocardium OBOL:automatic trabecula carnea textus muscularis of muscle of heart OBOL:automatic trabecula carnea textus muscularis of myocardium OBOL:automatic A bone that is part of a head [Automatically generated definition]. EMAPA:35996 MA:0000576 SCTID:118646007 adult head bone adult head bone organ bone of adult head bone of head bone organ of adult head bone organ of head head bone organ uberon craniofacial bone UBERON:0003457 Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone A bone that is part of a head [Automatically generated definition]. OBOL:automatic adult head bone OBOL:automatic adult head bone organ OBOL:automatic bone of adult head OBOL:automatic bone of head OBOL:automatic bone organ of adult head OBOL:automatic bone organ of head OBOL:automatic head bone organ OBOL:automatic craniofacial bone http://orcid.org/0000-0002-6601-2165 A bone that is part of a neck [Automatically generated definition]. EMAPA:37246 MA:0000584 bone of neck bone of neck (volume) bone organ of neck bone organ of neck (volume) neck (volume) bone neck (volume) bone organ neck bone organ uberon UBERON:0003458 neck bone A bone that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37246 MA:th bone of neck OBOL:automatic bone of neck (volume) OBOL:automatic bone organ of neck OBOL:automatic bone organ of neck (volume) OBOL:automatic neck (volume) bone OBOL:automatic neck (volume) bone organ OBOL:automatic neck bone organ OBOL:automatic A bone that is part of a facial skeleton [Automatically generated definition]. test whether 'facial bone' is an exact synonym EMAPA:19019 EMAPA:35924 MA:0001482 MA:0003159 MESH:D005147 NCIT:C63706 SCTID:181799005 UMLS:C0015455 bone of facial skeleton facial bone facial skeleton bone uberon bone of viscerocranium viscerocranium bone UBERON:0003462 facial bone MA A bone that is part of a facial skeleton [Automatically generated definition]. OBOL:automatic MESH:D005147 https://github.com/biopragmatics/biomappings UMLS:C0015455 ncithesaurus:Facial_Bone bone of facial skeleton OBOL:automatic facial bone EMAPA:19019 facial skeleton bone OBOL:automatic bone of viscerocranium OBOL:automatic viscerocranium bone OBOL:automatic A bone that is part of a trunk [Automatically generated definition]. EMAPA:36583 MA:0000512 SCTID:427358002 bone of torso bone of trunk bone organ of torso bone organ of trunk torso bone torso bone organ trunk bone organ uberon UBERON:0003463 trunk bone A bone that is part of a trunk [Automatically generated definition]. OBOL:automatic bone of torso OBOL:automatic bone of trunk OBOL:automatic bone organ of torso OBOL:automatic bone organ of trunk OBOL:automatic torso bone OBOL:automatic torso bone organ OBOL:automatic trunk bone organ OBOL:automatic An artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37569 MA:0001804 uberon UBERON:0003469 respiratory system artery An artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37569 MA:th The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose. EMAPA:37430 FMA:49570 MA:0001917 SCTID:145137009 Wikipedia:Superior_labial_artery arteria labialis superior ramus labialis superior arteriae facialis superior labial artery superior labial branch of facial artery uberon UBERON:0003470 artery of upper lip FMA The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose. Wikipedia:Superior_labial_artery EMAPA:37430 MA:th arteria labialis superior Wikipedia:Superior_labial_artery ramus labialis superior arteriae facialis Wikipedia:Superior_labial_artery superior labial artery FMA:49570 superior labial branch of facial artery FMA:49570 The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 FMA:49567 MA:0001916 SCTID:145036002 Wikipedia:Inferior_labial_artery arteria labialis inferior inferior labial artery inferior labial branch of facial artery ramus labialis inferior (arteria facialis) ramus labialis inferior arteriae facialis uberon UBERON:0003471 artery of lower lip FMA The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. Wikipedia:Inferior_labial_artery EMAPA:37429 MA:th arteria labialis inferior Wikipedia:Inferior_labial_artery inferior labial artery FMA:49567 inferior labial branch of facial artery FMA:49567 ramus labialis inferior (arteria facialis) FMA:TA ramus labialis inferior arteriae facialis Wikipedia:Inferior_labial_artery An artery that is part of a thoracic cavity[cjm]. in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity EMAPA:37241 MA:0001902 MESH:D013895 uberon thoracic artery UBERON:0003473 thoracic cavity artery An artery that is part of a thoracic cavity[cjm]. https://sourceforge.net/tracker/index.php?func=detail&aid=3317815&group_id=76834&atid=1205376 in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity MA EMAPA:37241 MA:th thoracic artery MESH:A07.231.114.891 A vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37584 MA:0001809 MA:0001810 apparatus respiratorius vein respiratory system vein vein of apparatus respiratorius vein of respiratory system uberon UBERON:0003476 respiratory system venous blood vessel A vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37584 MA:th apparatus respiratorius vein OBOL:automatic respiratory system vein OBOL:automatic vein of apparatus respiratorius OBOL:automatic vein of respiratory system OBOL:automatic The inferior labial vein is the vein receiving blood from the upper lip. EMAPA:37204 FMA:52538 MA:0002255 SCTID:422755007 Wikipedia:Superior_labial_vein superior labial vein upper lip vein vena labialis superior uberon UBERON:0003477 vein of upper lip The inferior labial vein is the vein receiving blood from the upper lip. Wikipedia:Superior_labial_vein EMAPA:37204 MA:th superior labial vein FMA:52538 upper lip vein OBOL:automatic vena labialis superior The inferior labial vein is the vein receiving blood from the lower lip. EMAPA:37202 FMA:52541 MA:0002253 SCTID:422955002 Wikipedia:Inferior_labial_vein inferior labial vein lower lip vein vena labialis inferior uberon venae labiales inferiores UBERON:0003478 vein of lower lip http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png The inferior labial vein is the vein receiving blood from the lower lip. Wikipedia:Inferior_labial_vein EMAPA:37202 MA:th inferior labial vein FMA:52541 lower lip vein OBOL:automatic vena labialis inferior venae labiales inferiores Wikipedia:Inferior_labial_vein A vein that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37242 MA:0001903 cavity of chest vein cavity of thorax vein chest cavity vein pectoral cavity vein vein of cavity of chest vein of cavity of thorax vein of chest cavity vein of pectoral cavity vein of thoracic cavity uberon UBERON:0003479 thoracic cavity vein A vein that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37242 MA:th cavity of chest vein OBOL:automatic cavity of thorax vein OBOL:automatic chest cavity vein OBOL:automatic pectoral cavity vein OBOL:automatic vein of cavity of chest OBOL:automatic vein of cavity of thorax OBOL:automatic vein of chest cavity OBOL:automatic vein of pectoral cavity OBOL:automatic vein of thoracic cavity OBOL:automatic A vein that is part of a tail [Automatically generated definition]. see also caudal vein AAO:0011105 EMAPA:37761 MA:0002233 Wikipedia:Tail_vein XAO:0000393 post-vent region vein vein of post-vent region vein of tail uberon caudal vein UBERON:0003481 tail vein A vein that is part of a tail [Automatically generated definition]. OBOL:automatic Wikipedia:Tail_vein EMAPA:37761 MA:th post-vent region vein OBOL:automatic vein of post-vent region OBOL:automatic vein of tail OBOL:automatic caudal vein Wikipedia:Tail_vein An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37575 MA:0001808 apparatus respiratorius blood capillary endothelium apparatus respiratorius capillary endothelium apparatus respiratorius capillary vessel endothelium apparatus respiratorius endothelium of blood capillary apparatus respiratorius endothelium of capillary apparatus respiratorius endothelium of capillary vessel blood capillary endothelium of apparatus respiratorius blood capillary endothelium of respiratory system capillary endothelium of apparatus respiratorius capillary endothelium of respiratory system capillary vessel endothelium of apparatus respiratorius capillary vessel endothelium of respiratory system endothelium of blood capillary of apparatus respiratorius endothelium of blood capillary of respiratory system endothelium of capillary of apparatus respiratorius endothelium of capillary of respiratory system endothelium of capillary vessel of apparatus respiratorius endothelium of capillary vessel of respiratory system respiratory system blood capillary endothelium respiratory system capillary vessel endothelium respiratory system endothelium of blood capillary respiratory system endothelium of capillary respiratory system endothelium of capillary vessel uberon UBERON:0003489 respiratory system capillary endothelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37575 MA:th apparatus respiratorius blood capillary endothelium OBOL:automatic apparatus respiratorius capillary endothelium OBOL:automatic apparatus respiratorius capillary vessel endothelium OBOL:automatic apparatus respiratorius endothelium of blood capillary OBOL:automatic apparatus respiratorius endothelium of capillary OBOL:automatic apparatus respiratorius endothelium of capillary vessel OBOL:automatic blood capillary endothelium of apparatus respiratorius OBOL:automatic blood capillary endothelium of respiratory system OBOL:automatic capillary endothelium of apparatus respiratorius OBOL:automatic capillary endothelium of respiratory system OBOL:automatic capillary vessel endothelium of apparatus respiratorius OBOL:automatic capillary vessel endothelium of respiratory system OBOL:automatic endothelium of blood capillary of apparatus respiratorius OBOL:automatic endothelium of blood capillary of respiratory system OBOL:automatic endothelium of capillary of apparatus respiratorius OBOL:automatic endothelium of capillary of respiratory system OBOL:automatic endothelium of capillary vessel of apparatus respiratorius OBOL:automatic endothelium of capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary endothelium OBOL:automatic respiratory system capillary vessel endothelium OBOL:automatic respiratory system endothelium of blood capillary OBOL:automatic respiratory system endothelium of capillary OBOL:automatic respiratory system endothelium of capillary vessel OBOL:automatic A venule that is part of a respiratory system [Automatically generated definition]. EMAPA:37587 MA:0001813 apparatus respiratorius venule venule of apparatus respiratorius venule of respiratory system uberon UBERON:0003494 respiratory system venule A venule that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37587 MA:th apparatus respiratorius venule OBOL:automatic venule of apparatus respiratorius OBOL:automatic venule of respiratory system OBOL:automatic An arteriole that is part of a respiratory system [Automatically generated definition]. EMAPA:37568 MA:0001803 uberon UBERON:0003495 respiratory system arteriole true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An arteriole that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37568 MA:th A blood vessel that is part of a head [Automatically generated definition]. EMAPA:36610 MA:0000575 SCTID:127865000 adult head blood vessel blood vessel of adult head blood vessel of head uberon UBERON:0003496 head blood vessel true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A blood vessel that is part of a head [Automatically generated definition]. OBOL:automatic adult head blood vessel OBOL:automatic blood vessel of adult head OBOL:automatic blood vessel of head OBOL:automatic A blood vessel that is part of an abdomen [Automatically generated definition]. MA:0000518 blood vessel of abdomen uberon UBERON:0003497 abdomen blood vessel UBERON:0012254 A blood vessel that is part of an abdomen [Automatically generated definition]. OBOL:automatic blood vessel of abdomen OBOL:automatic UBERON:0012254 abdominal aorta artery A blood vessel that is part of a heart [Automatically generated definition]. EMAPA:35397 MA:0002483 blood vessel of heart uberon cardiac blood vessel UBERON:0003498 heart blood vessel A blood vessel that is part of a heart [Automatically generated definition]. OBOL:automatic blood vessel of heart OBOL:automatic cardiac blood vessel EMAPA:35397 A blood vessel that is part of a brain [Automatically generated definition]. EMAPA:35182 MA:0002769 blood vessel of brain uberon UBERON:0003499 brain blood vessel A blood vessel that is part of a brain [Automatically generated definition]. OBOL:automatic blood vessel of brain OBOL:automatic A blood vessel that is part of a cornea [Automatically generated definition]. follow up on tracker item EMAPA:36611 MA:0001241 blood vessel of cornea cornea blood vessel uberon UBERON:0003500 corneal blood vessel A blood vessel that is part of a cornea [Automatically generated definition]. https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/tracker/index.php?func=detail&aid=3564332&group_id=36855&atid=440764 PMID:17051153 blood vessel of cornea OBOL:automatic cornea blood vessel OBOL:automatic A blood vessel that is part of a retina [Automatically generated definition]. EMAPA:36520 GAID:509 MA:0001317 MESH:D012171 SCTID:280692003 XAO:0004153 blood vessel of inner layer of eyeball blood vessel of retina blood vessel of tunica interna of eyeball inner layer of eyeball blood vessel retinal blood vessel tunica interna of eyeball blood vessel uberon UBERON:0003501 retina blood vessel A blood vessel that is part of a retina [Automatically generated definition]. OBOL:automatic blood vessel of inner layer of eyeball OBOL:automatic blood vessel of retina OBOL:automatic blood vessel of tunica interna of eyeball OBOL:automatic inner layer of eyeball blood vessel OBOL:automatic retinal blood vessel OBOL:automatic tunica interna of eyeball blood vessel OBOL:automatic A blood vessel that is part of a neck [Automatically generated definition]. EMAPA:37236 MA:0000583 blood vessel of neck blood vessel of neck (volume) neck (volume) blood vessel uberon UBERON:0003502 neck blood vessel A blood vessel that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37236 MA:th blood vessel of neck OBOL:automatic blood vessel of neck (volume) OBOL:automatic neck (volume) blood vessel OBOL:automatic A blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:35731 EMAPA:35995 MA:0001799 apparatus respiratorius blood vessel blood vessel of apparatus respiratorius blood vessel of respiratory system uberon UBERON:0003504 respiratory system blood vessel A blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius blood vessel OBOL:automatic blood vessel of apparatus respiratorius OBOL:automatic blood vessel of respiratory system OBOL:automatic A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. EMAPA:35144 MA:0000061 uberon UBERON:0003509 only in MA - supertype of artery, arteriole, aorta. arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. https://orcid.org/0000-0002-6601-2165 A blood vessel that is part of a iris [Automatically generated definition]. EMAPA:37387 MA:0001290 ZFA:0005568 blood vessel of iris uberon UBERON:0003511 iris blood vessel A blood vessel that is part of a iris [Automatically generated definition]. OBOL:automatic EMAPA:37387 MA:th blood vessel of iris OBOL:automatic A blood vessel that is part of a lung [Automatically generated definition]. EMAPA:32867 MA:0002457 blood vessel of lung uberon pulmonary vascular element UBERON:0003512 lung blood vessel A blood vessel that is part of a lung [Automatically generated definition]. OBOL:automatic blood vessel of lung OBOL:automatic pulmonary vascular element EMAPA:32867 A blood vessel that is part of a trunk [Automatically generated definition]. EMAPA:37237 MA:0000511 blood vessel of torso blood vessel of trunk torso blood vessel uberon UBERON:0003513 trunk blood vessel A blood vessel that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37237 MA:th blood vessel of torso OBOL:automatic blood vessel of trunk OBOL:automatic torso blood vessel OBOL:automatic A blood vessel that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37240 MA:0000554 blood vessel of cavity of chest blood vessel of cavity of thorax blood vessel of chest cavity blood vessel of pectoral cavity blood vessel of thoracic cavity cavity of chest blood vessel cavity of thorax blood vessel chest cavity blood vessel pectoral cavity blood vessel uberon UBERON:0003519 thoracic cavity blood vessel A blood vessel that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37240 MA:th blood vessel of cavity of chest OBOL:automatic blood vessel of cavity of thorax OBOL:automatic blood vessel of chest cavity OBOL:automatic blood vessel of pectoral cavity OBOL:automatic blood vessel of thoracic cavity OBOL:automatic cavity of chest blood vessel OBOL:automatic cavity of thorax blood vessel OBOL:automatic chest cavity blood vessel OBOL:automatic pectoral cavity blood vessel OBOL:automatic A blood vessel that is part of a pelvis [Automatically generated definition]. EMAPA:37244 MA:0000531 blood vessel of pelvis uberon UBERON:0003520 pelvis blood vessel A blood vessel that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37244 MA:th blood vessel of pelvis OBOL:automatic A blood vessel that is part of a tail [Automatically generated definition]. EMAPA:35848 MA:0000695 blood vessel of post-vent region blood vessel of tail post-vent region blood vessel uberon UBERON:0003524 tail blood vessel A blood vessel that is part of a tail [Automatically generated definition]. OBOL:automatic blood vessel of post-vent region OBOL:automatic blood vessel of tail OBOL:automatic post-vent region blood vessel OBOL:automatic A capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37574 MA:0001807 apparatus respiratorius blood capillary apparatus respiratorius capillary apparatus respiratorius capillary vessel blood capillary of apparatus respiratorius blood capillary of respiratory system capillary of apparatus respiratorius capillary of respiratory system capillary vessel of apparatus respiratorius capillary vessel of respiratory system respiratory system blood capillary respiratory system capillary vessel uberon UBERON:0003526 respiratory system capillary A capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37574 MA:th apparatus respiratorius blood capillary OBOL:automatic apparatus respiratorius capillary OBOL:automatic apparatus respiratorius capillary vessel OBOL:automatic blood capillary of apparatus respiratorius OBOL:automatic blood capillary of respiratory system OBOL:automatic capillary of apparatus respiratorius OBOL:automatic capillary of respiratory system OBOL:automatic capillary vessel of apparatus respiratorius OBOL:automatic capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary OBOL:automatic respiratory system capillary vessel OBOL:automatic A gray matter that is part of a brain [Automatically generated definition]. EMAPA:35184 MA:0000810 NCIT:C49333 UMLS:C1707348 brain grey matter brain grey substance gray matter of brain grey matter of brain grey substance of brain uberon UBERON:0003528 brain gray matter A gray matter that is part of a brain [Automatically generated definition]. OBOL:automatic UMLS:C1707348 ncithesaurus:Cerebral_Gray_Matter brain grey matter MA:0000810 brain grey substance OBOL:automatic gray matter of brain OBOL:automatic grey matter of brain OBOL:automatic grey substance of brain OBOL:automatic A zone of skin that is part of a tail [Automatically generated definition]. EMAPA:36502 MA:0000700 SCTID:67214004 post-vent region skin skin of post-vent region skin of tail uberon UBERON:0003534 tail skin A zone of skin that is part of a tail [Automatically generated definition]. OBOL:automatic post-vent region skin OBOL:automatic skin of post-vent region OBOL:automatic skin of tail OBOL:automatic A portion of connective tissue that is part of a head [Automatically generated definition]. EMAPA:16098 MA:0000577 adult head connective tissue adult head portion of connective tissue adult head textus connectivus connective tissue of adult head connective tissue of head head portion of connective tissue head textus connectivus portion of connective tissue of adult head portion of connective tissue of head textus connectivus of adult head textus connectivus of head uberon UBERON:0003566 head connective tissue A portion of connective tissue that is part of a head [Automatically generated definition]. OBOL:automatic adult head connective tissue OBOL:automatic adult head portion of connective tissue OBOL:automatic adult head textus connectivus OBOL:automatic connective tissue of adult head OBOL:automatic connective tissue of head OBOL:automatic head portion of connective tissue OBOL:automatic head textus connectivus OBOL:automatic portion of connective tissue of adult head OBOL:automatic portion of connective tissue of head OBOL:automatic textus connectivus of adult head OBOL:automatic textus connectivus of head OBOL:automatic A portion of connective tissue that is part of an abdomen [Automatically generated definition]. MA:0000519 abdomen portion of connective tissue abdomen textus connectivus connective tissue of abdomen portion of connective tissue of abdomen textus connectivus of abdomen uberon UBERON:0003567 abdomen connective tissue A portion of connective tissue that is part of an abdomen [Automatically generated definition]. OBOL:automatic abdomen portion of connective tissue OBOL:automatic abdomen textus connectivus OBOL:automatic connective tissue of abdomen OBOL:automatic portion of connective tissue of abdomen OBOL:automatic textus connectivus of abdomen OBOL:automatic A portion of connective tissue that is part of a neck [Automatically generated definition]. EMAPA:37250 MA:0000585 connective tissue of neck connective tissue of neck (volume) neck (volume) connective tissue neck (volume) portion of connective tissue neck (volume) textus connectivus neck portion of connective tissue neck textus connectivus portion of connective tissue of neck portion of connective tissue of neck (volume) textus connectivus of neck textus connectivus of neck (volume) uberon UBERON:0003568 neck connective tissue A portion of connective tissue that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37250 MA:th connective tissue of neck OBOL:automatic connective tissue of neck (volume) OBOL:automatic neck (volume) connective tissue OBOL:automatic neck (volume) portion of connective tissue OBOL:automatic neck (volume) textus connectivus OBOL:automatic neck portion of connective tissue OBOL:automatic neck textus connectivus OBOL:automatic portion of connective tissue of neck OBOL:automatic portion of connective tissue of neck (volume) OBOL:automatic textus connectivus of neck OBOL:automatic textus connectivus of neck (volume) OBOL:automatic A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:35968 EMAPA:35977 MA:0001814 apparatus respiratorius connective tissue apparatus respiratorius portion of connective tissue apparatus respiratorius textus connectivus connective tissue of apparatus respiratorius connective tissue of respiratory system portion of connective tissue of apparatus respiratorius portion of connective tissue of respiratory system respiratory system portion of connective tissue respiratory system textus connectivus textus connectivus of apparatus respiratorius textus connectivus of respiratory system uberon UBERON:0003570 respiratory system connective tissue A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius connective tissue OBOL:automatic apparatus respiratorius portion of connective tissue OBOL:automatic apparatus respiratorius textus connectivus OBOL:automatic connective tissue of apparatus respiratorius OBOL:automatic connective tissue of respiratory system OBOL:automatic portion of connective tissue of apparatus respiratorius OBOL:automatic portion of connective tissue of respiratory system OBOL:automatic respiratory system portion of connective tissue OBOL:automatic respiratory system textus connectivus OBOL:automatic textus connectivus of apparatus respiratorius OBOL:automatic textus connectivus of respiratory system OBOL:automatic A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37548 MA:0002409 connective tissue of lower respiratory tract lower respiratory tract portion of connective tissue lower respiratory tract textus connectivus portion of connective tissue of lower respiratory tract textus connectivus of lower respiratory tract uberon UBERON:0003580 lower respiratory tract connective tissue A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37548 MA:th connective tissue of lower respiratory tract OBOL:automatic lower respiratory tract portion of connective tissue OBOL:automatic lower respiratory tract textus connectivus OBOL:automatic portion of connective tissue of lower respiratory tract OBOL:automatic textus connectivus of lower respiratory tract OBOL:automatic A portion of connective tissue that is part of a dermis [Automatically generated definition]. EMAPA:36509 MA:0000799 connective tissue of dermis dermis portion of connective tissue dermis textus connectivus portion of connective tissue of dermis textus connectivus of dermis uberon UBERON:0003585 dermis connective tissue A portion of connective tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic connective tissue of dermis OBOL:automatic dermis portion of connective tissue OBOL:automatic dermis textus connectivus OBOL:automatic portion of connective tissue of dermis OBOL:automatic textus connectivus of dermis OBOL:automatic A portion of connective tissue that is part of a trunk [Automatically generated definition]. EMAPA:37252 MA:0000513 connective tissue of torso connective tissue of trunk portion of connective tissue of torso portion of connective tissue of trunk textus connectivus of torso textus connectivus of trunk torso connective tissue torso portion of connective tissue torso textus connectivus trunk portion of connective tissue trunk textus connectivus uberon UBERON:0003586 trunk connective tissue A portion of connective tissue that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37252 MA:th connective tissue of torso OBOL:automatic connective tissue of trunk OBOL:automatic portion of connective tissue of torso OBOL:automatic portion of connective tissue of trunk OBOL:automatic textus connectivus of torso OBOL:automatic textus connectivus of trunk OBOL:automatic torso connective tissue OBOL:automatic torso portion of connective tissue OBOL:automatic torso textus connectivus OBOL:automatic trunk portion of connective tissue OBOL:automatic trunk textus connectivus OBOL:automatic A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37255 MA:0000555 cavity of chest connective tissue cavity of chest portion of connective tissue cavity of chest textus connectivus cavity of thorax connective tissue cavity of thorax portion of connective tissue cavity of thorax textus connectivus chest cavity connective tissue chest cavity portion of connective tissue chest cavity textus connectivus connective tissue of cavity of chest connective tissue of cavity of thorax connective tissue of chest cavity connective tissue of pectoral cavity connective tissue of thoracic cavity pectoral cavity connective tissue pectoral cavity portion of connective tissue pectoral cavity textus connectivus portion of connective tissue of cavity of chest portion of connective tissue of cavity of thorax portion of connective tissue of chest cavity portion of connective tissue of pectoral cavity portion of connective tissue of thoracic cavity textus connectivus of cavity of chest textus connectivus of cavity of thorax textus connectivus of chest cavity textus connectivus of pectoral cavity textus connectivus of thoracic cavity thoracic cavity portion of connective tissue thoracic cavity textus connectivus uberon UBERON:0003593 thoracic cavity connective tissue A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37255 MA:th cavity of chest connective tissue OBOL:automatic cavity of chest portion of connective tissue OBOL:automatic cavity of chest textus connectivus OBOL:automatic cavity of thorax connective tissue OBOL:automatic cavity of thorax portion of connective tissue OBOL:automatic cavity of thorax textus connectivus OBOL:automatic chest cavity connective tissue OBOL:automatic chest cavity portion of connective tissue OBOL:automatic chest cavity textus connectivus OBOL:automatic connective tissue of cavity of chest OBOL:automatic connective tissue of cavity of thorax OBOL:automatic connective tissue of chest cavity OBOL:automatic connective tissue of pectoral cavity OBOL:automatic connective tissue of thoracic cavity OBOL:automatic pectoral cavity connective tissue OBOL:automatic pectoral cavity portion of connective tissue OBOL:automatic pectoral cavity textus connectivus OBOL:automatic portion of connective tissue of cavity of chest OBOL:automatic portion of connective tissue of cavity of thorax OBOL:automatic portion of connective tissue of chest cavity OBOL:automatic portion of connective tissue of pectoral cavity OBOL:automatic portion of connective tissue of thoracic cavity OBOL:automatic textus connectivus of cavity of chest OBOL:automatic textus connectivus of cavity of thorax OBOL:automatic textus connectivus of chest cavity OBOL:automatic textus connectivus of pectoral cavity OBOL:automatic textus connectivus of thoracic cavity OBOL:automatic thoracic cavity portion of connective tissue OBOL:automatic thoracic cavity textus connectivus OBOL:automatic A portion of connective tissue that is part of a pelvis [Automatically generated definition]. EMAPA:37257 MA:0000533 connective tissue of pelvis pelvis portion of connective tissue pelvis textus connectivus portion of connective tissue of pelvis textus connectivus of pelvis uberon UBERON:0003594 pelvis connective tissue A portion of connective tissue that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37257 MA:th connective tissue of pelvis OBOL:automatic pelvis portion of connective tissue OBOL:automatic pelvis textus connectivus OBOL:automatic portion of connective tissue of pelvis OBOL:automatic textus connectivus of pelvis OBOL:automatic A portion of connective tissue that is part of a tail [Automatically generated definition]. EMAPA:16749 MA:0000697 connective tissue of post-vent region connective tissue of tail portion of connective tissue of post-vent region portion of connective tissue of tail post-vent region connective tissue post-vent region portion of connective tissue post-vent region textus connectivus tail portion of connective tissue tail textus connectivus textus connectivus of post-vent region textus connectivus of tail uberon UBERON:0003599 tail connective tissue A portion of connective tissue that is part of a tail [Automatically generated definition]. OBOL:automatic connective tissue of post-vent region OBOL:automatic connective tissue of tail OBOL:automatic portion of connective tissue of post-vent region OBOL:automatic portion of connective tissue of tail OBOL:automatic post-vent region connective tissue OBOL:automatic post-vent region portion of connective tissue OBOL:automatic post-vent region textus connectivus OBOL:automatic tail portion of connective tissue OBOL:automatic tail textus connectivus OBOL:automatic textus connectivus of post-vent region OBOL:automatic textus connectivus of tail OBOL:automatic A cartilage that is part of a neck [Automatically generated definition]. EMAPA:37251 MA:0000586 cartilage of neck cartilage of neck (volume) neck (volume) cartilage uberon UBERON:0003601 neck cartilage A cartilage that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37251 MA:th cartilage of neck OBOL:automatic cartilage of neck (volume) OBOL:automatic neck (volume) cartilage OBOL:automatic A cartilage that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37547 MA:0001819 NCIT:C49256 UMLS:C1708759 cartilage of lower respiratory tract uberon UBERON:0003603 lower respiratory tract cartilage A cartilage that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37547 MA:th UMLS:C1708759 ncithesaurus:Lower_Respiratory_Tract_Cartilage cartilage of lower respiratory tract OBOL:automatic A skin gland that is part of a camera-type eye [Automatically generated definition]. EMAPA:37530 MA:0002451 camera-type eye skin gland camera-type eye skin glands camera-type eye skin glands set skin gland of camera-type eye skin gland of vertebrate eye skin glands of camera-type eye skin glands of vertebrate eye skin glands set of camera-type eye skin glands set of vertebrate eye vertebrate eye skin gland vertebrate eye skin glands vertebrate eye skin glands set uberon UBERON:0003605 eye skin gland A skin gland that is part of a camera-type eye [Automatically generated definition]. OBOL:automatic EMAPA:37530 MA:th camera-type eye skin gland OBOL:automatic camera-type eye skin glands OBOL:automatic camera-type eye skin glands set OBOL:automatic skin gland of camera-type eye OBOL:automatic skin gland of vertebrate eye OBOL:automatic skin glands of camera-type eye OBOL:automatic skin glands of vertebrate eye OBOL:automatic skin glands set of camera-type eye OBOL:automatic skin glands set of vertebrate eye OBOL:automatic vertebrate eye skin gland OBOL:automatic vertebrate eye skin glands OBOL:automatic vertebrate eye skin glands set OBOL:automatic The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MA:0002859 adult aorta elastic connective tissue adult aorta elastic tissue adult aorta textus connectivus elasticus aorta elastic connective tissue aorta elastic lamina aorta elastic laminae aorta textus connectivus elasticus dorsal aorta elastic connective tissue dorsal aorta elastic tissue dorsal aorta textus connectivus elasticus elastic connective tissue of adult aorta elastic connective tissue of aorta elastic connective tissue of dorsal aorta elastic connective tissue of trunk of aortic tree elastic tissue of adult aorta elastic tissue of aorta elastic tissue of dorsal aorta elastic tissue of trunk of aortic tree textus connectivus elasticus of adult aorta textus connectivus elasticus of aorta textus connectivus elasticus of dorsal aorta textus connectivus elasticus of trunk of aortic tree trunk of aortic tree elastic connective tissue trunk of aortic tree elastic tissue trunk of aortic tree textus connectivus elasticus uberon UBERON:0003609 aorta elastic tissue The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MP:0009862 adult aorta elastic connective tissue OBOL:automatic adult aorta elastic tissue OBOL:automatic adult aorta textus connectivus elasticus OBOL:automatic aorta elastic connective tissue OBOL:automatic aorta elastic lamina MP:0009862 aorta elastic laminae MP:0009862 aorta textus connectivus elasticus OBOL:automatic dorsal aorta elastic connective tissue OBOL:automatic dorsal aorta elastic tissue OBOL:automatic dorsal aorta textus connectivus elasticus OBOL:automatic elastic connective tissue of adult aorta OBOL:automatic elastic connective tissue of aorta OBOL:automatic elastic connective tissue of dorsal aorta OBOL:automatic elastic connective tissue of trunk of aortic tree OBOL:automatic elastic tissue of adult aorta OBOL:automatic elastic tissue of aorta OBOL:automatic elastic tissue of dorsal aorta OBOL:automatic elastic tissue of trunk of aortic tree OBOL:automatic textus connectivus elasticus of adult aorta OBOL:automatic textus connectivus elasticus of aorta OBOL:automatic textus connectivus elasticus of dorsal aorta OBOL:automatic textus connectivus elasticus of trunk of aortic tree OBOL:automatic trunk of aortic tree elastic connective tissue OBOL:automatic trunk of aortic tree elastic tissue OBOL:automatic trunk of aortic tree textus connectivus elasticus OBOL:automatic The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MA:0002858 cardiac elastic tissue elastic connective tissue of heart elastic tissue of heart heart elastic connective tissue heart textus connectivus elasticus textus connectivus elasticus of heart uberon UBERON:0003610 heart elastic tissue The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MP:0009863 cardiac elastic tissue MP:0009863 elastic connective tissue of heart OBOL:automatic elastic tissue of heart OBOL:automatic heart elastic connective tissue OBOL:automatic heart textus connectivus elasticus OBOL:automatic textus connectivus elasticus of heart OBOL:automatic An elastic tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37579 MA:0001820 apparatus respiratorius elastic connective tissue apparatus respiratorius elastic tissue apparatus respiratorius textus connectivus elasticus elastic connective tissue of apparatus respiratorius elastic connective tissue of respiratory system elastic tissue of apparatus respiratorius elastic tissue of respiratory system respiratory system elastic connective tissue respiratory system textus connectivus elasticus textus connectivus elasticus of apparatus respiratorius textus connectivus elasticus of respiratory system uberon UBERON:0003611 respiratory system elastic tissue An elastic tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37579 MA:th apparatus respiratorius elastic connective tissue OBOL:automatic apparatus respiratorius elastic tissue OBOL:automatic apparatus respiratorius textus connectivus elasticus OBOL:automatic elastic connective tissue of apparatus respiratorius OBOL:automatic elastic connective tissue of respiratory system OBOL:automatic elastic tissue of apparatus respiratorius OBOL:automatic elastic tissue of respiratory system OBOL:automatic respiratory system elastic connective tissue OBOL:automatic respiratory system textus connectivus elasticus OBOL:automatic textus connectivus elasticus of apparatus respiratorius OBOL:automatic textus connectivus elasticus of respiratory system OBOL:automatic An elastic tissue that is part of a circulatory system [Automatically generated definition]. MA:0002857 cardiovascular system elastic connective tissue cardiovascular system textus connectivus elasticus circulatory system elastic connective tissue circulatory system elastic tissue circulatory system textus connectivus elasticus elastic connective tissue of cardiovascular system elastic connective tissue of circulatory system elastic tissue of cardiovascular system elastic tissue of circulatory system textus connectivus elasticus of cardiovascular system textus connectivus elasticus of circulatory system uberon UBERON:0003613 cardiovascular system elastic tissue An elastic tissue that is part of a circulatory system [Automatically generated definition]. OBOL:automatic cardiovascular system elastic connective tissue OBOL:automatic cardiovascular system textus connectivus elasticus OBOL:automatic circulatory system elastic connective tissue OBOL:automatic circulatory system elastic tissue OBOL:automatic circulatory system textus connectivus elasticus OBOL:automatic elastic connective tissue of cardiovascular system OBOL:automatic elastic connective tissue of circulatory system OBOL:automatic elastic tissue of cardiovascular system OBOL:automatic elastic tissue of circulatory system OBOL:automatic textus connectivus elasticus of cardiovascular system OBOL:automatic textus connectivus elasticus of circulatory system OBOL:automatic Elastic tissue layer that lines a blood vessel layer. elastic lamina elastic laminae EMAPA:36300 MA:0002856 blood vessel elastic connective tissue blood vessel textus connectivus elasticus elastic connective tissue of blood vessel elastic tissue of blood vessel textus connectivus elasticus of blood vessel vascular elastic lamina vascular elastic laminae vascular elastic tissue uberon UBERON:0003614 blood vessel elastic tissue Elastic tissue layer that lines a blood vessel layer. http://orcid.org/0000-0002-6601-2165 https://sourceforge.net/p/obo/mammalian-phenotype-requests/2026/ elastic lamina MP:0006083 elastic laminae MP:0006083 blood vessel elastic connective tissue OBOL:automatic blood vessel textus connectivus elasticus OBOL:automatic elastic connective tissue of blood vessel OBOL:automatic elastic tissue of blood vessel OBOL:automatic textus connectivus elasticus of blood vessel OBOL:automatic vascular elastic lamina http://orcid.org/0000-0002-6601-2165 vascular elastic laminae http://orcid.org/0000-0002-6601-2165 vascular elastic tissue MP:0006083 Elastic tissue that is part of a lung [Automatically generated definition]. MA:0002860 elastic connective tissue of lung elastic tissue of lung lung elastic connective tissue lung textus connectivus elasticus textus connectivus elasticus of lung pulmonary elastic fiber uberon UBERON:0003615 lung elastic tissue Elastic tissue that is part of a lung [Automatically generated definition]. OBOL:automatic elastic connective tissue of lung OBOL:automatic elastic tissue of lung OBOL:automatic lung elastic connective tissue OBOL:automatic lung textus connectivus elasticus OBOL:automatic textus connectivus elasticus of lung OBOL:automatic pulmonary elastic fiber http://orcid.org/0000-0002-6601-2165 The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. EMAPA:35138 FMA:74433 MA:0002903 SCTID:48467007 adult aorta tunica media dorsal aorta tunica media trunk of aortic tree tunica media tunica media of adult aorta tunica media of aorta tunica media of dorsal aorta tunica media of trunk of aortic tree uberon UBERON:0003618 aorta tunica media The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. MP:0009873 adult aorta tunica media OBOL:automatic dorsal aorta tunica media OBOL:automatic trunk of aortic tree tunica media OBOL:automatic tunica media of adult aorta OBOL:automatic tunica media of aorta OBOL:automatic tunica media of dorsal aorta OBOL:automatic tunica media of trunk of aortic tree OBOL:automatic The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. BTO:0005553 EMAPA:35137 FMA:74419 MA:0002904 SCTID:362031007 adult aorta tunica intima dorsal aorta tunica intima trunk of aortic tree tunica intima tunica intima of adult aorta tunica intima of aorta tunica intima of dorsal aorta tunica intima of trunk of aortic tree uberon UBERON:0003619 aorta tunica intima The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. MP:0009872 adult aorta tunica intima OBOL:automatic dorsal aorta tunica intima OBOL:automatic trunk of aortic tree tunica intima OBOL:automatic tunica intima of adult aorta OBOL:automatic tunica intima of aorta OBOL:automatic tunica intima of dorsal aorta OBOL:automatic tunica intima of trunk of aortic tree OBOL:automatic An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:37565 MA:0001800 uberon UBERON:0003643 respiratory system arterial blood vessel An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37565 MA:th A muscle organ that attaches to a tail vertebra [Automatically generated definition]. the BTO class may possibly refer to an invertebrate structure AAO:0000081 BTO:0001905 EMAPA:37759 MA:0000699 SCTID:113230005 caudal muscle muscle organ of post-vent region muscle organ of tail post-vent region muscle organ tail muscle tail muscle organ uberon UBERON:0003665 post-anal tail muscle A muscle organ that attaches to a tail vertebra [Automatically generated definition]. OBOL:automatic the BTO class may possibly refer to an invertebrate structure BTO EMAPA:37759 MA:th muscle organ of post-vent region OBOL:automatic muscle organ of tail OBOL:automatic post-vent region muscle organ OBOL:automatic tail muscle MA:0000699 tail muscle organ OBOL:automatic The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity EFO:0000213 EMAPA:36505 FMA:12266 GAID:17 MA:0003057 MESH:D034841 NCIT:C12664 SCTID:361294009 UMLS:C0230168 Wikipedia:Abdominal_cavity galen:AbdominalCavity cavity of abdominal compartment cavity of compartment of abdomen space of abdominal compartment uberon cavitas abdominis UBERON:0003684 abdominal cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). UBERON:cjm in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity FMA UMLS:C0230168 ncithesaurus:Abdominal_Cavity cavity of abdominal compartment FMA:12266 cavity of compartment of abdomen FMA:12266 space of abdominal compartment FMA:12266 cavitas abdominis GAID:17 Wikipedia:Abdominal_cavity In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] AAO:0010826 BTO:0006035 EMAPA:37868 FMA:75306 GAID:228 MESH:D005539 NCIT:C12495 SCTID:244679008 TAO:0002045 UMLS:C0016519 Wikipedia:Foramen_magnum ZFA:0005387 uberon UBERON:0003687 Design pattern notes: check whether this fits the foramen design pattern foramen magnum http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Wikipedia:Foramen_magnum Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] 2012-08-14 TAO:0002045 TAO TAO:wd BTO:0006035 https://github.com/biopragmatics/biomappings EMAPA:37868 MA:th UMLS:C0016519 ncithesaurus:Foramen_Magnum The Atlanto-axial joint is of a complicated nature, comprising no fewer than four distinct joints. There is a pivot articulation between the odontoid process of the axis and the ring formed by the anterior arch and the transverse ligament of the atlas. FMA:25524 GAID:250 MESH:D001268 NCIT:C32157 SCTID:361832004 UMLS:C0004168 Wikipedia:Atlanto-axial_joint atlanto axial joint atlantoaxial joint uberon articulatio atlantoaxialis articulatio atlantoepistrophica atlantoaxial lateral atlanto-axial joint median atlanto-axial joint UBERON:0003694 atlanto-axial joint http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png The Atlanto-axial joint is of a complicated nature, comprising no fewer than four distinct joints. There is a pivot articulation between the odontoid process of the axis and the ring formed by the anterior arch and the transverse ligament of the atlas. Wikipedia:Atlanto-axial_joint UMLS:C0004168 ncithesaurus:Atlanto-axial_Joint atlanto axial joint GAID:250 atlantoaxial joint GAID:250 articulatio atlantoaxialis Wikipedia:Atlanto-axial_joint articulatio atlantoepistrophica Wikipedia:Atlanto-axial_joint atlantoaxial Wikipedia:Atlanto-axial_joint lateral atlanto-axial joint Wikipedia:Atlanto-axial_joint median atlanto-axial joint Wikipedia:Atlanto-axial_joint The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. EMAPA:37064 FMA:10429 FMA:259054 GAID:26 MESH:D034861 NCIT:C77608 SCTID:181613000 UMLS:C0836916 Wikipedia:Abdominal_wall paries abdominalis wall of abdomen wall of abdomen proper uberon abdominal wall proper layers of the abdominal wall paries abdominalis UBERON:0003697 abdominal wall http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. ncithesaurus:Abdominal_Wall EMAPA:37064 MA:th UMLS:C0836916 ncithesaurus:Abdominal_Wall paries abdominalis Wikipedia:Abdominal_wall wall of abdomen FMA:259054 wall of abdomen proper FMA:10429 abdominal wall proper FMA:10429 layers of the abdominal wall Wikipedia:Abdominal_wall paries abdominalis Wikipedia:Abdominal_wall Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct FMA:14678 GAID:281 MA:0002659 MESH:D017734 NCIT:C32573 SCTID:276158002 UMLS:C0206187 uberon bile duct extrahepatic part extrahepatic biliary system UBERON:0003703 extrahepatic bile duct Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. MESH:A03.159.183.079 UMLS:C0206187 ncithesaurus:Extrahepatic_Bile_Duct bile duct extrahepatic part MA:0002659 extrahepatic biliary system GAID:281 Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO] FMA:15766 GAID:287 MA:0001630 MESH:D001653 NCIT:C12677 SCTID:362193005 TAO:0005169 UMLS:C0005401 ZFA:0005169 bile duct intrahepatic part uberon intrahepatic biliary system UBERON:0003704 intrahepatic bile duct FMA MA Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. MESH:A03.159.183.158 Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO] 2012-08-14 TAO:0005169 TAO ZFIN:curator UMLS:C0005401 ncithesaurus:Intrahepatic_Bile_Duct bile duct intrahepatic part MA:0001630 The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava. EHDAA2:0000182 EHDAA:9868 FMA:4723 GAID:529 MESH:D016121 NCIT:C32816 SCTID:181371003 UMLS:C0006095 Wikipedia:Brachiocephalic_vein galen:BrachiocephalicVein brachiocephalic venous tree innominate vein uberon innomiate vein innominate trunk innominate vein innominate veins vena brachiocephalica venae anonyma UBERON:0003711 brachiocephalic vein http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava. Wikipedia:Brachiocephalic_vein UMLS:C0006095 ncithesaurus:Innominate_Vein brachiocephalic venous tree FMA:4723 innominate vein FMA:4723 innomiate vein Wikipedia:Brachiocephalic_vein innominate trunk Wikipedia:Brachiocephalic_vein innominate vein GAID:529 Wikipedia:Brachiocephalic_vein innominate veins Wikipedia:Brachiocephalic_vein vena brachiocephalica Wikipedia:Brachiocephalic_vein venae anonyma Wikipedia:Brachiocephalic_vein A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. EMAPA:37226 FMA:14331 GAID:541 MA:0002164 MESH:D013162 NCIT:C33608 SCTID:278029005 UMLS:C0038001 Wikipedia:Splenic_vein galen:SplenicVein vena splenica uberon lienal vein vena lienalis UBERON:0003713 splenic vein http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. ncithesaurus:Splenic_Vein EMAPA:37226 MA:th UMLS:C0038001 ncithesaurus:Splenic_Vein vena splenica FMA:14331 FMA:TA lienal vein MA:0002164 Wikipedia:Splenic_vein vena lienalis Wikipedia:Splenic_vein Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] FMA definition includes vasculature AAO:0000325 AEO:0000123 EHDAA2:0003123 FMA:9642 GAID:609 MESH:D009417 NCIT:C13052 SCTID:91728009 UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue uberon UBERON:0003714 neural tissue Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. FMA:9642 One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] 2012-06-20 AAO:0000325 AAO AAO:LAP FMA definition includes vasculature FMA UMLS:C0027757 ncithesaurus:Nervous_Tissue nerve tissue FMA:9642 nervous tissue FMA:9642 portion of neural tissue FMA:9642 The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers BAMS:spn EMAPA:37959 FMA:5883 GAID:800 MESH:D013153 SCTID:264198001 Wikipedia:Splanchnic_nerves uberon splanchnic nerves visceral nerve UBERON:0003715 splanchnic nerve The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. MP:0008318 EMAPA:37959 MA:th splanchnic nerves BAMS:spn visceral nerve Wikipedia:Splanchnic_nerves The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls. FMA:5860 GAID:857 MESH:D013900 SCTID:360498003 Wikipedia:Thoracic_nerves neuronames:1725 nervus thoracis thoracic spinal nerve uberon nervi thoracici pectoral nerve UBERON:0003726 thoracic nerve The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls. MESH:A08.800.800.720.800 nervus thoracis FMA:5860 FMA:TA thoracic spinal nerve FMA:5860 nervi thoracici Wikipedia:Thoracic_nerves pectoral nerve GAID:857 The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. EMAPA:18227 FMA:6028 GAID:858 MESH:D007367 NCIT:C32825 SCTID:279568001 UMLS:C1285089 Wikipedia:Intercostal_nerves anterior ramus of thoracic nerve anterior ramus of thoracic spinal nerve ramus anterior, nervus thoracicus thoracic anterior ramus ventral ramus of thoracic spinal nerve uberon nervi intercostales UBERON:0003727 intercostal nerve http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray819.png The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. Wikipedia:Intercostal_nerves UMLS:C1285089 ncithesaurus:Intercostal_Nerve anterior ramus of thoracic nerve FMA:6028 anterior ramus of thoracic spinal nerve FMA:6028 ramus anterior, nervus thoracicus FMA:6028 thoracic anterior ramus FMA:6028 ventral ramus of thoracic spinal nerve FMA:6028 nervi intercostales Wikipedia:Intercostal_nerves A mucous membrane that lines the mouth. this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa) the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. BTO:0002860 CALOHA:TS-0716 EMAPA:26937 FMA:59660 GAID:951 MA:0002794 MESH:D009061 NCIT:C77637 UMLS:C0026639 Wikipedia:Oral_mucosa mouth mucosa mouth mucous membrane mouth organ mucosa mucosa of mouth mucous membrane of mouth oral mucous membrane oral part of viscerocranial mucosa tunica mucosa oris uberon buccal mucosa mucosal lining of mouth oral mucosa tunica mucosa oris UBERON:0003729 mouth mucosa A mucous membrane that lines the mouth. http://orcid.org/0000-0002-6601-2165 the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. Wikipedia:Oral_mucosa UMLS:C0026639 ncithesaurus:Oral_Mucosa mouth mucosa FMA:59660 mouth mucous membrane OBOL:accepted mouth organ mucosa OBOL:accepted mucosa of mouth OBOL:accepted mucous membrane of mouth FMA:59660 oral part of viscerocranial mucosa FMA:59660 tunica mucosa oris FMA:59660 FMA:TA buccal mucosa GAID:951 mucosal lining of mouth MA:0002794 oral mucosa GAID:951 tunica mucosa oris Wikipedia:Oral_mucosa A nerve that is part of a thorax [Automatically generated definition]. EMAPA:37265 MA:0000562 MESH:D013900 SCTID:359876006 nerve of thorax thoracic segment nerve thorax nerve uberon upper body nerve UBERON:0003824 nerve of thoracic segment A nerve that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37265 MA:th nerve of thorax OBOL:automatic thoracic segment nerve MA:0000562 thorax nerve OBOL:automatic upper body nerve MA:0000562 A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37061 MA:0000528 abdominal segment nerve uberon UBERON:0003825 nerve of abdominal segment A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37061 MA:th abdominal segment nerve MA:0000528 A bone that is part of a thorax [Automatically generated definition]. EMAPA:37247 MA:0000559 SCTID:426649006 bone of thorax bone organ of thorax thorax bone thorax bone organ uberon upper body bone UBERON:0003827 thoracic segment bone A bone that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37247 MA:th bone of thorax OBOL:automatic bone organ of thorax OBOL:automatic thorax bone OBOL:automatic thorax bone organ OBOL:automatic upper body bone MA:0000559 A bone that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37058 MA:0000525 abdominal segment of trunk bone abdominal segment of trunk bone organ bone of abdominal segment of trunk bone organ of abdominal segment of trunk uberon UBERON:0003828 abdominal segment bone A bone that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37058 MA:th abdominal segment of trunk bone OBOL:automatic abdominal segment of trunk bone organ OBOL:automatic bone of abdominal segment of trunk OBOL:automatic bone organ of abdominal segment of trunk OBOL:automatic Any muscle organ that is part of a thorax [Automatically generated definition]. MA:0000561 muscle organ of thorax thorax muscle organ uberon upper body muscle UBERON:0003830 thoracic segment muscle prolog Any muscle organ that is part of a thorax [Automatically generated definition]. OBOL:automatic muscle organ of thorax OBOL:automatic thorax muscle organ OBOL:automatic upper body muscle MA:0000561 Any muscle organ that is part of a respiratory system [Automatically generated definition]. EMAPA:35733 MA:0001828 apparatus respiratorius muscle organ muscle organ of apparatus respiratorius muscle organ of respiratory system respiratory system muscle organ uberon UBERON:0003831 respiratory system muscle Any muscle organ that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius muscle organ OBOL:automatic muscle organ of apparatus respiratorius OBOL:automatic muscle organ of respiratory system OBOL:automatic respiratory system muscle organ OBOL:automatic Any muscle organ that is part of a esophagus [Automatically generated definition]. merge muscle and muscle layer? EMAPA:26983 MA:0002682 SCTID:360961009 esophageal muscle esophagus muscle organ gullet muscle organ muscle organ of esophagus muscle organ of gullet muscle organ of oesophagus oesophagus muscle organ uberon UBERON:0003832 esophagus muscle MA Any muscle organ that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus muscle organ OBOL:automatic gullet muscle organ OBOL:automatic muscle organ of esophagus OBOL:automatic muscle organ of gullet OBOL:automatic muscle organ of oesophagus OBOL:automatic oesophagus muscle organ OBOL:automatic A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37060 MA:0000527 abdominal segment of trunk muscle organ muscle organ of abdominal segment of trunk uberon UBERON:0003833 abdominal segment muscle A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37060 MA:th abdominal segment of trunk muscle organ OBOL:automatic muscle organ of abdominal segment of trunk OBOL:automatic A blood vessel that is part of a thorax [Automatically generated definition]. EMAPA:37238 MA:0000558 blood vessel of thorax thorax blood vessel uberon upper body blood vessel UBERON:0003834 thoracic segment blood vessel A blood vessel that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37238 MA:th blood vessel of thorax OBOL:automatic thorax blood vessel OBOL:automatic upper body blood vessel MA:0000558 A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37057 MA:0000524 abdominal segment of trunk blood vessel blood vessel of abdominal segment of trunk uberon UBERON:0003835 abdominal segment blood vessel A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37057 MA:th abdominal segment of trunk blood vessel OBOL:automatic blood vessel of abdominal segment of trunk OBOL:automatic A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37063 FMA:264898 MA:0000530 abdominal segment of trunk skin skin of abdominal segment of trunk uberon UBERON:0003836 abdominal segment skin A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37063 MA:th abdominal segment of trunk skin OBOL:automatic skin of abdominal segment of trunk OBOL:automatic A portion of connective tissue that is part of a thorax [Automatically generated definition]. EMAPA:37253 MA:0000560 connective tissue of thorax portion of connective tissue of thorax textus connectivus of thorax thorax connective tissue thorax portion of connective tissue thorax textus connectivus uberon upper body connective tissue UBERON:0003837 thoracic segment connective tissue A portion of connective tissue that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37253 MA:th connective tissue of thorax OBOL:automatic portion of connective tissue of thorax OBOL:automatic textus connectivus of thorax OBOL:automatic thorax connective tissue OBOL:automatic thorax portion of connective tissue OBOL:automatic thorax textus connectivus OBOL:automatic upper body connective tissue MA:0000560 A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37059 MA:0000526 abdominal segment of trunk connective tissue abdominal segment of trunk portion of connective tissue abdominal segment of trunk textus connectivus connective tissue of abdominal segment of trunk portion of connective tissue of abdominal segment of trunk textus connectivus of abdominal segment of trunk uberon UBERON:0003838 abdominal segment connective tissue A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37059 MA:th abdominal segment of trunk connective tissue OBOL:automatic abdominal segment of trunk portion of connective tissue OBOL:automatic abdominal segment of trunk textus connectivus OBOL:automatic connective tissue of abdominal segment of trunk OBOL:automatic portion of connective tissue of abdominal segment of trunk OBOL:automatic textus connectivus of abdominal segment of trunk OBOL:automatic An anatomical space that surrounded_by a neural tube. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] UBERON:0005713 AAO:0011073 EHDAA2:0001269 EHDAA:2889 EHDAA:914 EMAPA:16167 VHOG:0001119 XAO:0000252 cavity of neural tube lumen of neural tube neural tube neural lumen prosencoel uberon central lumen neural lumen neurocoel UBERON:0003842 neural tube lumen An anatomical space that surrounded_by a neural tube. OBOL:automatic (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001119 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ cavity of neural tube https://orcid.org/0000-0002-6601-2165 lumen of neural tube https://orcid.org/0000-0002-6601-2165 neural tube neural lumen EHDAA2:0001269 neural lumen EHDAA:2889 neurocoel VHOG:0001119 In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. EHDAA2:0000719 EHDAA:8703 SCTID:278192008 VHOG:0001340 Wikipedia:Gonadal_vein gonad vein gonada vein vein of gonad vein of gonada uberon UBERON:0003848 gonadal vein http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. Wikipedia:Gonadal_vein gonad vein OBOL:automatic gonada vein OBOL:automatic vein of gonad OBOL:automatic vein of gonada OBOL:automatic A neural crest that has_potential_to_developmentally_contribute_to a midbrain. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003591 EHDAA2:0001101 EHDAA:360 TAO:0000935 VHOG:0000796 ZFA:0000935 mesencephalic neural crest neural crest midbrain uberon UBERON:0003849 mesencephalic neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a midbrain. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000796 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ mesencephalic neural crest ZFA:0000935 neural crest midbrain ZFA:0000935 A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. Cranial neural crest that is part of the hindbrain.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0001628 EHDAA:362 EMAPA:35747 TAO:0007063 VHOG:0001210 ZFA:0007063 neural crest hindbrain rhombencephalic neural crest uberon rhombomere neural crest UBERON:0003852 rhombencephalon neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. OBOL:automatic Cranial neural crest that is part of the hindbrain.[TAO] 2012-08-14 TAO:0007063 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001210 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ neural crest hindbrain ZFA:0007063 rhombencephalic neural crest ZFA:0007063 rhombomere neural crest EMAPA:35747 A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] EHDAA:696 EMAPA:16163 EMAPA:16881 VHOG:0001006 neural crest spinal cord uberon spinal neural crest UBERON:0003853 spinal cord neural crest A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] 2012-09-17 VHOG:0001006 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ neural crest spinal cord VHOG:0001006 spinal neural crest VHOG:0001006 A neural plate that develops_from a future spinal cord. Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] FMA:312957 TAO:0007021 VHOG:0000439 ZFA:0007021 neural plate of spinal cord uberon UBERON:0003854 spinal cord neural plate ZFA A neural plate that develops_from a future spinal cord. OBOL:automatic Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000439 VHOG http://bgee.unil.ch/ (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] 2012-09-17 VHOG:0000439 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ neural plate of spinal cord OBOL:automatic Mesenchyme that is part of a developing gonad [Automatically generated definition]. EHDAA:5012 EMAPA:16858 EMAPA:17385 VHOG:0001090 gonada mesenchyme mesenchyme of gonad mesenchyme of gonada uberon UBERON:0003855 gonad mesenchyme Mesenchyme that is part of a developing gonad [Automatically generated definition]. OBOL:automatic gonada mesenchyme OBOL:automatic mesenchyme of gonad OBOL:automatic mesenchyme of gonada OBOL:automatic A presumptive structure that has the potential to develop into a ganglion. uberon UBERON:0003869 presumptive ganglion A presumptive structure that has the potential to develop into a ganglion. OBOL:automatic An anatomical cavity that has the potential to develop into a coelemic cavity lumen. future coelomic cavity lumen uberon body cavity precursor UBERON:0003886 future coelemic cavity lumen An anatomical cavity that has the potential to develop into a coelemic cavity lumen. OBOL:automatic The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 UMLS:C1512940 VHOG:0000316 Wikipedia:Intraembryonic_coelom somatic coelom uberon UBERON:0003887 intraembryonic coelom Wikipedia The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. MGI:anna MP:0012187 (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] 2012-09-17 VHOG:0000316 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 http://bgee.unil.ch/ UMLS:C1512940 ncithesaurus:Intraembryonic_Coelom somatic coelom Wikipedia:Intraembryonic_coelom Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. stromal FMA:81494 NCIT:C67387 UMLS:C0927195 uberon stromal connective tissue UBERON:0003891 stroma Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. http://orcid.org/0000-0002-6601-2165 UMLS:C0927195 ncithesaurus:Stroma_Connective_Tissue A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ AAO:0011058 BTO:0003391 EFO:0002577 EFO:0003428 EHDAA2:0000744 EHDAA:973 EMAPA:16847 NCIT:C34277 TAO:0000124 UMLS:C0734013 UMLS:C1514451 XAO:0003266 ZFA:0000124 embryological hepatic plate primordium of the liver uberon hepatic plate liver bud liver endoderm UBERON:0003894 liver primordium EHDAA2 XAO EHDAA2 ventral foregut endoderm Zaret 1996 A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. ISBN:3211492755 UMLS:C0734013 ncithesaurus:Hepatic_Cord UMLS:C1514451 ncithesaurus:Primordium_of_the_Liver embryological hepatic plate https://orcid.org/0000-0002-6601-2165 primordium of the liver ncithesaurus:Primordium_of_the_Liver hepatic plate EHDAA2:0000744 liver bud XAO:0003266 ZFA:0000124 liver endoderm EFO:0002577 One of the skeletal muscles of the head and neck, spine, and ribs. EHDAA:5982 EMAPA:18167 MA:0003153 RETIRED_EHDAA2:0000160 TAO:0001954 uberon UBERON:0003897 axial muscle One of the skeletal muscles of the head and neck, spine, and ribs. HP:0003327 A portion of skeletal muscle tissue in the trunk. SCTID:244848007 skeletal muscle of torso skeletal muscle tissue of torso skeletal muscle tissue of trunk torso skeletal muscle torso skeletal muscle tissue trunk skeletal muscle trunk skeletal muscle tissue uberon UBERON:0003898 skeletal muscle tissue of trunk https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A portion of skeletal muscle tissue in the trunk. http://orcid.org/0000-0002-6601-2165 skeletal muscle of torso OBOL:automatic skeletal muscle tissue of torso OBOL:automatic skeletal muscle tissue of trunk OBOL:automatic torso skeletal muscle OBOL:automatic torso skeletal muscle tissue OBOL:automatic trunk skeletal muscle OBOL:automatic trunk skeletal muscle tissue OBOL:automatic The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011095 BTO:0000929 CALOHA:TS-0685 EHDAA2:0001253 EHDAA:4763 EMAPA:17171 EMAPA:18590 FMA:58628 MA:0000277 NCIT:C33166 TAO:0000046 UMLS:C1518263 VHOG:0000535 XAO:0003216 ZFA:0000046 neural layer of retina neural retina neuroretina stratum nervosum (retina) stratum nervosum retinae uberon neural retinal epithelium UBERON:0003902 retinal neural layer Bgee:AN The part of the retina that contains neurons and photoreceptor cells[GO]. GO:0003407 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000535 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C1518263 ncithesaurus:Neural_Retina neural layer of retina FMA:58628 neural retina XAO:0003216 ZFA:0000046 neuroretina ZFA:0000046 stratum nervosum (retina) FMA:58628 stratum nervosum retinae FMA:58628 FMA:TA neural retinal epithelium MA:000027 Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]. Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO] sinusoidal some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). FMA:63131 SCTID:340163004 TAO:0005261 Wikipedia:Sinusoid_(blood_vessel) ZFA:0005261 sinusoidal blood vessel sinusoidal blood vessel endothelium uberon endothelium of irregular blood filled space sinusoidal capillary sinusoidal endothelium UBERON:0003909 sinusoid Wikipedia ZFA Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]. Wikipedia:Sinusoid_(blood_vessel) Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO] 2012-08-14 TAO:0005261 TAO ZFIN:curator some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). FMA sinusoidal blood vessel endothelium ZFA:0005261 sinusoidal capillary http://www.medilexicon.com/medicaldictionary.php?t=13986 Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 epithelial tube Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GO:0060562 PMID:12526790 FBbt:00007474 Any endothelium that has the quality of being cylindrical [Automatically generated definition]. uberon UBERON:0003915 endothelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. OBOL:automatic A blood vessel that carries blood from the capillaries toward the heart. EMAPA:35932 FMA:86188 MA:0000066 segment of venous tree organ venous tree organ segment uberon UBERON:0003920 Compare to: vein venous blood vessel A blood vessel that carries blood from the capillaries toward the heart. http://www.thefreedictionary.com/venous+blood+vessel segment of venous tree organ FMA:86188 venous tree organ segment FMA:86188 Embryonic structure that develops into pancreatic bud. in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds revisit after standardizing terms 'primordium', 'anlagen', 'bud' EFO:0002579 EFO:0003434 EHDAA2:0001382 EHDAA:2163 EMAPA:17066 FMA:79792 TAO:0000254 XAO:0001101 ZFA:0000254 pancreatic primordium uberon pancreatic anlage pancreatic endoderm primordial pancreas UBERON:0003921 pancreas primordium http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png Wikipedia Embryonic structure that develops into pancreatic bud. Wikipedia:Pancreas#Embryological_development in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds EHDAA2 pancreatic anlage ZFA:0000254 pancreatic endoderm EFO:0002579 primordial pancreas FMA:79792 The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. EFO:0003470 EMAPA:35645 NCIT:C34242 SCTID:360398004 TAO:0001390 UMLS:C1283285 Wikipedia:Pancreatic_bud ZFA:0001390 pancreatic bud pancreatic buds uberon pancreas epithelium pancreatic anlage UBERON:0003922 pancreatic epithelial bud http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 EHDAA2 Wikipedia:Pancreas#Embryological_development zebrafish Wikipedia:Pancreatic_bud EHDAA2-inferred The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. PMID:16417468 Wikipedia:Pancreatic_bud UMLS:C1283285 ncithesaurus:Pancreatic_Bud pancreatic bud ZFA:0001390 pancreatic buds TAO:0001390 pancreas epithelium EMAPA:35645 Pancreatic bud that gives rise to the accessory pancreatic duct. The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] AAO:0011031 EFO:0003465 EHDAA2:0001385 EMAPA:17067 SCTID:361435005 TAO:0001370 VHOG:0001428 Wikipedia:Pancreatic_bud XAO:0000467 ZFA:0001370 pancreas dorsal primordium duct bud pancreas primordium dorsal bud primary pancreatic bud uberon dorsal pancreas anlage dorsal pancreatic anlage posterior pancreatic anlage posterior pancreatic bud UBERON:0003923 dorsal pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 XAO Pancreatic bud that gives rise to the accessory pancreatic duct. Wikipedia:Pancreatic_bud The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] 2012-06-20 AAO:0011031 AAO XAO:curator In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001428 VHOG DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000) http://bgee.unil.ch/ pancreas dorsal primordium duct bud EHDAA2:0001385 primary pancreatic bud XAO:0000467 Pancreatic bud that gives rise to the major pancreatic duct. In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP] the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship. AAO:0011111 EFO:0003464 EHDAA2:0001389 EMAPA:17256 SCTID:361437002 TAO:0001369 VHOG:0001429 Wikipedia:Pancreatic_bud XAO:0001103 ZFA:0001369 pancreas primordium ventral bud pancreas ventral primordium duct bud uberon anterior pancreatic anlage anterior pancreatic bud ventral pancreas anlage ventral pancreatic anlage UBERON:0003924 ventral pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 PMID:16417468 WP Pancreatic bud that gives rise to the major pancreatic duct. Wikipedia:Pancreatic_bud In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001429 VHOG DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000) http://bgee.unil.ch/ pancreas ventral primordium duct bud EHDAA2:0001389 A duct that is part of a digestive system [Automatically generated definition]. TAO:0005162 ZFA:0005162 duct of digestive system duct of gastrointestinal system gastrointestinal system duct uberon UBERON:0003928 digestive system duct A duct that is part of a digestive system [Automatically generated definition]. OBOL:automatic duct of digestive system OBOL:automatic duct of gastrointestinal system OBOL:automatic gastrointestinal system duct OBOL:automatic An epithelium that lines the lumen of the digestive tract. Epithelium lining the lumen of the gut.[TAO] BTO:0000956 EHDAA2:0004567 EMAPA:32928 FBbt:00047166 MA:0003201 NCIT:C12963 TAO:0005123 UMLS:C0836205 XAO:0003200 ZFA:0005123 digestive tract epithelial tissue epithelial tissue of digestive tract epithelial tissue of gut epithelium of digestive tract epithelium of gut gastrodermis gut epithelial tissue gut epithelium uberon alimentary tract epithelium UBERON:0003929 digestive tract epithelium An epithelium that lines the lumen of the digestive tract. http://orcid.org/0000-0002-6601-2165 Epithelium lining the lumen of the gut.[TAO] 2012-08-14 TAO:0005123 TAO ZFIN:curator FBbt:00047166 UMLS:C0836205 ncithesaurus:Gut_Epithelium digestive tract epithelial tissue OBOL:automatic epithelial tissue of digestive tract OBOL:automatic epithelial tissue of gut OBOL:automatic epithelium of digestive tract OBOL:automatic epithelium of gut OBOL:automatic gastrodermis NCBITaxon:6073 https://orcid.org/0000-0003-3308-6245 gut epithelial tissue OBOL:automatic gut epithelium EHDAA2:0004567 MA:0003201 ZFA:0005123 alimentary tract epithelium OBOL:automatic A cartilage element of chondrocranium. Example: neurocranial trabecula. EFO:0003690 TAO:0001461 ZFA:0001461 cartilage of chondrocranium cartilaginous element of chondrocranium chondrocranium cartilage neurocranium cartilage uberon UBERON:0003932 cartilage element of chondrocranium A cartilage element of chondrocranium. Example: neurocranial trabecula. https://orcid.org/0000-0002-6601-2165 cartilage of chondrocranium OBOL:accepted cartilaginous element of chondrocranium OBOL:accepted chondrocranium cartilage ZFA:0001461 neurocranium cartilage ZFA:0001461 A cartilage element that is part of the cranial skeleton. Cartilage which is part of the cranium.[TAO] TAO:0001458 ZFA:0001458 cartilage of cranium cranium cartilage uberon cranial cartilages UBERON:0003933 cranial cartilage A cartilage element that is part of the cranial skeleton. ZFA:0001458 https://orcid.org/0000-0002-6601-2165 Cartilage which is part of the cranium.[TAO] 2012-08-14 TAO:0001458 TAO ZFIN:curator cartilage of cranium OBOL:automatic cranium cartilage OBOL:automatic cranial cartilages ZFA:0001458 Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. BTO:0006162 MA:0001751 genitalia gland gland of genitalia gland of reproductive system reproductive gland reproductive system gland sex gland uberon UBERON:0003937 reproductive gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MP:0000653 BTO:0006162 https://github.com/biopragmatics/biomappings genitalia gland OBOL:automatic gland of genitalia MP:0000653 gland of reproductive system OBOL:automatic reproductive gland MA:0001751 reproductive system gland OBOL:automatic sex gland MP:0000653 The sensory system for the sense of touch and pain. The neural tissue involved in the transmission of sensory signals MP defines this in a may more appropriate to somatosensory cortex UBERON:0014511 EMAPA:37954 NLXANAT:090818 Wikipedia:Somatosensory_system neuronames:2887 somatic sensory system system for detection of somatic senses uberon UBERON:0003942 somatosensory system The sensory system for the sense of touch and pain. NLXANAT:090818 The neural tissue involved in the transmission of sensory signals MP:0000959 MP defines this in a may more appropriate to somatosensory cortex MP EMAPA:37954 MA:th The anterior segment of the lamellated connective tissue layer of the cornea. anterior stroma EMAPA:37414 cornea anterior stroma uberon UBERON:0003952 anterior stroma of cornea lexical The anterior segment of the lamellated connective tissue layer of the cornea. MP:0003093 anterior stroma MP:0003093 EMAPA:37414 MA:th cornea anterior stroma MP:0003093 The posterior segment of the lamellated connective tissue layer of the cornea. posterior stroma EMAPA:37415 cornea posterior stroma uberon UBERON:0003953 posterior stroma of cornea lexical The posterior segment of the lamellated connective tissue layer of the cornea. MP:0003094 posterior stroma MP:0003094 EMAPA:37415 MA:th cornea posterior stroma MP:0003094 The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity. EMAPA:37841 cutaneous elastic fiber dermal elastic fiber uberon UBERON:0003967 cutaneous elastic tissue The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity. MP:0008418 EMAPA:37841 MA:th cutaneous elastic fiber MP:0008418 dermal elastic fiber MP:0008418 The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. BTO:0003099 FMA:45654 SCTID:303518005 female internal genitalia internal female genital organ internal genitalia of female reproductive system uberon organa genitalia feminina interna UBERON:0003975 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 internal female genitalia The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. MP:0009209 female internal genitalia FMA:45654 internal female genital organ BTO:0003099 internal genitalia of female reproductive system OBOL:automatic organa genitalia feminina interna BTO:0003099 The connection between the embryo proper and extraembryonic tissues. uberon UBERON:0004015 embryonic-extraembryonic boundary The connection between the embryo proper and extraembryonic tissues. MP:0003890 A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. Not to be confused with 'dermatome segment of skin'. AAO:0011028 AEO:0001017 BTO:0006248 EHDAA2_RETIRED:0003428 EHDAA:1719 EHDAA:1725 EHDAA:1731 EHDAA:1737 EMAPA:32838 FMA:295656 NCIT:C61572 UMLS:C0180383 Wikipedia:Dermatome_(embryology) XAO:0000220 cutis plate dermatomal mesenchyme uberon epimere mesoderm mesenchyma dermatomiale UBERON:0004016 dermatome http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. AEO:0001017 AEO:JB BTO:0006248 https://github.com/biopragmatics/biomappings UMLS:C0180383 ncithesaurus:Dermatome cutis plate Wikipedia:Cutis_plate dermatomal mesenchyme Wikipedia:Cutis_plate mesenchyma dermatomiale Wikipedia:Dermatomal_mesenchyme The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells. As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] germinal neuroepithelial layer germinal neuroepithelium original neural tube uberon UBERON:0004022 germinal neuroepithelium NCBIBook:NBK10047 The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells. MP:0004261 http://www.ncbi.nlm.nih.gov/books/NBK10047 germinal neuroepithelial layer http://orcid.org/0000-0002-6601-2165 germinal neuroepithelium NCBIBook:NBK10047 original neural tube NCBIBook:NBK10047 One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP]. In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule) BTO:0002840 EMAPA:37440 TAO:0005164 ZFA:0005164 bile ductule biliary ductule ductuli biliferi uberon bile capillary biliary ductule cholangiole terminal cholangiole UBERON:0004058 biliary ductule BTO One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP]. BTO:0002840 MP:0009494 In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule) ZFA EMAPA:37440 MA:th bile ductule BTO:0002840 biliary ductule http://www.mondofacto.com/facts/dictionary?ductuli+biliferi ductuli biliferi http://www.mondofacto.com/facts/dictionary?ductuli+biliferi bile capillary BTO:0002840 biliary ductule BTO:0002840 cholangiole BTO:0002840 terminal cholangiole http://orcid.org/0000-0002-6601-2165 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen ependymal layer EMAPA:17152 EMAPA:35362 EMAPA_RETIRED:16783 MA:0003193 neural tube ependymal layer neural tube ventricular germinal zone neural tube ventricular zone neural tube ependymal zone uberon UBERON:0004060 neural tube ventricular layer NCBIBook:NBK10047 NCBIBook:NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. MP:0009689 http://www.ncbi.nlm.nih.gov/books/NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen MP:0009689 ependymal layer NCBIBook:NBK10047 neural tube ependymal layer NCBIBook:NBK10047 neural tube ventricular germinal zone NCBIBook:NBK10047 neural tube ventricular zone MP:0009689 neural tube ependymal zone MP:0009689 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. EMAPA:17148 EMAPA:35360 neuronames:1367 neural tube intermediate zone uberon future brain marginal layer UBERON:0004061 neural tube mantle layer NCBIBook:NBK10047 by division NCBIBook:NBK10047 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. MP:0009690 http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube intermediate zone MP:0009690 http://www.ncbi.nlm.nih.gov/books/NBK10047 future brain marginal layer EMAPA:35360 The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter. EMAPA:17151 neuronames:1368 neural tube marginal zone uberon brain marginal zone UBERON:0004062 neural tube marginal layer forms from axons The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter. MP:0009691 http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube marginal zone MP:0009691 The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. AAO:0010561 EFO:0001904 NCIT:C34111 UMLS:C1511061 Wikipedia:Basal_plate_(neural_tube) neuronames:1372 basal plate basal plate of neural tube spinal cord basal plate uberon motor part of neural tube ventral part of neural tube UBERON:0004064 neural tube basal plate Shh Swenson The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. MP:0009693 Wikipedia:Basal_plate_(neural_tube) http://www.ncbi.nlm.nih.gov/books/NBK10047 UMLS:C1511061 ncithesaurus:Basal_Plate basal plate of neural tube Wikipedia:Basal_plate_(neural_tube) spinal cord basal plate MP:0009693 The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout. UBERON:0006237 EHDAA2:0000578 EHDAA:4778 EMAPA:16681 FMA:293101 NCIT:C34182 SCTID:361486000 UMLS:C1517321 VHOG:0001319 Wikipedia:Frontonasal_prominence embryonic frontonasal prominence uberon forebrain prominence frontonasal mass frontonasal process prominentia frontonasalis UBERON:0004066 frontonasal prominence http://upload.wikimedia.org/wikipedia/commons/9/98/Gray44.png The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout. MP:0009901 UMLS:C1517321 ncithesaurus:Frontonasal_Prominence embryonic frontonasal prominence http://orcid.org/0000-0002-6601-2165 forebrain prominence MP:0009901 frontonasal mass MP:0009901 frontonasal process MP:0009901 prominentia frontonasalis Wikipedia:Frontonasal_prominence The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it. Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity. EHDAA2:0001076 EHDAA:4792 EMAPA:16808 FMA:295858 SCTID:308877001 VHOG:0000804 Wikipedia:Medial_nasal_prominence medial nasal process medial-nasal process prominentia nasalis medialis uberon medial nasal swelling nasomedial prominence UBERON:0004068 medial nasal prominence http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png EHDAA2 Wikipedia The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it. MP:0009903 Wikipedia:Medial_nasal_prominence medial nasal process EHDAA2:0001076 medial-nasal process EMAPA:16808 prominentia nasalis medialis Wikipedia:Medial_nasal_prominence medial nasal swelling https://orcid.org/0000-0002-6601-2165 nasomedial prominence https://orcid.org/0000-0002-6601-2165 Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. AAO:0010215 BTO:0001438 EMAPA:18415 FMA:321896 GAID:547 MA:0000068 MESH:D014684 NCIT:C12817 SCTID:244405007 UMLS:C0042460 Wikipedia:Venae_cavae uberon caval vein venae cavae UBERON:0004087 vena cava http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. Wikipedia:Venae_cavae http://orcid.org/0000-0002-6601-2165 UMLS:C0042460 ncithesaurus:Vena_Cava venae cavae Wikipedia:Venae_cavae The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present. note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye in HP covers eyelid, eyebrow. FMA:260119 content of orbital part of eye eye region orbital part of face uberon ocular and peri-ocular region ocular region orbital content orbital part of eye UBERON:0004088 orbital region The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present. http://orcid.org/0000-0002-6601-2165 in HP covers eyelid, eyebrow. HP:0000284 content of orbital part of eye FMA:260119 eye region http://orcid.org/0000-0002-6601-2165 orbital part of face http://orcid.org/0000-0002-6601-2165 orbital content FMA:260119 orbital part of eye FMA:72951 The middle of the face including the nose and its associated bony structures[MW]. this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface. midfacial EMAPA:32806 FMA:285406 MA:0001910 uberon lower face midface/lower face snout UBERON:0004089 midface The middle of the face including the nose and its associated bony structures[MW]. HP:0000309 http://www.merriam-webster.com/medical/midface snout MA:0001910 2 Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 SCTID:346902003 Wikipedia:Foramen foramen foramina uberon opening ostia ostium UBERON:0004111 anatomical conduit Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 FMA has both conduit and conduit space. In EHDAA2 this is a surface feature FMA foramen EHDAA2:0003080 foramina https://orcid.org/0000-0002-6601-2165 ostia A vasculature that is part of a iris [Automatically generated definition]. ZFA:0005568 iris blood vessels iris vascular network iris vasculature vascular network of iris uberon UBERON:0004118 vasculature of iris A vasculature that is part of a iris [Automatically generated definition]. OBOL:automatic iris blood vessels ZFA:0005568 iris vascular network OBOL:automatic vascular network of iris OBOL:automatic An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes uberon UBERON:0004119 endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. https://orcid.org/0000-0002-6601-2165 An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. https://orcid.org/0000-0002-6601-2165 mesodermal derivative FBbt:00025998 An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. https://orcid.org/0000-0002-6601-2165 ectodermal deriviative FBbt:00025990 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] genitourinary urogenital AAO:0000624 BILA:0000122 BTO:0003091 EFO:0003864 EHDAA:1013 EMAPA:16367 EV:0100094 FMA:280610 GAID:362 MESH:D014566 NCIT:C12810 SCTID:278861008 UMLS:C0042066 VHOG:0000286 XAO:0000140 galen:GenitoUrinarySystem urogenital system uberon GU tract UG tract Urogenitalsystem genito-urinary system genitourinary tract urogenital tract UBERON:0004122 genitourinary system Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. VHOG:0000286 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] 2012-06-20 AAO:0000624 AAO AAO:EJS relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] 2012-06-20 AAO:0000624 AAO Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] 2012-09-17 VHOG:0000286 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633 http://bgee.unil.ch/ UMLS:C0042066 ncithesaurus:Genitourinary_System Urogenitalsystem BTO:0003091 genito-urinary system FMA:280610 urogenital tract BTO:0003091 Any of the layers of the myocardium. Example: compact layer, trabecular layer. EMAPA:37475 MA:0000080 layer of myocardium myocardium layer uberon UBERON:0004123 myocardial layer Any of the layers of the myocardium. Example: compact layer, trabecular layer. http://orcid.org/0000-0002-6601-2165 EMAPA:37475 MA:th The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA]. The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO] EFO:0003706 MA:0002866 TAO:0005059 ZFA:0005059 myocardial trabecular layer trabecular layer uberon heart muscle trabecula heart muscle trabeculae myocardial trabeculae carneae trabecula of heart muscle trabeculae UBERON:0004124 myocardium trabecular layer The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA]. ZFA:0005059 The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO] 2012-08-14 TAO:0005059 TAO ZFIN:curator trabecular layer ZFA:0005059 heart muscle trabeculae myocardial trabeculae carneae trabeculae TAO:0005059 A myocardium trabecular layer that is part of a cardiac ventricle. TODO - check FMA FMA:83511 TAO:0005060 ZFA:0005060 myocardium of region of ventricle trabecular cardiac ventricle muscle ventricular trabecular myocardium uberon UBERON:0004126 trabecular layer of ventricle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A myocardium trabecular layer that is part of a cardiac ventricle. OBOL:automatic myocardium of region of ventricle FMA:83511 trabecular cardiac ventricle muscle GO:0003222 ventricular trabecular myocardium GO:0003222 The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 FMA:293357 NCIT:C34236 SCTID:362864008 TAO:0000050 UMLS:C0231106 VHOG:0000165 Wikipedia:Optic_vesicles XAO:0000228 ZFA:0000050 uberon evagination eye vesicle ocular vesicle optic vesicles UBERON:0004128 Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288] optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png ZFA GO-def ZFA The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. GO:0003404 Wikipedia:Optic_vesicles (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] 2012-09-17 VHOG:0000165 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C0231106 ncithesaurus:Optic_Vesicle eye vesicle XAO:0000228 ocular vesicle VHOG:0000165 optic vesicles ZFA:0000050 Missing definition for term UBERON:0004133. Please replace it using linked reference. salivary nucleus uberon UBERON:0004133 salivatory nucleus Missing definition for term UBERON:0004133. Please replace it using linked reference. GO:0021751 salivary nucleus GO:0021751 The first recognizable structure derived from the heart field. TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 myocardial plate uberon cardiac crescent cardiogenic crescent heart rudiment UBERON:0004139 cardiogenic plate The first recognizable structure derived from the heart field. GO:0003142 (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] 2012-09-17 VHOG:0000975 VHOG PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) http://bgee.unil.ch/ myocardial plate EHDAA2:0000215 cardiac crescent EMAPA:16106 cardiogenic crescent GO:0003142 A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field uberon FHF PHF heart field UBERON:0004140 primary heart field GO:0003128 https://orcid.org/0000-0003-3308-6245 A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. GO:0003138 GOC:mtg_heart GOC:rl this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] GO first heart field XAO:0004185 primary heart field PMID:17276708 XAO:0004185 FHF XAO:0004185 PHF XAO:0004185 heart field XAO:0004185 An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 NCIT:C34161 TAO:0000360 XAO:0000337 ZFA:0000360 embryonic heart tube endocardial heart tube endocardial tube uberon UBERON:0004141 heart tube ZFA-modified An epithelial tube that will give rise to the mature heart. GO:0003143 GOC:mtg_heart the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. MP:0012700 embryonic heart tube GO:0003143 endocardial heart tube MP:0012700 endocardial tube XAO:0000337 The outflow tract septum is a partition in the outflow tract. XAO:0004141 uberon UBERON:0004142 outflow tract septum The outflow tract septum is a partition in the outflow tract. GO:0003148 The outflow tract is the portion of the heart through which blood flows into the arteries. Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616] EHDAA2:0001351 EHDAA:464 EHDAA:798 EMAPA:16346 MA:0000100 VHOG:0000670 XAO:0004139 cardiac outflow tract heart outflow tract uberon arterial (outflow) pole UBERON:0004145 outflow tract The outflow tract is the portion of the heart through which blood flows into the arteries. GO:0003151 cardiac outflow tract PMID:20735616 arterial (outflow) pole PMID:20735616 The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles. the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles. HPS His-Purkinji network VCS ventricular conduction system uberon UBERON:0004146 His-Purkinje system cjm GO PMID:12626327 PMID:21234997 github:michaelerice The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles. GO:0003164 https://github.com/geneontology/go-ontology/issues/12451 the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles. http://medical-dictionary.thefreedictionary.com/His-Purkinje+system HPS Vein of heart that drains the myocardium. EHDAA2:0004507 EMAPA:37137 FMA:12846 NCIT:C12878 NCIT:C12882 SCTID:277726009 UMLS:C0226654 UMLS:C0226737 Wikipedia:Coronary_circulation ZFA:0005814 galen:CoronaryVein cardiac vein coronary vein heart vein vein of heart uberon coronary vein UBERON:0004148 cardiac vein https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA Vein of heart that drains the myocardium. http://orcid.org/0000-0002-6601-2165 EMAPA:37137 MA:th UMLS:C0226654 ncithesaurus:Cardiac_Vein UMLS:C0226737 ncithesaurus:Coronary_Vein cardiac vein FMA:12846 coronary vein ZFA:0005814 heart vein OBOL:automatic vein of heart OBOL:automatic coronary vein Wikipedia:Coronary_circulation A cardiac chamber surrounds an enclosed cavity within the heart. FMA:7095 SCTID:276456008 chamber of heart heart chamber uberon UBERON:0004151 generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus cardiac chamber A cardiac chamber surrounds an enclosed cavity within the heart. GO:0003205 An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium. propepicardial Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA] EMAPA:36025 ZFA:0005808 proepicardial cluster proepicardial organ uberon UBERON:0004160 proepicardium todo check other taxa ZFA An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium. GO:0003342 http://en.wiktionary.org/wiki/proepicardium proepicardial cluster ZFA:0005808 proepicardial organ ZFIN:ZDB-PUB-080218-16 A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2:0001829 EHDAA:736 EMAPA:16318 FMA:295593 NCIT:C34296 SCTID:308819008 UMLS:C0231004 VHOG:0000019 Wikipedia:Septum_transversum transverse septum uberon UBERON:0004161 septum transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. VHOG:0000019 Wikipedia:Septum_transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] 2012-09-17 VHOG:0000019 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/transverse+septum In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000019 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2 UMLS:C0231004 ncithesaurus:Septum_Transversum transverse septum https://orcid.org/0000-0002-6601-2165 The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. FMA:45652 internal genitalia internal genitals uberon internal reproductive organ internal sex organ UBERON:0004175 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 internal genitalia The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. GO:0035260 The external genitalia are the outer sex organs, such as the penis or vulva in mammals. FMA:45643 SCTID:362207005 external genitalia uberon external reproductive organ external sex organ UBERON:0004176 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia The external genitalia are the outer sex organs, such as the penis or vulva in mammals. GO:0035261 Organ that is part of the hematopoietic system. consider splitting out lymph organ, compare with lymph node the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. the FMA class 'lymphoid organ' is a general anatomical term BTO:0004605 EMAPA:37665 FMA:7143 MA:0000747 SCTID:361338006 haematological system organ haemopoietic system organ hematopoeitic organ hematopoietic system organ organ of haematological system organ of haemopoietic system organ of hematopoietic system organ of organa haemopoietica organa haemopoietica organ hematopoeitic or lymphoid organ lymph organ lymphoid organ uberon UBERON:0004177 hemopoietic organ Organ that is part of the hematopoietic system. GOC:Obol the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs the FMA class 'lymphoid organ' is a general anatomical term FMA EMAPA:37665 MA:th haematological system organ OBOL:automatic haemopoietic system organ OBOL:automatic hematopoietic system organ OBOL:automatic organ of haematological system OBOL:automatic organ of haemopoietic system OBOL:automatic organ of hematopoietic system OBOL:automatic organ of organa haemopoietica OBOL:automatic organa haemopoietica organ OBOL:automatic lymph organ MA:0000747 lymphoid organ BTO:0004605 FMA:7143 The nonstriated, involuntary muscle tissue located in the wall of the aorta. BTO:0001685 CALOHA:TS-0048 EFO:0002775 EMAPA:35135 MA:0000702 NCIT:C49191 UMLS:C1706825 aorta non-striated muscle aorta smooth muscle aortic smooth muscle uberon UBERON:0004178 aorta smooth muscle tissue The nonstriated, involuntary muscle tissue located in the wall of the aorta. MGI:csmith MP:0009865 UMLS:C1706825 ncithesaurus:Aorta_Smooth_Muscle_Tissue aorta non-striated muscle OBOL:automatic aorta smooth muscle OBOL:automatic aortic smooth muscle BTO:0001685 A portions of the gut that is derived from endoderm. EMAPA:32930 endodermal gut gut endoderm uberon UBERON:0004185 endodermal part of digestive tract A portions of the gut that is derived from endoderm. GO:0061031 gut endoderm EMAPA:32930 A nerve that is part of a back [Automatically generated definition]. EMAPA:37268 MA:0000497 nerve of back uberon UBERON:0004215 back nerve A nerve that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37268 MA:th nerve of back OBOL:automatic A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35469 MA:0001547 involuntary muscle of large intestine large intestine involuntary muscle large intestine non-striated muscle large intestine smooth muscle tissue non-striated muscle of large intestine smooth muscle of large intestine smooth muscle tissue of large intestine uberon UBERON:0004220 large intestine smooth muscle MA consider merging A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA involuntary muscle of large intestine OBOL:automatic large intestine involuntary muscle OBOL:automatic large intestine non-striated muscle OBOL:automatic large intestine smooth muscle tissue OBOL:automatic non-striated muscle of large intestine OBOL:automatic smooth muscle of large intestine OBOL:automatic smooth muscle tissue of large intestine OBOL:automatic A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa BTO:0000643 EMAPA:35441 EMAPA:35443 MA:0001539 NCIT:C49243 UMLS:C1708547 bowel involuntary muscle bowel non-striated muscle bowel smooth muscle bowel smooth muscle tissue intestine involuntary muscle intestine non-striated muscle intestine smooth muscle tissue involuntary muscle of bowel involuntary muscle of intestine non-striated muscle of bowel non-striated muscle of intestine smooth muscle of bowel smooth muscle of intestine smooth muscle tissue of bowel smooth muscle tissue of intestine uberon intestinal muscularis intestinal smooth muscle UBERON:0004221 intestine smooth muscle consider merging A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA UMLS:C1708547 ncithesaurus:Intestinal_Smooth_Muscle_Tissue bowel involuntary muscle OBOL:automatic bowel non-striated muscle OBOL:automatic bowel smooth muscle OBOL:automatic bowel smooth muscle tissue OBOL:automatic intestine involuntary muscle OBOL:automatic intestine non-striated muscle OBOL:automatic intestine smooth muscle tissue OBOL:automatic involuntary muscle of bowel OBOL:automatic involuntary muscle of intestine OBOL:automatic non-striated muscle of bowel OBOL:automatic non-striated muscle of intestine OBOL:automatic smooth muscle of bowel OBOL:automatic smooth muscle of intestine OBOL:automatic smooth muscle tissue of bowel OBOL:automatic smooth muscle tissue of intestine OBOL:automatic intestinal muscularis EMAPA:35441 intestinal smooth muscle BTO:0000643 A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. BTO:0001818 EMAPA:35823 MA:0001627 involuntary muscle of stomach involuntary muscle of ventriculus non-striated muscle of stomach non-striated muscle of ventriculus smooth muscle of stomach smooth muscle of ventriculus smooth muscle tissue of stomach smooth muscle tissue of ventriculus stomach involuntary muscle stomach non-striated muscle stomach smooth muscle tissue ventriculus involuntary muscle ventriculus non-striated muscle ventriculus smooth muscle ventriculus smooth muscle tissue uberon gastric muscle gastric smooth muscle stomach muscle UBERON:0004222 stomach smooth muscle A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. OBOL:automatic involuntary muscle of stomach OBOL:automatic involuntary muscle of ventriculus OBOL:automatic non-striated muscle of stomach OBOL:automatic non-striated muscle of ventriculus OBOL:automatic smooth muscle of stomach OBOL:automatic smooth muscle of ventriculus OBOL:automatic smooth muscle tissue of stomach OBOL:automatic smooth muscle tissue of ventriculus OBOL:automatic stomach involuntary muscle OBOL:automatic stomach non-striated muscle OBOL:automatic stomach smooth muscle tissue OBOL:automatic ventriculus involuntary muscle OBOL:automatic ventriculus non-striated muscle OBOL:automatic ventriculus smooth muscle OBOL:automatic ventriculus smooth muscle tissue OBOL:automatic gastric muscle BTO:0001818 gastric smooth muscle MA:0001627 stomach muscle BTO:0001818 A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. BTO:0001660 EMAPA:35734 MA:0001830 respiratory smooth muscle smooth muscle of respiratory system uberon airway smooth muscle airway smooth muscle cell UBERON:0004225 respiratory system smooth muscle A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic respiratory smooth muscle BTO:0001660 smooth muscle of respiratory system OBOL:automatic airway smooth muscle BTO:0001660 airway smooth muscle cell BTO:0001660 A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. EMAPA:35117 MA:0001523 smooth muscle tissue of gastrointestinal system uberon UBERON:0004226 gastrointestinal system smooth muscle A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. OBOL:automatic smooth muscle tissue of gastrointestinal system OBOL:automatic A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37394 MA:0001532 anal part of perineum involuntary muscle anal part of perineum non-striated muscle anal part of perineum smooth muscle anal part of perineum smooth muscle tissue anal region involuntary muscle anal region non-striated muscle anal region smooth muscle tissue anal triangle involuntary muscle anal triangle non-striated muscle anal triangle smooth muscle anal triangle smooth muscle tissue involuntary muscle of anal part of perineum involuntary muscle of anal region involuntary muscle of anal triangle non-striated muscle of anal part of perineum non-striated muscle of anal region non-striated muscle of anal triangle smooth muscle of anal part of perineum smooth muscle of anal region smooth muscle of anal triangle smooth muscle tissue of anal part of perineum smooth muscle tissue of anal region smooth muscle tissue of anal triangle uberon UBERON:0004231 anal region smooth muscle A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37394 MA:th anal part of perineum involuntary muscle OBOL:automatic anal part of perineum non-striated muscle OBOL:automatic anal part of perineum smooth muscle OBOL:automatic anal part of perineum smooth muscle tissue OBOL:automatic anal region involuntary muscle OBOL:automatic anal region non-striated muscle OBOL:automatic anal region smooth muscle tissue OBOL:automatic anal triangle involuntary muscle OBOL:automatic anal triangle non-striated muscle OBOL:automatic anal triangle smooth muscle OBOL:automatic anal triangle smooth muscle tissue OBOL:automatic involuntary muscle of anal part of perineum OBOL:automatic involuntary muscle of anal region OBOL:automatic involuntary muscle of anal triangle OBOL:automatic non-striated muscle of anal part of perineum OBOL:automatic non-striated muscle of anal region OBOL:automatic non-striated muscle of anal triangle OBOL:automatic smooth muscle of anal part of perineum OBOL:automatic smooth muscle of anal region OBOL:automatic smooth muscle of anal triangle OBOL:automatic smooth muscle tissue of anal part of perineum OBOL:automatic smooth muscle tissue of anal region OBOL:automatic smooth muscle tissue of anal triangle OBOL:automatic A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:35520 MA:0002410 involuntary muscle of lower respiratory tract lower respiratory tract involuntary muscle lower respiratory tract non-striated muscle lower respiratory tract smooth muscle tissue non-striated muscle of lower respiratory tract smooth muscle of lower respiratory tract smooth muscle tissue of lower respiratory tract uberon UBERON:0004233 lower respiratory tract smooth muscle A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic involuntary muscle of lower respiratory tract OBOL:automatic lower respiratory tract involuntary muscle OBOL:automatic lower respiratory tract non-striated muscle OBOL:automatic lower respiratory tract smooth muscle tissue OBOL:automatic non-striated muscle of lower respiratory tract OBOL:automatic smooth muscle of lower respiratory tract OBOL:automatic smooth muscle tissue of lower respiratory tract OBOL:automatic A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. see notes for muscle of iris. BTO:0000655 EMAPA:35448 FMA:312338 MA:0001270 involuntary muscle of iris iridial smooth muscle iris involuntary muscle iris non-striated muscle iris smooth muscle tissue non-striated muscle of iris smooth muscle of iris smooth muscle tissue of iris uberon UBERON:0004234 iris smooth muscle MA A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. OBOL:automatic involuntary muscle of iris OBOL:automatic iridial smooth muscle http://orcid.org/0000-0002-6601-2165 iris involuntary muscle OBOL:automatic iris non-striated muscle OBOL:automatic iris smooth muscle tissue OBOL:automatic non-striated muscle of iris OBOL:automatic smooth muscle of iris OBOL:automatic smooth muscle tissue of iris OBOL:automatic A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. EMAPA:36287 FMA:312251 MA:0000706 uberon UBERON:0004236 arteriole smooth muscle A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. OBOL:automatic Smooth muscle found within, and composing the majority of the wall of blood vessels. Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension. UBERON:0010508 BTO:0001431 CALOHA:TS-1107 EMAPA:35177 MA:0000710 MESH:D009131 NCIT:C33853 TAO:0005321 UMLS:C1519956 Wikipedia:Vascular_smooth_muscle ZFA:0005321 blood vessel involuntary muscle blood vessel non-striated muscle blood vessel smooth muscle tissue involuntary muscle of blood vessel non-striated muscle of blood vessel smooth muscle of blood vessel smooth muscle tissue of blood vessel vascular smooth muscle vascular smooth muscle tissue uberon UBERON:0004237 blood vessel smooth muscle Smooth muscle found within, and composing the majority of the wall of blood vessels. Wikipedia:Vascular_smooth_muscle UMLS:C1519956 ncithesaurus:Vascular_Smooth_Muscle_Tissue blood vessel involuntary muscle OBOL:automatic blood vessel non-striated muscle OBOL:automatic blood vessel smooth muscle tissue OBOL:automatic involuntary muscle of blood vessel OBOL:automatic non-striated muscle of blood vessel OBOL:automatic smooth muscle of blood vessel OBOL:automatic smooth muscle tissue of blood vessel OBOL:automatic vascular smooth muscle ZFA:0005321 A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition]. EMAPA:35807 MA:0000757 involuntary muscle of spleen non-striated muscle of spleen smooth muscle of spleen smooth muscle tissue of spleen spleen involuntary muscle spleen non-striated muscle spleen smooth muscle tissue uberon UBERON:0004238 spleen smooth muscle A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition]. OBOL:automatic involuntary muscle of spleen OBOL:automatic non-striated muscle of spleen OBOL:automatic smooth muscle of spleen OBOL:automatic smooth muscle tissue of spleen OBOL:automatic spleen involuntary muscle OBOL:automatic spleen non-striated muscle OBOL:automatic spleen smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35783 MA:0001559 involuntary muscle of small bowel involuntary muscle of small intestine non-striated muscle of small bowel non-striated muscle of small intestine small bowel involuntary muscle small bowel non-striated muscle small bowel smooth muscle small bowel smooth muscle tissue small intestine involuntary muscle small intestine non-striated muscle small intestine smooth muscle tissue smooth muscle of small bowel smooth muscle of small intestine smooth muscle tissue of small bowel smooth muscle tissue of small intestine uberon UBERON:0004239 small intestine smooth muscle consider merging A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA involuntary muscle of small bowel OBOL:automatic involuntary muscle of small intestine OBOL:automatic non-striated muscle of small bowel OBOL:automatic non-striated muscle of small intestine OBOL:automatic small bowel involuntary muscle OBOL:automatic small bowel non-striated muscle OBOL:automatic small bowel smooth muscle OBOL:automatic small bowel smooth muscle tissue OBOL:automatic small intestine involuntary muscle OBOL:automatic small intestine non-striated muscle OBOL:automatic small intestine smooth muscle tissue OBOL:automatic smooth muscle of small bowel OBOL:automatic smooth muscle of small intestine OBOL:automatic smooth muscle tissue of small bowel OBOL:automatic smooth muscle tissue of small intestine OBOL:automatic A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition]. EMAPA:35373 MA:0001635 NCIT:C49483 UMLS:C1708179 gall bladder involuntary muscle gall bladder non-striated muscle gall bladder smooth muscle gall bladder smooth muscle tissue gallbladder involuntary muscle gallbladder non-striated muscle gallbladder smooth muscle tissue involuntary muscle of gall bladder involuntary muscle of gallbladder non-striated muscle of gall bladder non-striated muscle of gallbladder smooth muscle of gall bladder smooth muscle of gallbladder smooth muscle tissue of gall bladder smooth muscle tissue of gallbladder uberon biliary smooth muscle UBERON:0004240 gallbladder smooth muscle A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition]. OBOL:automatic UMLS:C1708179 ncithesaurus:Gallbladder_Smooth_Muscle_Tissue gall bladder involuntary muscle OBOL:automatic gall bladder non-striated muscle OBOL:automatic gall bladder smooth muscle OBOL:automatic gall bladder smooth muscle tissue OBOL:automatic gallbladder involuntary muscle OBOL:automatic gallbladder non-striated muscle OBOL:automatic involuntary muscle of gall bladder OBOL:automatic involuntary muscle of gallbladder OBOL:automatic non-striated muscle of gall bladder OBOL:automatic non-striated muscle of gallbladder OBOL:automatic smooth muscle of gall bladder OBOL:automatic smooth muscle of gallbladder OBOL:automatic smooth muscle tissue of gall bladder OBOL:automatic smooth muscle tissue of gallbladder OBOL:automatic biliary smooth muscle MA:0001635 A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. EMAPA:37708 MA:0000492 involuntary muscle of outflow tract non-striated muscle of outflow tract outflow tract involuntary muscle outflow tract non-striated muscle outflow tract smooth muscle tissue smooth muscle of outflow tract smooth muscle tissue of outflow tract uberon UBERON:0004246 outflow tract smooth muscle A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37708 MA:th involuntary muscle of outflow tract OBOL:automatic non-striated muscle of outflow tract OBOL:automatic outflow tract involuntary muscle OBOL:automatic outflow tract non-striated muscle OBOL:automatic outflow tract smooth muscle tissue OBOL:automatic smooth muscle of outflow tract OBOL:automatic smooth muscle tissue of outflow tract OBOL:automatic A bone that is part of the dorsal region of an animal. this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37248 MA:0000494 uberon back bone bone of back dorsal region bone UBERON:0004247 bone of dorsum A bone that is part of the dorsal region of an animal. http://orcid.org/0000-0002-6601-2165 EMAPA:37248 MA:th back bone MA:0000494 bone of back OBOL:automatic dorsal region bone http://orcid.org/0000-0002-6601-2165 Any muscle organ that is part of a skin of body [Automatically generated definition]. review as part of general integumentary system review - part of skin, or more generally, integumental system in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only UBERON:0015797 EMAPA:18187 EMAPA:35776 MA:0002710 MA:0003139 integumental system muscle muscle of integumental system muscle organ of skin skin muscle organ uberon UBERON:0004253 skin muscle Any muscle organ that is part of a skin of body [Automatically generated definition]. OBOL:automatic in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only MA integumental system muscle MA:0003139 muscle of integumental system EMAPA:18187 muscle organ of skin OBOL:automatic skin muscle organ OBOL:automatic A blood vessel that is part of a back [Automatically generated definition]. EMAPA:37243 MA:0000493 blood vessel of back uberon UBERON:0004258 back blood vessel A blood vessel that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37243 MA:th blood vessel of back OBOL:automatic A myocardium that is part of a outflow tract [Automatically generated definition]. (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] EHDAA2:0001358 EMAPA:35623 MA:0000489 VHOG:0000603 cardiac muscle of outflow tract heart muscle of outflow tract heart myocardium of outflow tract muscle of heart of outflow tract myocardium of outflow tract outflow tract cardiac muscle outflow tract heart muscle outflow tract heart myocardium outflow tract muscle of heart uberon UBERON:0004265 outflow tract myocardium A myocardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] 2012-09-17 VHOG:0000603 VHOG PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997) http://bgee.unil.ch/ cardiac muscle of outflow tract OBOL:automatic heart muscle of outflow tract OBOL:automatic heart myocardium of outflow tract OBOL:automatic muscle of heart of outflow tract OBOL:automatic myocardium of outflow tract OBOL:automatic outflow tract cardiac muscle OBOL:automatic outflow tract heart muscle OBOL:automatic outflow tract heart myocardium OBOL:automatic outflow tract muscle of heart OBOL:automatic A portion of connective tissue that is part of a back [Automatically generated definition]. EMAPA:37256 MA:0000495 uberon mesenchyne of back UBERON:0004267 back connective tissue A portion of connective tissue that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37256 MA:th mesenchyne of back OBOL:automatic A pericardium that is part of a outflow tract [Automatically generated definition]. EMAPA:37707 MA:0000491 pericardium of outflow tract uberon UBERON:0004271 outflow tract pericardium A pericardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37707 MA:th pericardium of outflow tract OBOL:automatic A muscle that is part of the eye region. AAO:0000156 EMAPA:35335 MA:0000271 uberon UBERON:0004277 eye muscle MA A muscle that is part of the eye region. OBOL:automatic Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 EMAPA:17213 FMA:23875 GAID:177 MA:0003006 MAT:0000032 MESH:D012863 MIAA:0000032 SCTID:361378004 VSAO:0000026 Wikipedia:Skeleton XAO:0004053 galen:Skeleton set of all bones set of bones of body uberon UBERON:0004288 skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] 2012-08-14 VSAO:0000026 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] Portion of somites that gives rise to dermis and muscles.[AAO] all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] AAO:0010572 AEO:0000214 EHDAA2:0003259 EMAPA:31109 FMA:295654 NCIT:C34140 TAO:0001513 UMLS:C1511786 VHOG:0000676 ZFA:0001513 uberon dermamyotome dermomyotomes UBERON:0004290 dermomyotome AEO AEO EHDAA2 ZFA The bilaminar epithelium formed from the myotome and dermatome. AEO:0000214 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] 2012-08-14 TAO:0001513 TAO ZFIN:curator Portion of somites that gives rise to dermis and muscles.[AAO] 2012-06-20 AAO:0010572 AAO AAO:EJS all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. http://medical-dictionary.thefreedictionary.com/dermomyotome Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] 2012-09-17 VHOG:0000676 VHOG DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006) http://bgee.unil.ch/ UMLS:C1511786 ncithesaurus:Dermomyotome dermamyotome VHOG:0000676 dermomyotomes VHOG:0000676 A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone rudimentary heart uberon UBERON:0004291 heart rudiment A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] 2012-08-14 TAO:0000115 TAO ZFIN:curator heart cone GO:0003313 rudimentary heart ZFA:0000115 Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP] EMAPA:36645 FMA:9496 Wikipedia:Cardiac_skeleton cardiac fibrous skeleton fibrous skeleton of heart heart fibrous skeleton skeleton of heart uberon anulus fibrosus dexter cordis anulus fibrosus sinister cordis trigona fibrosa trigonum fibrosum dextrum cordis trigonum fibrosum sinistrum cordis UBERON:0004292 cardiac skeleton http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. GO:0003204 Wikipedia:Cardiac_skeleton cardiac fibrous skeleton EMAPA:36645 heart fibrous skeleton GO:0003204 skeleton of heart FMA:9496 anulus fibrosus dexter cordis Wikipedia:Cardiac_skeleton anulus fibrosus sinister cordis Wikipedia:Cardiac_skeleton trigona fibrosa Wikipedia:Cardiac_skeleton trigonum fibrosum dextrum cordis Wikipedia:Cardiac_skeleton trigonum fibrosum sinistrum cordis Wikipedia:Cardiac_skeleton A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. EMAPA:37573 MA:0001806 smooth muscle tissue of blood vessel of respiratory system uberon UBERON:0004297 respiratory system blood vessel smooth muscle A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37573 MA:th smooth muscle tissue of blood vessel of respiratory system OBOL:automatic Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition. distinction between trophectoderm and trophoblast unclear/inconsistent in many sources The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] (...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG] trophectodermal BTO has this has part of the trophoblast BTO:0001840 EHDAA2:0002091 EHDAA:56 EMAPA:16046 VHOG:0000979 uberon UBERON:0004345 trophectoderm EHDAA2 EHDAA2 EHDAA2 Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition. MP:0005028 The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0000979 VHOG http://bgee.unil.ch/ (...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000979 VHOG ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106 http://bgee.unil.ch/ BTO has this has part of the trophoblast BTO The embryonic structure that gives rise to the corneal ectoderm. EHDAA:938 EMAPA:16322 RETIRED_EHDAA2:0001308 VHOG:0001296 uberon UBERON:0004348 optic eminence The embryonic structure that gives rise to the corneal ectoderm. MP:0006305 Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. note that media, dorsal fins etc have AERs. Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] Proliferative region that is part of the developing fin fold or fin.[TAO] relationship loss: subclass proliferative region (TAO:0000098)[TAO] The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop AAO:0010760 EMAPA:32744 NCIT:C34109 TAO:0002146 UMLS:C1516037 Wikipedia:Apical_ectodermal_ridge XAO:0004121 ZFA:0001702 apical epidermal ridge uberon AER crista ectodermalis apicalis UBERON:0004356 apical ectodermal ridge http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. MP:0001676 Wikipedia:Apical_ectodermal_ridge Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] 2012-06-20 AAO:0010760 AAO AAO:EJS Proliferative region that is part of the developing fin fold or fin.[TAO] 2012-08-14 TAO:0002146 TAO ZFIN:curator relationship loss: subclass proliferative region (TAO:0000098)[TAO] 2012-08-14 TAO:0002146 TAO The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold PMID:20574421 UMLS:C1516037 ncithesaurus:Apical_Ectodermal_Ridge apical epidermal ridge XAO:0004121 AER MP:0001676 crista ectodermalis apicalis Wikipedia:Apical_ectodermal_ridge An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] VHOG:0001258 limb - fin bud paired appendage bud paired limb/fin bud uberon UBERON:0004357 Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056] paired limb/fin bud An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. ISBN:9780878932504 MP:0005650 https://orcid.org/0000-0002-6601-2165 The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] 2012-09-17 VHOG:0001258 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) http://bgee.unil.ch/ limb - fin bud VHOG:0001258 paired limb/fin bud VHOG:0001258 The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries. The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 1 AAO:0010364 CALOHA:TS-2089 EHDAA2:0000006 EHDAA:573 EMAPA:16118 FMA:293019 MFMO:0000095 NCIT:C34175 SCTID:308767008 TAO:0001595 UMLS:C1517197 VHOG:0000296 Wikipedia:First_pharyngeal_arch XAO:0000097 ZFA:0001612 1st pharyngeal arch branchial arch 1 first branchial arch first pharyngeal arch first visceral arch mandibular arch visceral arch 1 uberon 1st arch 1st visceral arch arcus pharyngeus primus UBERON:0004362 pharyngeal arch 1 http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries. http://orcid.org/0000-0002-6601-2165 The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010364 AAO XAO:EJS the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery MP:0006337,MGI:smb A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000296 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ UMLS:C1517197 ncithesaurus:First_Pharyngeal_Arch branchial arch 1 first branchial arch first visceral arch visceral arch 1 1st arch EHDAA2:0000006 1st visceral arch VHOG:0000296 arcus pharyngeus primus Wikipedia:First_pharyngeal_arch One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]. add specific artery derivatives Do not confuse with arch of aorta. Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches UBERON:0004342 AAO:0010414 EFO:0003695 EHDAA2:0000186 EHDAA:398 EHDAA:7327 EMAPA:16684 NCIT:C32123 TAO:0005004 UMLS:C0003489 VHOG:0000122 Wikipedia:Aortic_arches XAO:0000341 ZFA:0005004 PAA aortic arch aortic arches branchial aortic arches branchial arch artery embryonic aortic arch artery pharyngeal arch artery uberon a. arcuum pharyngeorum aortic arch artery arteriae arcuum pharyngeorum branchial aortic arches pharyngeal arch arteries pharyngeal arch artery UBERON:0004363 pharyngeal arch artery http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png ZFA One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]. MP:0002672 Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] 2012-09-17 VHOG:0000122 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/aortic+arches When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000122 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0003489 ncithesaurus:Aortic_Arch PAA MP:0002672 aortic arch ZFA:0005004 aortic arches ZFA:0005004 branchial aortic arches ZFIN:ZDB-PUB-080512-6 branchial arch artery EMAPA:16684 embryonic aortic arch artery EMAPA:16684 MP:0002672 pharyngeal arch artery MP:0002672 a. arcuum pharyngeorum Wikipedia:Aortic_arches aortic arch artery EMAPA:16684 arteriae arcuum pharyngeorum Wikipedia:Aortic_arches branchial aortic arches ZFA:0005004 ZFIN:ZDB-PUB-080512-6 pharyngeal arch arteries pharyngeal arch artery VHOG:0000122 Thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta. derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast. BTO:0001715 EMAPA:16059 epamniotic cone placenta - ectoplacental cone uberon UBERON:0004364 ectoplacental cone Thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta. MP:0001717 PMID:19829370 derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast. PMID:19829370 Blood vessel that is connected to the yolk sac. EMAPA:36494 uberon UBERON:0004365 vitelline blood vessel Blood vessel that is connected to the yolk sac. http://orcid.org/0000-0002-6601-2165 A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] EMAPA:18804 FMA:58309 GAID:894 MA:0001246 MESH:D003886 NCIT:C32454 SCTID:281076002 TAO:0002157 UMLS:C0011665 Wikipedia:Descemet%27s_membrane ZFA:0001686 Descemet membrane Descemet's posterior elastic lamina lamina limitans posterior lamina limitans posterior corneae posterior limiting lamina posterior limiting lamina of cornea posterior limiting membrane uberon UBERON:0004367 The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed) Descemet's membrane https://github.com/obophenotype/uberon/issues/15 Cline et al lexical A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. MP:0004285 https://github.com/obophenotype/uberon/issues/15 Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] 2016-05-01 TAO:0002157 ZFIN ZFIN:ZDB-PUB-061010-3 https://orcid.org/0000-0001-9114-8737 UMLS:C0011665 ncithesaurus:Descemet_s_Membrane Descemet's posterior elastic lamina FMA:58309 lamina limitans posterior FMA:58309 lamina limitans posterior corneae FMA:58309 FMA:TA posterior limiting lamina MA:0001246 posterior limiting lamina of cornea FMA:58309 posterior limiting membrane ZFA:0001686 A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals FMA:58273 MA:0001240 NCIT:C32226 SCTID:281075003 TAO:0002155 UMLS:C0229127 Wikipedia:Bowman%27s_membrane ZFA:0001684 Bowman's anterior elastic lamina Bowman's layer Bowman's membrane anterior elastic lamina anterior limiting lamina anterior limiting lamina of cornea lamina limitans anterior (cornea) lamina limitans anterior corneae uberon Reichert's membrane anterior limiting membrane UBERON:0004370 anterior limiting lamina of cornea lexical A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. ncithesaurus:Bowman_s_Membrane Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] 2012-08-14 TAO:0002155 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0229127 ncithesaurus:Bowman_s_Membrane Bowman's anterior elastic lamina FMA:58273 Bowman's layer FMA:58273 Bowman's membrane FMA:58273 anterior elastic lamina ZFA:0001684 anterior limiting lamina MA:0001240 anterior limiting lamina of cornea FMA:58273 lamina limitans anterior (cornea) FMA:58273 lamina limitans anterior corneae FMA:58273 FMA:TA Reichert's membrane http://sourceforge.net/tracker/?func=detail&aid=2956371&group_id=76834&atid=974957 anterior limiting membrane ZFA:0001684 Vascular network that is connected to the yolk sac. Wikipedia:Vitelline_circulation uberon omphalomesenteric system vitelline bloos vessel system vitelline system UBERON:0004374 vitelline vasculature Vascular network that is connected to the yolk sac. http://orcid.org/0000-0002-6601-2165 omphalomesenteric system https://orcid.org/0000-0002-6601-2165 vitelline bloos vessel system https://orcid.org/0000-0002-6601-2165 vitelline system https://orcid.org/0000-0002-6601-2165 A bone that is part of an appendage [Automatically generated definition]. appendage bone bone of appendage bone of free segment of appendicular skeleton uberon UBERON:0004375 bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. OBOL:automatic A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar) it's not clear if the XAO class belongs here or below EMAPA:37722 MA:0002869 XAO:0003077 uberon presacral vertebra UBERON:0004451 trunk or cervical vertebra A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. UBERONREF:0000006 it's not clear if the XAO class belongs here or below XAO EMAPA:37722 MA:th presacral vertebra MA:0002869 An embryo at the neurula stage. UBERON:0007013 BILA:0000061 BTO:0001766 NCIT:C34229 UMLS:C1518306 neurula uberon UBERON:0004455 neurula embryo An embryo at the neurula stage. http://orcid.org/0000-0002-6601-2165 UMLS:C1518306 ncithesaurus:Neurula neurula BTO:0001766 Sum of all sensory systems in an organism. note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon UBERON:0004456 entire sense organ system Sum of all sensory systems in an organism. http://orcid.org/0000-0002-6601-2165 sense organ system FMA:78499 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. EMAPA:18171 FMA:71287 head musculature muscle group of head muscles of head musculi capitis set of muscles of head uberon UBERON:0004461 This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376 skeletal musculature of head https://github.com/obophenotype/mouse-anatomy-ontology/issues/4 https://github.com/obophenotype/uberon/issues/1405 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. OBOL:automatic head musculature FMA:71287 muscle group of head FMA:71287 muscles of head FMA:71287 musculi capitis FMA:71287 FMA:TA set of muscles of head FMA:71287 Any collection of muscles that is part of a thorax [Automatically generated definition]. BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO:0000508 EMAPA:37260 FMA:71293 muscle group of thorax muscles of thorax musculi thoracis set of muscles of thorax thoracic musculature uberon UBERON:0004464 musculature of thorax Any collection of muscles that is part of a thorax [Automatically generated definition]. OBOL:automatic BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO EMAPA:37260 MA:th muscle group of thorax FMA:71293 muscles of thorax FMA:71293 musculi thoracis FMA:71293 FMA:TA set of muscles of thorax FMA:71293 thoracic musculature FMA:71293 Any collection of muscles that is part of a neck [Automatically generated definition]. AAO:0000091 EMAPA:36050 FMA:71290 MESH:D009334 cervical muscles muscle group of neck muscles of neck musculi cervicis musculi colli neck musculature set of muscles of neck uberon UBERON:0004465 musculature of neck Any collection of muscles that is part of a neck [Automatically generated definition]. OBOL:automatic cervical muscles AAO:0000091 muscle group of neck FMA:71290 muscles of neck FMA:71290 musculi cervicis FMA:71290 FMA:TA musculi colli FMA:71290 FMA:TA neck musculature FMA:71290 set of muscles of neck FMA:71290 FMA:33061 muscle group of vertebral column uberon UBERON:0004468 set of muscles of vertebral column muscle group of vertebral column FMA:33061 Any collection of muscles that is part of a back [Automatically generated definition]. FMA:71291 muscle group of back muscles of back musculi dorsi set of muscles of back uberon UBERON:0004469 musculature of back Any collection of muscles that is part of a back [Automatically generated definition]. OBOL:automatic muscle group of back FMA:71291 muscles of back FMA:71291 musculi dorsi FMA:71291 FMA:TA set of muscles of back FMA:71291 Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. we merge two FMA classes here UBERON:0004485 UBERON:0005633 AAO:0000427 EHDAA2:0001429 EMAPA:18184 FMA:50205 FMA:50248 muscle group of pelvic girdle muscle group of pelvis pelvic girdle muscle system pelvic girdle muscles pelvic girdle musculature set of muscles of pelvic girdle uberon muscular system of pelvis set of muscles of pelvis UBERON:0004470 musculature of pelvic girdle Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic we merge two FMA classes here FMA muscle group of pelvic girdle FMA:50205 muscle group of pelvis FMA:50248 pelvic girdle muscle system EHDAA2:0001429 pelvic girdle muscles AAO:0000427 pelvic girdle musculature FMA:50205 set of muscles of pelvic girdle FMA:50205 muscular system of pelvis FMA:50248 set of muscles of pelvis FMA:50248 A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. AAO:0000423 EMAPA:37857 FMA:33519 muscle group of pectoral girdle pectoral girdle muscles pectoral girdle musculature set of muscles of pectoral girdle uberon UBERON:0004471 musculature of pectoral girdle A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. https://orcid.org/0000-0002-6601-2165 EMAPA:37857 MA:th muscle group of pectoral girdle FMA:33519 pectoral girdle muscles AAO:0000423 pectoral girdle musculature FMA:33519 set of muscles of pectoral girdle FMA:33519 Any collection of muscles that is part of a face. originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose FMA:71288 entire facial musculature facial muscles muscle group of face musculi faciei uberon set of facial muscles set of muscles of face UBERON:0004473 musculature of face Any collection of muscles that is part of a face. OBOL:automatic entire facial musculature https://orcid.org/0000-0002-6601-2165 facial muscles FMA:71288 muscle group of face FMA:71288 musculi faciei FMA:71288 FMA:TA set of facial muscles FMA:71288 set of muscles of face FMA:71288 Any collection of muscles that is part of a trunk [Automatically generated definition]. currently defined by location rather than attachment AAO:0011572 EFO:0003531 FMA:50187 muscle group of trunk set of muscles of trunk uberon muscular system of trunk UBERON:0004479 musculature of trunk Any collection of muscles that is part of a trunk [Automatically generated definition]. OBOL:automatic muscle group of trunk FMA:50187 set of muscles of trunk FMA:50187 muscular system of trunk FMA:50187 A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. FMA:7283 atrial cardiac muscle tissue atrial heart muscle cardiac atrium muscle uberon atrial myocardium UBERON:0004490 cardiac muscle tissue of atrium A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. OBOL:automatic in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. GO atrial cardiac muscle tissue GO:0055009 atrial heart muscle GO:0055009 cardiac atrium muscle GO:0055009 atrial myocardium GO:0055009 GOC:mtg_heart A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. FMA:84083 interatrial septum cardiac muscle tissue interatrial septum heart muscle interatrial septum muscle interatrial septum myocardium uberon UBERON:0004491 cardiac muscle tissue of interatrial septum A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. OBOL:automatic interatrial septum cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 interatrial septum heart muscle http://orcid.org/0000-0002-6601-2165 interatrial septum muscle http://orcid.org/0000-0002-6601-2165 interatrial septum myocardium http://orcid.org/0000-0002-6601-2165 A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. FMA:226279 cardiac septum cardiac muscle tissue cardiac septum heart muscle cardiac septum muscle cardiac septum myocardium uberon UBERON:0004492 cardiac muscle tissue of cardiac septum A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. OBOL:automatic cardiac septum cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 cardiac septum heart muscle http://orcid.org/0000-0002-6601-2165 cardiac septum muscle http://orcid.org/0000-0002-6601-2165 cardiac septum myocardium http://orcid.org/0000-0002-6601-2165 A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. Note placement of MA class based on parthood relationship EMAPA:32688 FMA:261726 MA:0002441 uberon UBERON:0004493 cardiac muscle tissue of myocardium MA A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. OBOL:automatic A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. FMA:261898 uberon UBERON:0004495 skeletal muscle tissue of diaphragm A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. OBOL:automatic A muscle that is attached to a vertebra of the vertebral column. FMA:22594 vertebral column muscle uberon UBERON:0004518 muscle of vertebral column A muscle that is attached to a vertebra of the vertebral column. https://orcid.org/0000-0002-6601-2165 vertebral column muscle FMA:22594 A vasculature that is part of a muscle organ [Automatically generated definition]. FMA:87123 muscular organ vasculature uberon UBERON:0004521 vasculature of muscle organ A vasculature that is part of a muscle organ [Automatically generated definition]. OBOL:automatic muscular organ vasculature FMA:87123 A vasculature that is part of a musculoskeletal system [Automatically generated definition]. FMA:239607 uberon UBERON:0004522 vasculature of musculoskeletal system A vasculature that is part of a musculoskeletal system [Automatically generated definition]. OBOL:automatic A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. FMA:84429 uberon UBERON:0004525 cardiac muscle tissue of trabecula carnea of right ventricle true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. OBOL:automatic A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. FMA:84430 uberon UBERON:0004526 cardiac muscle tissue of trabecula carnea of left ventricle true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. OBOL:automatic Anatomical system that has as its parts the heart and blood vessels. we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 EHDAA2:0000216 EHDAA:394 EMAPA:16104 EMAPA:16370 EV:0100017 FMA:7161 GAID:467 MA:0000010 MAT:0000016 MESH:D002319 MIAA:0000016 NCIT:C12686 SCTID:278198007 TAO:0000010 UMLS:C0007226 VHOG:0000302 WikipediaCategory:Cardiovascular_system XAO:0000100 XAO:0001010 ZFA:0000010 uberon CV system Herz und Gefaesssystem UBERON:0004535 cardiovascular system Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000302 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 http://bgee.unil.ch/ UMLS:C0007226 ncithesaurus:Cardiovascular_System CV system BTO:0000088 Herz und Gefaesssystem BTO:0000088 A vascular network consisting of blood vessels. TAO:0001079 ZFA:0001079 blood vascular network set of blood vessels uberon blood system blood vessel system blood vessels UBERON:0004537 blood vasculature https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb A vascular network consisting of blood vessels. https://orcid.org/0000-0002-6601-2165 blood vessels TAO:0001079 An eye that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37362 FMA:12515 MA:0002949 NCIT:C119334 SCTID:362503005 left eyeball left orbital part of face left orbital region uberon UBERON:0004548 left eye https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb An eye that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37362 MA:th left eyeball FMA:12515 left orbital part of face FMA:54450 left orbital region FMA:54450 An eye that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37363 FMA:12514 MA:0002950 NCIT:C119333 SCTID:362502000 right eyeball right orbital part of face right orbital region uberon UBERON:0004549 right eye https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb An eye that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37363 MA:th right eyeball FMA:12514 right orbital part of face FMA:54449 right orbital region FMA:54449 The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. FMA:45623 Wikipedia:Systemic_circulation#Arteries systemic arterial circulatory system uberon UBERON:0004571 systemic arterial system MA-inferred The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. Wikipedia:Systemic_circulation#Arteries http://orcid.org/0000-0002-6601-2165 systemic arterial circulatory system FMA:45623 The part of the cardiovascular system consisting of all arteries. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004690 EHDAA2:0000143 EHDAA:396 EMAPA:16201 EMAPA:16371 MA:0002719 SCTID:362030008 VHOG:0000273 uberon UBERON:0004572 arterial system MA The part of the cardiovascular system consisting of all arteries. https://orcid.org/0000-0002-6601-2165 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000273 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. EMAPA:37126 FMA:66464 Wikipedia:Artery#Systemic_arteries systemic arterial subtree uberon UBERON:0004573 systemic artery An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. Wikipedia:Artery#Systemic_arteries http://orcid.org/0000-0002-6601-2165 EMAPA:37126 MA:th systemic arterial subtree FMA:66464 The part of the venous system that drains the general body tissues[Kardong]. In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] FMA:45626 Wikipedia:Systemic_venous_system systemic venous circulatory system uberon UBERON:0004581 systemic venous system The part of the venous system that drains the general body tissues[Kardong]. ISBN:0073040584 Wikipedia:Systemic_venous_system In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Wikipedia:Systemic_venous_system Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] FMA FMA:45626 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ systemic venous circulatory system FMA:45626 The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004692 EHDAA2:0002171 EHDAA:486 EMAPA:16240 MA:0002720 NCIT:C33858 SCTID:362060003 UMLS:C1267406 VHOG:0000277 vein system uberon UBERON:0004582 venous system MA The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. https://orcid.org/0000-0002-6601-2165 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ UMLS:C1267406 ncithesaurus:Venous_System A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. FMA class is not a subtype of muscle FMA:75004 NCIT:C28381 UMLS:C1409894 Wikipedia:Sphincter sphincter uberon circular muscle UBERON:0004590 sphincter muscle A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. Wikipedia:Sphincter FMA class is not a subtype of muscle FMA UMLS:C1409894 ncithesaurus:Sphincter An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart. BTO:0000766 CALOHA:TS-2155 EMAPA:35176 MA:0000709 NCIT:C53395 TAO:0005257 UMLS:C1706972 ZFA:0005257 uberon UBERON:0004638 blood vessel endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart. https://orcid.org/0000-0002-6601-2165 UMLS:C1706972 ncithesaurus:Blood_Vessel_Endothelium The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein. should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP] EMAPA:35499 FMA:14471 MA:0002494 NCIT:C32732 SCTID:362194004 UMLS:C0227518 Wikipedia:Lobules_of_liver hepatic lobule lobuli hepatici lobulus hepaticus uberon lobules of liver lobuli hepatis UBERON:0004647 liver lobule FMA FMA MA The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein. ISBN:0-683-40008-8 MP:0008987 UMLS:C0227518 ncithesaurus:Hepatic_Lobule hepatic lobule FMA:14471 lobuli hepatici lobulus hepaticus FMA:14471 lobules of liver Wikipedia:Lobules_of_liver lobuli hepatis Wikipedia:Lobules_of_liver An anatomical wall that is part of an aorta, enclosing the luminal space. EMAPA:35139 FMA:14156 MA:0002901 aortic wall wall of aorta uberon UBERON:0004663 aorta wall An anatomical wall that is part of an aorta, enclosing the luminal space. http://orcid.org/0000-0002-6601-2165 aortic wall FMA:14156 wall of aorta FMA:14156 The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers. EMAPA:35136 FMA:14283 MA:0002902 SCTID:24996002 tunica adventitia of aorta uberon UBERON:0004664 aorta tunica adventitia The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers. ISBN:0-683-40008-8 MP:0009871 tunica adventitia of aorta FMA:14283 The membranous portion of the wall between the two lower chambers of the heart. The membranous septum is the upper part of ventricular septum[GO:0003149]. UBERON:0004143 membranous septum ventricle membranous septum ventricular membranous septum EHDAA2:0004596 EMAPA:18246 FMA:7135 MA:0002939 SCTID:278228007 VHOG:0000927 cardiac ventricular membranous septum membranous interventricular septum membranous part interventricular septum membranous part of interventricular septum membranous portion of interventricular septum pars membranacea (septi interventricularis) pars membranacea septi interventricularis uberon membranous interventricular septum UBERON:0004666 interventricular septum membranous part Wikipedia The membranous portion of the wall between the two lower chambers of the heart. MP:0008823 The membranous septum is the upper part of ventricular septum[GO:0003149]. GO:0003149 membranous septum GO:0003149 ventricle membranous septum VT:0000018 ventricular membranous septum MP:0008823 cardiac ventricular membranous septum http://orcid.org/0000-0002-6601-2165 membranous interventricular septum FMA:7135 membranous part interventricular septum VHOG:0000927 membranous part of interventricular septum FMA:7135 membranous portion of interventricular septum FMA:7135 pars membranacea (septi interventricularis) FMA:7135 pars membranacea septi interventricularis FMA:7135 FMA:TA membranous interventricular septum MA:0002939 The muscular portion of the wall between the two lower chambers of the heart. The muscular septum is the lower part of the ventricular septum[GO] UBERON:0004144 muscular septum EHDAA2:0000885 EHDAA:2607 EMAPA:18247 FMA:7134 MA:0002940 RETIRED_EHDAA2:0000888 cardiac ventricular muscular septum muscular interventricular septum muscular part interventricular septum muscular part of interventricular septum pars muscularis (septi interventricularis) pars muscularis septi interventricularis septum membranaceum ventricular muscular septum uberon muscular interventricular septum UBERON:0004667 interventricular septum muscular part The muscular portion of the wall between the two lower chambers of the heart. Wikipedia:Interventricular_septum#Portions http://orcid.org/0000-0002-6601-2165 The muscular septum is the lower part of the ventricular septum[GO] GO:0003150 muscular septum GO:0003150 cardiac ventricular muscular septum http://orcid.org/0000-0002-6601-2165 muscular interventricular septum FMA:7134 muscular part of interventricular septum FMA:7134 pars muscularis (septi interventricularis) FMA:7134 pars muscularis septi interventricularis FMA:7134 FMA:TA septum membranaceum muscular interventricular septum MA:0002940 The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. BAMS:RA EMAPA:35721 FMA:84017 MA:0003147 MESH:D011903 NCIT:C97335 NLXANAT:20090205 TAO:0001429 UMLS:C0034671 Wikipedia:Raphe_nuclei ZFA:0001429 neuronames:2495 nuclei raphes raphe nuclei raphe nuclei set uberon nuclei raphes raphe cluster raphe nucleus raphe of mesenchephalon set of raphe nuclei UBERON:0004684 we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei' raphe nuclei http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png GO Wikipedia Wikipedia The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. NLXANAT:20090205 https://sourceforge.net/tracker/?func=detail&aid=3248146&group_id=36855&atid=440764 UMLS:C0034671 ncithesaurus:Raphe_Nuclei nuclei raphes FMA:84017 FMA:TA raphe nuclei FMA:84017 NLXANAT:20090205 raphe nuclei set FMA:84017 nuclei raphes Wikipedia:Raphe_nuclei raphe cluster Wikipedia:Raphe_nuclei raphe nucleus ZFA:0001429 raphe of mesenchephalon BAMS:RA set of raphe nuclei FMA:84017 The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. EMAPA:37496 FMA:10636 MA:0001939 SCTID:244225009 Wikipedia:Costocervical_trunk costocervical trunk trunk of costocervical artery uberon truncus costocervicalis UBERON:0004688 costo-cervical trunk http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. Wikipedia:Costocervical_trunk EMAPA:37496 MA:th costocervical trunk FMA:10636 trunk of costocervical artery FMA:10636 truncus costocervicalis Wikipedia:Costocervical_trunk A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. EMAPA:36503 MA:0000704 uberon UBERON:0004695 arterial system smooth muscle A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. OBOL:automatic A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. EMAPA:36613 MA:0000715 uberon UBERON:0004696 venous system smooth muscle A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. OBOL:automatic An endothelium that is part of a vena cava [Automatically generated definition]. EMAPA:37800 MA:0000713 NCIT:C49318 UMLS:C1710623 uberon UBERON:0004698 vena cava endothelium An endothelium that is part of a vena cava [Automatically generated definition]. OBOL:automatic EMAPA:37800 MA:th UMLS:C1710623 ncithesaurus:Vena_Cava_Endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] MA:0000490 VHOG:0001524 uberon UBERON:0004699 outflow tract endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] 2012-09-17 VHOG:0001524 VHOG DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001) http://bgee.unil.ch/ An endothelium that is part of an arterial system [Automatically generated definition]. EMAPA:35145 MA:0000703 NCIT:C49329 UMLS:C1706849 uberon UBERON:0004700 arterial system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. OBOL:automatic UMLS:C1706849 ncithesaurus:Arterial_System_Endothelium An endothelium that is part of a venous system [Automatically generated definition]. EMAPA:35907 MA:0000714 NCIT:C49320 UMLS:C1710626 uberon UBERON:0004701 venous system endothelium An endothelium that is part of a venous system [Automatically generated definition]. OBOL:automatic UMLS:C1710626 ncithesaurus:Venous_System_Endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. EMAPA:35732 MA:0001805 uberon UBERON:0004702 respiratory system blood vessel endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches. TODO - check relationship to bulbus arteriosus A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] EHDAA2:0000197 EHDAA:438 EHDAA:768 EMAPA:16333 FMA:70300 NCIT:C34114 SCTID:361525002 UMLS:C1284055 Wikipedia:Bulbus_cordis primitive right ventricle endocardium uberon UBERON:0004706 bulbus cordis http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches. ISBN:0-683-40008-8 MP:0010568 A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] 2012-08-14 TAO:0000173 TAO ZFIN:curator UMLS:C1284055 ncithesaurus:Bulbus_Cordis primitive right ventricle endocardium EHDAA2:0000197 An appendage that is part of an appendage girdle complex. this class is the union of the classes limb, pectoral fin and pelvic fin. UBERON:0009872 VSAO:0000067 girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage paired appendage uberon UBERON:0004708 paired limb/fin VSAO VSAO definitional An appendage that is part of an appendage girdle complex. UBERON:cjm https://github.com/geneontology/go-ontology/issues/9029 girdle-associated appendage https://orcid.org/0000-0002-6601-2165 limb or fin https://orcid.org/0000-0002-6601-2165 limb/fin https://orcid.org/0000-0002-6601-2165 pectoral or pelvic appendage https://orcid.org/0000-0002-6601-2165 pelvic/pectoral appendage https://orcid.org/0000-0002-6601-2165 jointed paired lateral appendage https://orcid.org/0000-0002-6601-2165 paired appendage VSAO:0000067 Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. UBERON:0009876 posterior appendage VSAO:0000126 hindlimb/pelvic fin pelvic appendage pelvic limb/fin posterior limb/fin posterior paired appendage uberon UBERON:0004709 pelvic appendage definitional lexical Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. VSAO:0000150 hindlimb/pelvic fin https://orcid.org/0000-0002-6601-2165 pelvic appendage VSAO:0000126 pelvic limb/fin https://orcid.org/0000-0002-6601-2165 posterior paired appendage VSAO:0000126 Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues. While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] UBERON:0009875 anterior appendage VHOG:0001753 VSAO:0000125 anterior limb/fin anterior paired appendage forelimb - pectoral fin forelimb or pectoral fin forelimb/pectoral fin pectoral limb/fin uberon UBERON:0004710 pectoral appendage definitional lexical Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues. VSAO:0000150-modified While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] 2012-09-17 VHOG:0001753 VHOG DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004) http://bgee.unil.ch/ anterior limb/fin https://orcid.org/0000-0002-6601-2165 anterior paired appendage VSAO:0000148 forelimb - pectoral fin VHOG:0001753 forelimb or pectoral fin https://orcid.org/0000-0002-6601-2165 forelimb/pectoral fin https://orcid.org/0000-0002-6601-2165 pectoral limb/fin https://orcid.org/0000-0002-6601-2165 The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. BTO:0001744 CALOHA:TS-0497 EMAPA:18638 GAID:536 MA:0002154 MESH:D007601 NCIT:C12738 SCTID:244403000 UMLS:C0022427 Wikipedia:Jugular_vein uberon jugular vena jugularis UBERON:0004711 jugular vein http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. Wikipedia:Jugular_vein UMLS:C0022427 ncithesaurus:Jugular_Vein vena jugularis BTO:0001744 The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus AEO:0000194 BTO:0003834 EHDAA2:0000001 EHDAA2:0003235 EMAPA:36040 NCIT:C34131 UMLS:C1516779 Wikipedia:Conceptus embryo plus adnexa uberon UBERON:0004716 conceptus The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. BTO:0003834 Wikipedia:Conceptus UMLS:C1516779 ncithesaurus:Conceptus Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. WBls:0000023 uberon UBERON:0004729 nematode larval stage https://github.com/obophenotype/uberon/issues/567 Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. GO:0002119 A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted A metameric segment of the central nervous system.[ZFA] 2009-06-18T09:00:04Z NLX:147842 TAO:0001328 Wikipedia:Neuromere ZFA:0001328 neural tube metameric segment neural tube segment neuromere neuromeres uberon neural metamere neural segment UBERON:0004731 neuromere A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). DOI:10.1016/j.tins.2013.06.004 https://github.com/obophenotype/uberon/issues/318 A metameric segment of the central nervous system.[ZFA] 2012-08-14 TAO:0001328 TAO ZFIN:curator neural tube metameric segment http://orcid.org/0000-0002-6601-2165 neuromeres TAO:0001328 Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451) uberon neuromere UBERON:0004732 segmental subdivision of nervous system Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. FBbt:00005140 http://orcid.org/0000-0002-6601-2165 neuromere FBbt:00005140 An organ subunit that is part of a hindbrain [Automatically generated definition]. FMA:61998 hindbrain segment segment of hindbrain uberon UBERON:0004733 segmental subdivision of hindbrain An organ subunit that is part of a hindbrain [Automatically generated definition]. OBOL:automatic hindbrain segment FMA:61998 segment of hindbrain FMA:61998 Organism at the gastrula stage. We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 MIAA:0000179 NCIT:C34057 NCIT:C34058 UMLS:C0017199 UMLS:C1284022 Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst gastrula embryo uberon blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ UBERON:0004734 gastrula Organism at the gastrula stage. Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst We explicitly merge the NCITA terms here NCIT FBbt:00005317 UMLS:C0017199 ncithesaurus:Gastrula UMLS:C1284022 ncithesaurus:Trilaminar_Embryonic_Disc gastrula embryo BILA:0000060 blastocystis trilaminaris https://orcid.org/0000-0002-6601-2165 tri-laminar disc https://orcid.org/0000-0002-6601-2165 tri-laminar disk https://orcid.org/0000-0002-6601-2165 trilaminar blastocyst https://orcid.org/0000-0002-6601-2165 trilaminar blastoderm https://orcid.org/0000-0002-6601-2165 trilaminar disc https://orcid.org/0000-0002-6601-2165 trilaminar disk https://orcid.org/0000-0002-6601-2165 trilaminar germ https://orcid.org/0000-0002-6601-2165 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 SCTID:309311006 VSAO:0000015 XAO:0004038 ZFA:0005619 uberon UBERON:0004755 Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue VSAO 2012-08-14 VSAO:0000015 VSAO A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. GO_REF:0000034 PSPUB:0000170 VSAO:0000015 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/134 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] 2012-08-14 VSAO:0000015 taken from version of VSAO used in TAO and used directly in Uberon VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 EMAPA:37744 MA:th Dermis-derived entity that is made of skeletal tissue. dermal element uberon UBERON:0004756 dermal skeletal element Dermis-derived entity that is made of skeletal tissue. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/206 dermal element VSAO:curator A gland that is part of an anal canal [Automatically generated definition]. EMAPA:27221 EMAPA:27233 EMAPA:27543 FMA:15720 FMA:15724 NCIT:C32068 SCTID:245448005 UMLS:C0162322 Wikipedia:Anal_gland gland of anal canal uberon anal gland anal sac gland of anus rectal gland UBERON:0004760 gland of anal canal A gland that is part of an anal canal [Automatically generated definition]. OBOL:automatic Wikipedia:Anal_gland UMLS:C0162322 ncithesaurus:Anal_Gland gland of anal canal OBOL:automatic anal sac Wikipedia:Anal_gland The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) AAO:0000094 AAO:0010153 EHDAA:6031 FMA:76621 NCIT:C34121 SCTID:155540009 UMLS:C1516496 Wikipedia:Chondrocranium XAO:0003059 cartilaginous chondocranium cartiligionous skeletal structure of skull uberon cartilaginous skull chondocranium embryonic chondocranium neurocranium UBERON:0004761 cartilaginous neurocranium FMA PMC1571569 The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. Wikipedia:Chondrocranium in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) FMA UMLS:C1516496 ncithesaurus:Chondrocranium chondocranium Wikipedia:Chondrocranium neurocranium Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes) MA:0002837 Wikipedia:Intramembranous_ossification uberon UBERON:0004764 intramembranous bone tissue Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. GO:0001957 Wikipedia:Intramembranous_ossification note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes) MA Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure uberon UBERON:0004765 skeletal element VSAO Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] 2012-08-14 VSAO:0000128 VSAO PSPUB:0000170 Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] 2012-08-14 TAO:0001890 TAO TAO:VSAO_workshop A bone that is part of a cranium. here cranium = skull - mandible SCTID:181792001 cranium bone uberon UBERON:0004766 cranial bone A bone that is part of a cranium. UBERON:automatic cranium bone UBERON:automatic Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular. Do not manually classify under here - bones are automatically classified lower jaw bone uberon UBERON:0004768 bone of lower jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular. https://orcid.org/0000-0002-6601-2165 Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 SCTID:361827000 VSAO:0000181 joint system set of all joints of body uberon set of all joints set of joints of body UBERON:0004770 articular system FMA Anatomical system that consists of all the joints of the body. VSAO:0000181 joint system FMA:23878 set of all joints of body FMA:23878 set of joints of body FMA:23878 A submucosa that is part of a respiratory system [Automatically generated definition]. EMAPA:37578 MA:0001822 apparatus respiratorius submucosa submucosa of apparatus respiratorius submucosa of respiratory system uberon UBERON:0004777 respiratory system submucosa A submucosa that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37578 MA:th apparatus respiratorius submucosa OBOL:automatic submucosa of apparatus respiratorius OBOL:automatic submucosa of respiratory system OBOL:automatic A lamina propria that is part of a respiratory system [Automatically generated definition]. EMAPA:37576 MA:0001821 apparatus respiratorius lamina propria apparatus respiratorius lamina propria mucosa lamina propria mucosa of apparatus respiratorius lamina propria mucosa of respiratory system lamina propria of apparatus respiratorius lamina propria of respiratory system respiratory system lamina propria mucosa uberon UBERON:0004779 respiratory system lamina propria true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37576 MA:th apparatus respiratorius lamina propria OBOL:automatic apparatus respiratorius lamina propria mucosa OBOL:automatic lamina propria mucosa of apparatus respiratorius OBOL:automatic lamina propria mucosa of respiratory system OBOL:automatic lamina propria of apparatus respiratorius OBOL:automatic lamina propria of respiratory system OBOL:automatic respiratory system lamina propria mucosa OBOL:automatic A lamina propria that is part of a gastrointestinal system. MA:0001899 NCIT:C49299 UMLS:C1708197 uberon UBERON:0004780 gastrointestinal system lamina propria true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a gastrointestinal system. OBOL:automatic UMLS:C1708197 ncithesaurus:Gastrointestinal_Tract_Lamina_Propria A lamina propria that is part of a gallbladder [Automatically generated definition]. EMAPA:35371 FMA:278594 MA:0001633 NCIT:C49228 UMLS:C1708175 gall bladder lamina propria gall bladder lamina propria mucosa gallbladder lamina propria mucosa lamina propria mucosa of gall bladder lamina propria mucosa of gallbladder lamina propria of gall bladder lamina propria of gallbladder uberon biliary lamina propria UBERON:0004781 gallbladder lamina propria true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a gallbladder [Automatically generated definition]. OBOL:automatic UMLS:C1708175 ncithesaurus:Gallbladder_Lamina_Propria gall bladder lamina propria OBOL:automatic gall bladder lamina propria mucosa OBOL:automatic lamina propria mucosa of gall bladder OBOL:automatic lamina propria mucosa of gallbladder OBOL:automatic lamina propria of gall bladder OBOL:automatic lamina propria of gallbladder OBOL:automatic biliary lamina propria MA:0001633 A serous membrane that is part of a digestive system [Automatically generated definition]. EMAPA:37592 MA:0001522 digestive system serosa digestive system serous membrane gastrointestinal system serous membrane serosa of digestive system serosa of gastrointestinal system serous membrane of digestive system serous membrane of gastrointestinal system uberon UBERON:0004782 gastrointestinal system serosa A serous membrane that is part of a digestive system [Automatically generated definition]. OBOL:automatic EMAPA:37592 MA:th digestive system serosa OBOL:automatic digestive system serous membrane OBOL:automatic gastrointestinal system serous membrane OBOL:automatic serosa of digestive system OBOL:automatic serosa of gastrointestinal system OBOL:automatic serous membrane of digestive system OBOL:automatic serous membrane of gastrointestinal system OBOL:automatic A serous membrane that is part of a gallbladder [Automatically generated definition]. EMAPA:35372 FMA:14659 MA:0001634 SCTID:362197006 gall bladder serosa gall bladder serous membrane gallbladder serous membrane serosa of gall bladder serosa of gallbladder serous coat of gallbladder serous membrane of gall bladder serous membrane of gallbladder tunica serosa (vesica biliaris) tunica serosa vesicae biliaris uberon biliary serosa UBERON:0004783 gallbladder serosa A serous membrane that is part of a gallbladder [Automatically generated definition]. OBOL:automatic gall bladder serosa OBOL:automatic gallbladder serous membrane OBOL:automatic serosa of gall bladder OBOL:automatic serosa of gallbladder OBOL:automatic serous coat of gallbladder FMA:14659 serous membrane of gall bladder OBOL:automatic serous membrane of gallbladder OBOL:automatic tunica serosa (vesica biliaris) FMA:14659 tunica serosa vesicae biliaris FMA:14659 FMA:TA biliary serosa MA:0001634 An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. FMA:13884 MA:0002791 NCIT:C119295 anatomical wall of cardiac ventricle anatomical wall of heart ventricle anatomical wall of lower chamber of heart anatomical wall of ventricle of heart cardiac ventricle anatomical wall cardiac ventricle wall heart ventricle anatomical wall lower chamber of heart anatomical wall lower chamber of heart wall ventricle of heart anatomical wall ventricle of heart wall ventricular wall wall of cardiac ventricle wall of heart ventricle wall of lower chamber of heart wall of ventricle of heart uberon wall of ventricle UBERON:0004784 heart ventricle wall An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. OBOL:automatic anatomical wall of cardiac ventricle OBOL:automatic anatomical wall of heart ventricle OBOL:automatic anatomical wall of lower chamber of heart OBOL:automatic anatomical wall of ventricle of heart OBOL:automatic cardiac ventricle anatomical wall OBOL:automatic cardiac ventricle wall OBOL:automatic heart ventricle anatomical wall OBOL:automatic lower chamber of heart anatomical wall OBOL:automatic lower chamber of heart wall OBOL:automatic ventricle of heart anatomical wall OBOL:automatic ventricle of heart wall OBOL:automatic ventricular wall FMA:13884 wall of cardiac ventricle OBOL:automatic wall of heart ventricle OBOL:automatic wall of lower chamber of heart OBOL:automatic wall of ventricle of heart OBOL:automatic wall of ventricle MA:0002791 The mucous membrane lining the respiratory tract. TODO - split respiratory tract mucosa from respiratory system mucosa BTO:0000973 EMAPA:18334 EMAPA:37577 FMA:302092 GAID:304 MA:0001827 MESH:D020545 apparatus respiratorius mucosa apparatus respiratorius mucosa of organ apparatus respiratorius mucous membrane mucosa of apparatus respiratorius mucosa of organ of apparatus respiratorius mucosa of organ of respiratory system mucosa of respiratory system mucous membrane of apparatus respiratorius mucous membrane of respiratory system respiratory system mucosa of organ respiratory system mucous membrane uberon laryngeal mucous membrane respiratory mucosa respiratory tract mucosa UBERON:0004785 respiratory system mucosa The mucous membrane lining the respiratory tract. MESH:A04.760 MGI:cwg MP:0002277 EMAPA:37577 MA:th apparatus respiratorius mucosa OBOL:automatic apparatus respiratorius mucosa of organ OBOL:automatic apparatus respiratorius mucous membrane OBOL:automatic mucosa of apparatus respiratorius OBOL:automatic mucosa of organ of apparatus respiratorius OBOL:automatic mucosa of organ of respiratory system OBOL:automatic mucosa of respiratory system OBOL:automatic mucous membrane of apparatus respiratorius OBOL:automatic mucous membrane of respiratory system OBOL:automatic respiratory system mucosa of organ OBOL:automatic respiratory system mucous membrane OBOL:automatic laryngeal mucous membrane EMAPA:18334 respiratory mucosa BTO:0000973 A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 EMAPA:36591 MA:0001521 SCTID:410433007 digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut uberon UBERON:0004786 The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa PMID:16417468 PMID:16417468 PMID:16417468 BTO-modified A mucosa that is part of a gastrointestinal system. OBOL:automatic digestive tract mucosa https://orcid.org/0000-0002-6601-2165 gut mucosa BTO:0000546 gut mucuous membrane https://orcid.org/0000-0002-6601-2165 mucosa of gut https://orcid.org/0000-0002-6601-2165 A mucous gland that is part of the skin. See comments for 'skin mucus' EMAPA:35775 MA:0000148 mucous gland of entire skin mucous gland of skin of body skin mucus gland skin of body mucous gland uberon UBERON:0004790 skin mucous gland A mucous gland that is part of the skin. http://orcid.org/0000-0002-6601-2165 mucous gland of entire skin OBOL:automatic mucous gland of skin of body OBOL:automatic skin mucus gland OBOL:automatic skin of body mucous gland OBOL:automatic A secretion that is part of a endocrine pancreas [Automatically generated definition]. MA:0002517 NCIT:C33255 UMLS:C1518866 endocrine pancreas secretion pancreatic endocrine secretion pars endocrina pancreatis secretion secretion of pars endocrina pancreatis uberon UBERON:0004792 secretion of endocrine pancreas A secretion that is part of a endocrine pancreas [Automatically generated definition]. OBOL:automatic UMLS:C1518866 ncithesaurus:Pancreatic_Endocrine_Secretion endocrine pancreas secretion OBOL:automatic pancreatic endocrine secretion ncithesaurus:Pancreatic_Endocrine_Secretion pars endocrina pancreatis secretion OBOL:automatic secretion of pars endocrina pancreatis OBOL:automatic A secretion that is part of a exocrine pancreas [Automatically generated definition]. MA:0002518 NCIT:C33256 UMLS:C1518867 exocrine pancreas secretion pancreatic exocrine secretion pars exocrina pancreatis secretion secretion of pars exocrina pancreatis uberon UBERON:0004793 secretion of exocrine pancreas A secretion that is part of a exocrine pancreas [Automatically generated definition]. OBOL:automatic UMLS:C1518867 ncithesaurus:Pancreatic_Exocrine_Secretion exocrine pancreas secretion OBOL:automatic pancreatic exocrine secretion ncithesaurus:Pancreatic_Exocrine_Secretion pars exocrina pancreatis secretion OBOL:automatic secretion of pars exocrina pancreatis OBOL:automatic A secretion that is part of a esophagus [Automatically generated definition]. FMA:79662 MA:0002514 NCIT:C52555 UMLS:C0227179 esophageal secretion gullet secretion oesophagus secretion secretion of esophagus secretion of gullet secretion of oesophagus uberon UBERON:0004794 esophagus secretion A secretion that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C0227179 ncithesaurus:Esophagus_Secretion esophageal secretion FMA:79662 gullet secretion OBOL:automatic oesophagus secretion OBOL:automatic secretion of esophagus OBOL:automatic secretion of gullet OBOL:automatic secretion of oesophagus OBOL:automatic A secretion that is part of a pancreas [Automatically generated definition]. MA:0002516 NCIT:C13270 UMLS:C0030296 pancreatic secretion secretion of pancreas uberon UBERON:0004795 pancreas secretion A secretion that is part of a pancreas [Automatically generated definition]. OBOL:automatic UMLS:C0030296 ncithesaurus:Pancreatic_Secretion pancreatic secretion OBOL:automatic secretion of pancreas OBOL:automatic Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. EMAPA:36296 MA:0002854 uberon UBERON:0004797 blood vessel layer https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. http://orcid.org/0000-0002-6601-2165 The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. BTO:0000419 CALOHA:TS-0023 EMAPA:32827 MA:0001480 SCTID:321764001 VHOG:0000981 epithelial tissue of respiratory tract epithelium of respiratory tract respiratory tract epithelial tissue uberon airway epithelium respiratory epithelium UBERON:0004802 respiratory tract epithelium The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. ISBN:0-683-40008-8 MGI:anna MP:0010942 epithelial tissue of respiratory tract OBOL:automatic epithelium of respiratory tract OBOL:automatic respiratory tract epithelial tissue OBOL:automatic airway epithelium BTO:0000419 respiratory epithelium BTO:0000419 An epithelium that is part of a respiratory system [Automatically generated definition]. CALOHA:TS-0023 EMAPA:32826 MA:0001823 VHOG:0000981 apparatus respiratorius epithelial tissue apparatus respiratorius epithelium epithelial tissue of apparatus respiratorius epithelial tissue of respiratory system epithelium of apparatus respiratorius epithelium of respiratory system respiratory system epithelial tissue uberon UBERON:0004807 respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius epithelial tissue OBOL:automatic apparatus respiratorius epithelium OBOL:automatic epithelial tissue of apparatus respiratorius OBOL:automatic epithelial tissue of respiratory system OBOL:automatic epithelium of apparatus respiratorius OBOL:automatic epithelium of respiratory system OBOL:automatic respiratory system epithelial tissue OBOL:automatic An epithelium that is part of a digestive system [Automatically generated definition]. EMAPA:32683 MA:0001520 digestive system epithelial tissue digestive system epithelium epithelial tissue of digestive system epithelial tissue of gastrointestinal system epithelium of digestive system epithelium of gastrointestinal system gastrointestinal system epithelial tissue uberon UBERON:0004808 gastrointestinal system epithelium An epithelium that is part of a digestive system [Automatically generated definition]. OBOL:automatic digestive system epithelial tissue OBOL:automatic digestive system epithelium OBOL:automatic epithelial tissue of digestive system OBOL:automatic epithelial tissue of gastrointestinal system OBOL:automatic epithelium of digestive system OBOL:automatic epithelium of gastrointestinal system OBOL:automatic gastrointestinal system epithelial tissue OBOL:automatic An epithelium that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37549 MA:0001481 epithelial tissue of lower respiratory tract epithelium of lower respiratory tract lower respiratory tract epithelial tissue uberon UBERON:0004815 lower respiratory tract epithelium An epithelium that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37549 MA:th epithelial tissue of lower respiratory tract OBOL:automatic epithelium of lower respiratory tract OBOL:automatic lower respiratory tract epithelial tissue OBOL:automatic Any epithelium that lines one of the bile ducts. The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium. BTO:0000417 MA:0001629 NCIT:C43616 UMLS:C1711208 biliary duct epithelium epithelium of bile duct epithelium of biliary duct uberon UBERON:0004820 bile duct epithelium Any epithelium that lines one of the bile ducts. http://orcid.org/0000-0002-6601-2165 The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium. BTO:0000417 UMLS:C1711208 ncithesaurus:Bile_Duct_Epithelium biliary duct epithelium OBOL:automatic epithelium of bile duct OBOL:automatic epithelium of biliary duct OBOL:automatic An epithelium that is part of a extrahepatic bile duct [Automatically generated definition]. EHDAA2:0000742 EHDAA:3051 MA:0002661 NCIT:C43618 UMLS:C1711347 epithelial tissue of extrahepatic bile duct epithelium of extrahepatic bile duct extrahepatic bile duct epithelial tissue uberon UBERON:0004822 extrahepatic bile duct epithelium An epithelium that is part of a extrahepatic bile duct [Automatically generated definition]. OBOL:automatic UMLS:C1711347 ncithesaurus:Extrahepatic_Bile_Duct_Epithelium epithelial tissue of extrahepatic bile duct OBOL:automatic epithelium of extrahepatic bile duct OBOL:automatic extrahepatic bile duct epithelial tissue OBOL:automatic An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]. EHDAA2:0000743 EHDAA:3053 MA:0002662 NCIT:C43617 UMLS:C1708552 epithelial tissue of intrahepatic bile duct epithelium of intrahepatic bile duct intrahepatic bile duct epithelial tissue uberon UBERON:0004823 intrahepatic bile duct epithelium An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]. OBOL:automatic UMLS:C1708552 ncithesaurus:Intrahepatic_Bile_Duct_Epithelium epithelial tissue of intrahepatic bile duct OBOL:automatic epithelium of intrahepatic bile duct OBOL:automatic intrahepatic bile duct epithelial tissue OBOL:automatic A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37583 MA:0001829 respiratory system skeletal muscle tissue skeletal muscle of apparatus respiratorius skeletal muscle of respiratory system skeletal muscle tissue of apparatus respiratorius skeletal muscle tissue of respiratory system uberon UBERON:0004830 respiratory system skeletal muscle A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37583 MA:th respiratory system skeletal muscle tissue OBOL:automatic skeletal muscle of apparatus respiratorius OBOL:automatic skeletal muscle of respiratory system OBOL:automatic skeletal muscle tissue of apparatus respiratorius OBOL:automatic skeletal muscle tissue of respiratory system OBOL:automatic A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. EMAPA:36523 MA:0001572 esophagus skeletal muscle tissue skeletal muscle of esophagus uberon UBERON:0004831 Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal esophagus skeletal muscle A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus skeletal muscle tissue OBOL:automatic skeletal muscle of esophagus OBOL:automatic A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37393 MA:0001530 anal part of perineum skeletal muscle anal part of perineum skeletal muscle tissue anal region skeletal muscle tissue anal triangle skeletal muscle anal triangle skeletal muscle tissue skeletal muscle of anal part of perineum skeletal muscle of anal region skeletal muscle of anal triangle skeletal muscle tissue of anal part of perineum skeletal muscle tissue of anal region skeletal muscle tissue of anal triangle uberon UBERON:0004832 anal region skeletal muscle A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37393 MA:th anal part of perineum skeletal muscle OBOL:automatic anal part of perineum skeletal muscle tissue OBOL:automatic anal region skeletal muscle tissue OBOL:automatic anal triangle skeletal muscle OBOL:automatic anal triangle skeletal muscle tissue OBOL:automatic skeletal muscle of anal part of perineum OBOL:automatic skeletal muscle of anal region OBOL:automatic skeletal muscle of anal triangle OBOL:automatic skeletal muscle tissue of anal part of perineum OBOL:automatic skeletal muscle tissue of anal region OBOL:automatic skeletal muscle tissue of anal triangle OBOL:automatic A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips EMAPA:37642 MA:0001578 lip skeletal muscle tissue skeletal muscle of lip skeletal muscle tissue of lip uberon UBERON:0004833 lip skeletal muscle A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37642 MA:th lip skeletal muscle tissue OBOL:automatic skeletal muscle of lip OBOL:automatic skeletal muscle tissue of lip OBOL:automatic Smooth muscle tissue in all or part of a hepatic duct. EMAPA:37598 MA:0001640 uberon UBERON:0004834 hepatic duct smooth muscle Smooth muscle tissue in all or part of a hepatic duct. http://orcid.org/0000-0002-6601-2165 EMAPA:37598 MA:th An endothelium of artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37566 MA:0001801 apparatus respiratorius arterial endothelium apparatus respiratorius artery endothelium apparatus respiratorius endothelium of artery arterial endothelium of apparatus respiratorius arterial endothelium of respiratory system artery endothelium of apparatus respiratorius artery endothelium of respiratory system endothelium of artery of apparatus respiratorius endothelium of artery of respiratory system respiratory system artery endothelium respiratory system endothelium of artery uberon UBERON:0004848 respiratory system arterial endothelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An endothelium of artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37566 MA:th apparatus respiratorius arterial endothelium OBOL:automatic apparatus respiratorius artery endothelium OBOL:automatic apparatus respiratorius endothelium of artery OBOL:automatic arterial endothelium of apparatus respiratorius OBOL:automatic arterial endothelium of respiratory system OBOL:automatic artery endothelium of apparatus respiratorius OBOL:automatic artery endothelium of respiratory system OBOL:automatic endothelium of artery of apparatus respiratorius OBOL:automatic endothelium of artery of respiratory system OBOL:automatic respiratory system artery endothelium OBOL:automatic respiratory system endothelium of artery OBOL:automatic An endothelium of vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37585 MA:0001811 apparatus respiratorius endothelium of vein apparatus respiratorius vein endothelium apparatus respiratorius venous endothelium endothelium of vein of apparatus respiratorius endothelium of vein of respiratory system respiratory system endothelium of vein respiratory system vein endothelium vein endothelium of apparatus respiratorius vein endothelium of respiratory system venous endothelium of apparatus respiratorius venous endothelium of respiratory system uberon UBERON:0004849 respiratory system venous endothelium An endothelium of vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37585 MA:th apparatus respiratorius endothelium of vein OBOL:automatic apparatus respiratorius vein endothelium OBOL:automatic apparatus respiratorius venous endothelium OBOL:automatic endothelium of vein of apparatus respiratorius OBOL:automatic endothelium of vein of respiratory system OBOL:automatic respiratory system endothelium of vein OBOL:automatic respiratory system vein endothelium OBOL:automatic vein endothelium of apparatus respiratorius OBOL:automatic vein endothelium of respiratory system OBOL:automatic venous endothelium of apparatus respiratorius OBOL:automatic venous endothelium of respiratory system OBOL:automatic The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall. BTO:0000394 CALOHA:TS-0047 EFO:0002597 EMAPA:35134 MA:0000701 NCIT:C49190 UMLS:C1706824 adult aorta endothelium endothelium of adult aorta endothelium of aorta endothelium of trunk of aortic tree endothelium of trunk of systemic arterial tree trunk of aortic tree endothelium trunk of systemic arterial tree endothelium uberon aortic endothelium UBERON:0004851 aorta endothelium The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall. MGI:csmith MP:0009864 UMLS:C1706824 ncithesaurus:Aorta_Endothelium adult aorta endothelium OBOL:automatic endothelium of adult aorta OBOL:automatic endothelium of aorta OBOL:automatic endothelium of trunk of aortic tree OBOL:automatic endothelium of trunk of systemic arterial tree OBOL:automatic trunk of aortic tree endothelium OBOL:automatic trunk of systemic arterial tree endothelium OBOL:automatic aortic endothelium BTO:0000394 An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 MA:0000717 MESH:D004730 NCIT:C13053 TAO:0002171 UMLS:C0014261 VHOG:0001217 XAO:0000356 ZFA:0001639 uberon endothelia vascular endothelia UBERON:0004852 cardiovascular system endothelium An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001217 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C0014261 ncithesaurus:Vascular_Endothelium endothelia ZFA:0001639 vascular endothelia XAO:0000356 A mesentery that is part of a digestive system [Automatically generated definition]. EMAPA:37068 MA:0001900 digestive system mesentery mesentery of digestive system mesentery of gastrointestinal system uberon UBERON:0004854 gastrointestinal system mesentery A mesentery that is part of a digestive system [Automatically generated definition]. OBOL:automatic EMAPA:37068 MA:th digestive system mesentery OBOL:automatic mesentery of digestive system OBOL:automatic mesentery of gastrointestinal system OBOL:automatic A connective tissue that surrounds a skeletal muscle tissue. EMAPA:37743 MA:0002868 connective tissue of skeletal muscle connective tissue of skeletal muscle tissue portion of connective tissue of skeletal muscle portion of connective tissue of skeletal muscle tissue skeletal muscle portion of connective tissue skeletal muscle textus connectivus skeletal muscle tissue connective tissue skeletal muscle tissue portion of connective tissue skeletal muscle tissue textus connectivus textus connectivus of skeletal muscle textus connectivus of skeletal muscle tissue uberon skeletal muscle interstitial tissue skeletal muscle interstitum UBERON:0004857 skeletal muscle connective tissue A connective tissue that surrounds a skeletal muscle tissue. OBOL:automatic EMAPA:37743 MA:th connective tissue of skeletal muscle OBOL:automatic connective tissue of skeletal muscle tissue OBOL:automatic portion of connective tissue of skeletal muscle OBOL:automatic portion of connective tissue of skeletal muscle tissue OBOL:automatic skeletal muscle portion of connective tissue OBOL:automatic skeletal muscle textus connectivus OBOL:automatic skeletal muscle tissue connective tissue OBOL:automatic skeletal muscle tissue portion of connective tissue OBOL:automatic skeletal muscle tissue textus connectivus OBOL:automatic textus connectivus of skeletal muscle OBOL:automatic textus connectivus of skeletal muscle tissue OBOL:automatic skeletal muscle interstitial tissue MA:0002868 skeletal muscle interstitum MA:0002868 A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. EMAPA:35334 MA:0000267 eye-associated gland gland of eye uberon UBERON:0004859 Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands eye gland A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. http://orcid.org/0000-0002-6601-2165 eye-associated gland http://orcid.org/0000-0002-6601-2165 gland of eye OBOL:automatic A vasculature that is part of a retina [Automatically generated definition]. FMA:76552 MESH:D012171 XAO:0004153 retina vasculature retina vasculature of camera-type eye retinal blood vessels retinal blood vessels set retinal vasculature set of blood vessels of retina set of retinal blood vessels vasa sanguinea retinae uberon UBERON:0004864 vasculature of retina A vasculature that is part of a retina [Automatically generated definition]. OBOL:automatic PMID:21622558 PMID:2772405 michaelerice retina vasculature GO:0061298 retina vasculature of camera-type eye GO:0061298 retinal blood vessels FMA:76552 retinal blood vessels set FMA:76552 retinal vasculature OBOL:automatic set of blood vessels of retina OBOL:automatic set of retinal blood vessels FMA:76552 vasa sanguinea retinae FMA:76552 FMA:TA Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye. note that the AAO and ZFA class is a cavity AAO:0000343 FMA:84961 SCTID:280541000 Wikipedia:Orbit_(anatomy) ZFA:0005558 uberon orbit UBERON:0004867 orbital cavity Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye. http://orcid.org/0000-0002-6601-2165 note that the AAO and ZFA class is a cavity AAO https://github.com/obophenotype/uberon/issues/462 orbit AAO:0000343 Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 FMA:295568 Wikipedia:Lateral_plate_mesoderm#Division_into_layers XAO:0000276 inner layer of lateral plate mesoderm uberon splanchnic mesoderm UBERON:0004872 splanchnic layer of lateral plate mesoderm Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors BILA visceral mesoderm BILA:0000044 http://www.drugs.com/dict/visceral-mesoderm.html http://www.stedmans.com/ splanchnic mesoderm ISBN:9780878932504 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. TODO - check relationship to LPM EHDAA2:0001903 EHDAA:383 EMAPA:16181 FMA:295564 NCIT:C34303 UMLS:C1519472 VHOG:0000558 Wikipedia:Splanchnopleure uberon ventral splanchnic mesoderm UBERON:0004873 splanchnopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. Wikipedia:Splanchnopleure UMLS:C1519472 ncithesaurus:Splanchnopleure ventral splanchnic mesoderm Wikipedia:Intraembryonic_coelom A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ sources differ as to whether this is part-of or develops-from the LPM EHDAA2:0001847 EHDAA:381 EMAPA:16180 FMA:295566 NCIT:C34301 UMLS:C1519423 VHOG:0000557 Wikipedia:Somatopleure uberon UBERON:0004874 somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. Wikipedia:Somatopleure UMLS:C1519423 ncithesaurus:Somatopleure The central region of trunk mesoderm. This tissue forms the notochord. Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 ZFA:0000091 axial chorda mesoderm chorda mesoderm dorsal mesoderm presumptive notochord uberon UBERON:0004880 chordamesoderm The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 axial chorda mesoderm ZFA:0000091 dorsal mesoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest presumptive notochord ZFA:0000091 The mass of tissue made up of mesenchymal cells in the lung. EMAPA:32866 lung-associated mesenchyme mesenchyme of lung pulmonary mesenchyme uberon UBERON:0004883 lung mesenchyme The mass of tissue made up of mesenchymal cells in the lung. GO:0060484 lung-associated mesenchyme GO:0060484 mesenchyme of lung OBOL:automatic pulmonary mesenchyme GO:0060484 A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila. optic nerve BTO:0000966 EV:0100351 FBbt:00001956 TADS:0000232 optic nerve (generic) uberon UBERON:0004904 for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II) neuron projection bundle connecting eye with brain A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila. http://orcid.org/0000-0002-6601-2165 optic nerve BTO:0000966 FBbt:00001956 Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint uberon UBERON:0004905 articulation Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 FBbt:00005811 A portion of the gut that is derived from ectoderm. ectodermal gut gut ectoderm uberon UBERON:0004906 ectodermal part of digestive tract A portion of the gut that is derived from ectoderm. GO:0007439 gut ectoderm EMAPA:32930 The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L gut FMA:49179 NCIT:C33010 SCTID:279973004 UMLS:C0226875 Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract galen:LowerGastrointestinalTract lower GI tract lower gastrointestinal tract uberon UBERON:0004907 lower digestive tract The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 MA WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L FMA gut GO:0048565 UMLS:C0226875 ncithesaurus:Lower_Gastrointestinal_Tract The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus FMA:49177 NCIT:C33837 SCTID:181244000 UMLS:C0226874 Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract galen:UpperGastrointestinalTract upper GI tract upper gastrointestinal tract uberon UBERON:0004908 upper digestive tract The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus FMA UMLS:C0226874 ncithesaurus:Upper_Gastrointestinal_Tract An epithelium surrounding a gonad. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts EHDAA:4032 EHDAA:5931 NCIT:C32676 UMLS:C1517534 gonad epithelium gonadal epithelium uberon gonadal sheath UBERON:0004909 epithelium of gonad An epithelium surrounding a gonad. OBOL:automatic UMLS:C1517534 ncithesaurus:Germinal_Epithelium gonad epithelium OBOL:automatic gonadal epithelium OBOL:automatic gonadal sheath FBbt:00004859 An epithelium surrounding an ovary. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts BTO:0003661 ovarian epithelium ovary epithelium ovarian sheath uberon UBERON:0004911 epithelium of female gonad An epithelium surrounding an ovary. OBOL:automatic ovarian epithelium OBOL:automatic ovary epithelium OBOL:automatic ovarian sheath FBbt:00004896 EHDAA2:0000171 EMAPA:16561 EMAPA_RETIRED:16565 VHOG:0001351 uberon hepatic diverticulum UBERON:0004912 biliary bud http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png EHDAA2 EHDAA2 EHDAA2-modified hepatic diverticulum EMAPA:16561 A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct. Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO] CALOHA:TS-2348 FMA:15076 GAID:283 MESH:D014670 NCIT:C13011 SCTID:362200007 TAO:0005167 UMLS:C0042425 Wikipedia:Ampulla_of_Vater ZFA:0005167 galen:AmpullaOfVater Vater's ampulla ampulla biliaropancreatica ampulla of Vater ampulla of bile duct biliaropancreatic ampulla papilla Vateri uberon ampulla Vaterii ampulla hepatopancreatica papilla duodeni major UBERON:0004913 hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct. Wikipedia:Ampulla_of_Vater Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO] 2012-08-14 TAO:0005167 TAO ZFIN:ZDB-PUB-070212-11 ZFIN:ZDB-PUB-080414-12 UMLS:C0042425 ncithesaurus:Ampulla_of_Vater ampulla biliaropancreatica FMA:15076 FMA:TA ampulla of bile duct FMA:15076 papilla Vateri ZFA:0005167 ampulla Vaterii Wikipedia:Ampulla_of_Vater ampulla hepatopancreatica Wikipedia:Ampulla_of_Vater papilla duodeni major ZFA:0005167 One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct. EMAPA:18662 FMA:15953 MA:0003107 NCIT:C119578 SCTID:245389007 papilla duodenalis papilla of duodenum uberon papilla duodeni UBERON:0004914 duodenal papilla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct. http://medical-dictionary.thefreedictionary.com/duodenal+papilla papilla duodeni Wikipedia:Major_duodenal_papilla Muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP]. EMAPA:18663 FMA:15077 GAID:285 MESH:D009803 NCIT:C13065 SCTID:181271000 UMLS:C0028872 Wikipedia:Sphincter_of_ampulla Oddi's sphincter hepatopancreatic ampullary sphincter musculus sphincter ampullae musculus sphincter ampullae hepatopancreatica sphincter of Oddi sphincter of ampulla of vater uberon UBERON:0004915 sphincter of hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png Muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP]. Wikipedia:Sphincter_of_ampulla UMLS:C0028872 ncithesaurus:Sphincter_of_Oddi hepatopancreatic ampullary sphincter FMA:15077 musculus sphincter ampullae FMA:15077 musculus sphincter ampullae hepatopancreatica FMA:15077 FMA:TA sphincter of ampulla of vater FMA:15077 A sphincter muscle that is part of a anal region. EMAPA:36052 anal region sphincter sphincter analia uberon UBERON:0004916 anal sphincter A sphincter muscle that is part of a anal region. OBOL:automatic A proximal-distal subdivision of the digestive tract. intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. FBbt:00100315 FMA:71131 uberon alimentary system subdivision gut section intestinal tract segment of intestinal tract subdivision of alimentary system UBERON:0004921 subdivision of digestive tract A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 FBbt:00100315 alimentary system subdivision FMA:71131 gut section FBbt:00100315 subdivision of alimentary system FMA:71131 A part of a wall of an organ that forms a layer. FMA:82485 uberon UBERON:0004923 organ component layer A part of a wall of an organ that forms a layer. http://orcid.org/0000-0002-6601-2165 The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 FMA:75144 SCTID:19594009 pharyngeal submucosa pharynx submucosa tela submucosa pharyngea tela submucosa pharyngis uberon pharyngobasilar fascia submucous coat of pharynx submucous layer of pharynx UBERON:0004924 submucosa of pharynx The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 pharyngeal submucosa FMA:75144 pharynx submucosa OBOL:automatic tela submucosa pharyngea FMA:75144 FMA:TA tela submucosa pharyngis BTO:0002113 submucous coat of pharynx BTO:0002113 submucous layer of pharynx BTO:0002113 A submucosa that is part of a cystic duct [Automatically generated definition]. FMA:18013 cystic duct submucosa cystic ductal submucosa uberon UBERON:0004926 submucosa of cystic duct A submucosa that is part of a cystic duct [Automatically generated definition]. OBOL:automatic cystic duct submucosa OBOL:automatic cystic ductal submucosa FMA:18013 A submucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15027 sigmoid colon submucosa uberon UBERON:0004932 submucosa of sigmoid colon A submucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic sigmoid colon submucosa OBOL:automatic A submucosa that is part of a body of stomach [Automatically generated definition]. FMA:17059 body of stomach submucosa corpus gastricum (ventriculare) submucosa gastric body submucosa stomach body submucosa submucosa of corpus gastricum (ventriculare) submucosa of gastric body submucosa of stomach body uberon UBERON:0004934 submucosa of body of stomach A submucosa that is part of a body of stomach [Automatically generated definition]. OBOL:automatic body of stomach submucosa OBOL:automatic corpus gastricum (ventriculare) submucosa OBOL:automatic gastric body submucosa OBOL:automatic stomach body submucosa OBOL:automatic submucosa of corpus gastricum (ventriculare) OBOL:automatic submucosa of gastric body OBOL:automatic submucosa of stomach body OBOL:automatic A submucosa that is part of a pyloric antrum [Automatically generated definition]. FMA:17060 antrum of stomach submucosa pyloric antrum submucosa stomach pyloric antrum submucosa submucosa of antrum of stomach submucosa of stomach pyloric antrum uberon UBERON:0004936 submucosa of pyloric antrum A submucosa that is part of a pyloric antrum [Automatically generated definition]. OBOL:automatic antrum of stomach submucosa OBOL:automatic pyloric antrum submucosa OBOL:automatic stomach pyloric antrum submucosa OBOL:automatic submucosa of antrum of stomach OBOL:automatic submucosa of stomach pyloric antrum OBOL:automatic A submucosa that is part of a pylorus [Automatically generated definition]. EMAPA:27201 FMA:17462 pyloric part of stomach submucosa pyloric submucosa pylorus submucosa stomach pyloric region submucosa submucosa of pyloric part of stomach submucosa of stomach pyloric region uberon UBERON:0004937 submucosa of pylorus A submucosa that is part of a pylorus [Automatically generated definition]. OBOL:automatic pyloric part of stomach submucosa OBOL:automatic pylorus submucosa FMA:17462 OBOL:automatic stomach pyloric region submucosa OBOL:automatic submucosa of pyloric part of stomach OBOL:automatic submucosa of stomach pyloric region OBOL:automatic A submucosa that is part of a biliary tree [Automatically generated definition]. FMA:18009 biliary tract submucosa biliary tree submucosa submucosa of biliary tract uberon UBERON:0004938 submucosa of biliary tree A submucosa that is part of a biliary tree [Automatically generated definition]. OBOL:automatic biliary tract submucosa OBOL:automatic biliary tree submucosa OBOL:automatic submucosa of biliary tract OBOL:automatic A submucosa that is part of a common bile duct [Automatically generated definition]. FMA:18011 common bile duct submucosa common bile ductal submucosa ductus choledochus (biliaris) submucosa submucosa of ductus choledochus (biliaris) uberon UBERON:0004939 submucosa of common bile duct A submucosa that is part of a common bile duct [Automatically generated definition]. OBOL:automatic common bile duct submucosa OBOL:automatic common bile ductal submucosa FMA:18011 ductus choledochus (biliaris) submucosa OBOL:automatic submucosa of ductus choledochus (biliaris) OBOL:automatic A submucosa that is part of a common hepatic duct [Automatically generated definition]. FMA:18014 common hepatic duct submucosa common hepatic ductal submucosa hepatic duct submucosa submucosa of hepatic duct uberon UBERON:0004940 submucosa of common hepatic duct A submucosa that is part of a common hepatic duct [Automatically generated definition]. OBOL:automatic common hepatic duct submucosa OBOL:automatic common hepatic ductal submucosa FMA:18014 hepatic duct submucosa OBOL:automatic submucosa of hepatic duct OBOL:automatic A submucosa that is part of a right hepatic duct [Automatically generated definition]. FMA:18015 right hepatic duct submucosa right hepatic ductal submucosa uberon UBERON:0004941 submucosa of right hepatic duct A submucosa that is part of a right hepatic duct [Automatically generated definition]. OBOL:automatic right hepatic duct submucosa OBOL:automatic right hepatic ductal submucosa FMA:18015 A submucosa that is part of a left hepatic duct [Automatically generated definition]. FMA:18017 left hepatic duct submucosa left hepatic ductal submucosa uberon UBERON:0004942 submucosa of left hepatic duct A submucosa that is part of a left hepatic duct [Automatically generated definition]. OBOL:automatic left hepatic duct submucosa OBOL:automatic left hepatic ductal submucosa FMA:18017 A mucosa that is part of a cystic duct [Automatically generated definition]. FMA:14690 cystic duct mucosa cystic duct mucosa of organ cystic duct mucous membrane cystic duct organ mucosa cystic ductal mucosa mucosa of organ of cystic duct mucous membrane of cystic duct organ mucosa of cystic duct uberon UBERON:0004988 mucosa of cystic duct A mucosa that is part of a cystic duct [Automatically generated definition]. OBOL:automatic cystic duct mucosa OBOL:automatic cystic duct mucosa of organ OBOL:automatic cystic duct mucous membrane OBOL:automatic cystic duct organ mucosa OBOL:automatic cystic ductal mucosa FMA:14690 mucosa of organ of cystic duct OBOL:automatic mucous membrane of cystic duct OBOL:automatic organ mucosa of cystic duct OBOL:automatic A mucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15026 mucosa of organ of sigmoid colon mucous membrane of sigmoid colon organ mucosa of sigmoid colon sigmoid colon mucosa sigmoid colon mucosa of organ sigmoid colon mucous membrane sigmoid colon organ mucosa uberon UBERON:0004993 mucosa of sigmoid colon A mucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic mucosa of organ of sigmoid colon OBOL:automatic mucous membrane of sigmoid colon OBOL:automatic organ mucosa of sigmoid colon OBOL:automatic sigmoid colon mucosa OBOL:automatic sigmoid colon mucosa of organ OBOL:automatic sigmoid colon mucous membrane OBOL:automatic sigmoid colon organ mucosa OBOL:automatic A mucosa that is part of a body of stomach [Automatically generated definition]. FMA:17054 body of stomach mucosa body of stomach mucosa of organ body of stomach mucous membrane body of stomach organ mucosa corpus gastricum (ventriculare) mucosa corpus gastricum (ventriculare) mucosa of organ corpus gastricum (ventriculare) mucous membrane corpus gastricum (ventriculare) organ mucosa gastric body mucosa gastric body mucosa of organ gastric body mucous membrane gastric body organ mucosa mucosa of corpus gastricum (ventriculare) mucosa of gastric body mucosa of organ of body of stomach mucosa of organ of corpus gastricum (ventriculare) mucosa of organ of gastric body mucosa of organ of stomach body mucosa of stomach body mucous membrane of body of stomach mucous membrane of corpus gastricum (ventriculare) mucous membrane of gastric body mucous membrane of stomach body organ mucosa of body of stomach organ mucosa of corpus gastricum (ventriculare) organ mucosa of gastric body organ mucosa of stomach body stomach body mucosa stomach body mucosa of organ stomach body mucous membrane stomach body organ mucosa uberon UBERON:0004995 mucosa of body of stomach A mucosa that is part of a body of stomach [Automatically generated definition]. OBOL:automatic body of stomach mucosa OBOL:automatic body of stomach mucosa of organ OBOL:automatic body of stomach mucous membrane OBOL:automatic body of stomach organ mucosa OBOL:automatic corpus gastricum (ventriculare) mucosa OBOL:automatic corpus gastricum (ventriculare) mucosa of organ OBOL:automatic corpus gastricum (ventriculare) mucous membrane OBOL:automatic corpus gastricum (ventriculare) organ mucosa OBOL:automatic gastric body mucosa OBOL:automatic gastric body mucosa of organ OBOL:automatic gastric body mucous membrane OBOL:automatic gastric body organ mucosa OBOL:automatic mucosa of corpus gastricum (ventriculare) OBOL:automatic mucosa of gastric body OBOL:automatic mucosa of organ of body of stomach OBOL:automatic mucosa of organ of corpus gastricum (ventriculare) OBOL:automatic mucosa of organ of gastric body OBOL:automatic mucosa of organ of stomach body OBOL:automatic mucosa of stomach body OBOL:automatic mucous membrane of body of stomach OBOL:automatic mucous membrane of corpus gastricum (ventriculare) OBOL:automatic mucous membrane of gastric body OBOL:automatic mucous membrane of stomach body OBOL:automatic organ mucosa of body of stomach OBOL:automatic organ mucosa of corpus gastricum (ventriculare) OBOL:automatic organ mucosa of gastric body OBOL:automatic organ mucosa of stomach body OBOL:automatic stomach body mucosa OBOL:automatic stomach body mucosa of organ OBOL:automatic stomach body mucous membrane OBOL:automatic stomach body organ mucosa OBOL:automatic A mucosa that is part of a pyloric antrum [Automatically generated definition]. BTO:0004107 FMA:17055 antral mucosa antrum of stomach mucosa antrum of stomach mucosa of organ antrum of stomach mucous membrane antrum of stomach organ mucosa mucosa of antrum of stomach mucosa of organ of antrum of stomach mucosa of organ of pyloric antrum mucosa of organ of stomach pyloric antrum mucosa of stomach pyloric antrum mucous membrane of antrum of stomach mucous membrane of pyloric antrum mucous membrane of stomach pyloric antrum organ mucosa of antrum of stomach organ mucosa of pyloric antrum organ mucosa of stomach pyloric antrum pyloric antrum mucosa pyloric antrum mucosa of organ pyloric antrum mucous membrane pyloric antrum organ mucosa stomach pyloric antrum mucosa stomach pyloric antrum mucosa of organ stomach pyloric antrum mucous membrane stomach pyloric antrum organ mucosa uberon gastric antrum mucosa UBERON:0004997 mucosa of pyloric antrum BTO A mucosa that is part of a pyloric antrum [Automatically generated definition]. OBOL:automatic antral mucosa BTO:0004107 antrum of stomach mucosa OBOL:automatic antrum of stomach mucosa of organ OBOL:automatic antrum of stomach mucous membrane OBOL:automatic antrum of stomach organ mucosa OBOL:automatic mucosa of antrum of stomach OBOL:automatic mucosa of organ of antrum of stomach OBOL:automatic mucosa of organ of pyloric antrum OBOL:automatic mucosa of organ of stomach pyloric antrum OBOL:automatic mucosa of stomach pyloric antrum OBOL:automatic mucous membrane of antrum of stomach OBOL:automatic mucous membrane of pyloric antrum OBOL:automatic mucous membrane of stomach pyloric antrum OBOL:automatic organ mucosa of antrum of stomach OBOL:automatic organ mucosa of pyloric antrum OBOL:automatic organ mucosa of stomach pyloric antrum OBOL:automatic pyloric antrum mucosa OBOL:automatic pyloric antrum mucosa of organ OBOL:automatic pyloric antrum mucous membrane OBOL:automatic pyloric antrum organ mucosa OBOL:automatic stomach pyloric antrum mucosa OBOL:automatic stomach pyloric antrum mucosa of organ OBOL:automatic stomach pyloric antrum mucous membrane OBOL:automatic stomach pyloric antrum organ mucosa OBOL:automatic gastric antrum mucosa BTO:0004107 A mucosa that is part of a pylorus [Automatically generated definition]. BTO:0004110 EMAPA:27199 FMA:17461 mucosa of organ of pyloric part of stomach mucosa of organ of pylorus mucosa of organ of stomach pyloric region mucosa of pyloric part of stomach mucosa of stomach pyloric region mucous membrane of pyloric part of stomach mucous membrane of pylorus mucous membrane of stomach pyloric region organ mucosa of pyloric part of stomach organ mucosa of pylorus organ mucosa of stomach pyloric region pyloric part of stomach mucosa pyloric part of stomach mucosa of organ pyloric part of stomach mucous membrane pyloric part of stomach organ mucosa pylorus mucosa pylorus mucosa of organ pylorus mucous membrane pylorus organ mucosa stomach pyloric region mucosa stomach pyloric region mucosa of organ stomach pyloric region mucous membrane stomach pyloric region organ mucosa uberon antropyloric mucosa UBERON:0004998 mucosa of pylorus A mucosa that is part of a pylorus [Automatically generated definition]. OBOL:automatic mucosa of organ of pyloric part of stomach OBOL:automatic mucosa of organ of pylorus OBOL:automatic mucosa of organ of stomach pyloric region OBOL:automatic mucosa of pyloric part of stomach OBOL:automatic mucosa of stomach pyloric region OBOL:automatic mucous membrane of pyloric part of stomach OBOL:automatic mucous membrane of pylorus OBOL:automatic mucous membrane of stomach pyloric region OBOL:automatic organ mucosa of pyloric part of stomach OBOL:automatic organ mucosa of pylorus OBOL:automatic organ mucosa of stomach pyloric region OBOL:automatic pyloric part of stomach mucosa OBOL:automatic pyloric part of stomach mucosa of organ OBOL:automatic pyloric part of stomach mucous membrane OBOL:automatic pyloric part of stomach organ mucosa OBOL:automatic pylorus mucosa OBOL:automatic pylorus mucosa of organ OBOL:automatic pylorus mucous membrane OBOL:automatic pylorus organ mucosa OBOL:automatic stomach pyloric region mucosa OBOL:automatic stomach pyloric region mucosa of organ OBOL:automatic stomach pyloric region mucous membrane OBOL:automatic stomach pyloric region organ mucosa OBOL:automatic antropyloric mucosa BTO:0002984 A mucosa that is part of a biliary tree [Automatically generated definition]. FMA:14695 biliary tract mucosa biliary tract mucosa of organ biliary tract mucous membrane biliary tract organ mucosa biliary tree mucosa biliary tree mucosa of organ biliary tree mucous membrane biliary tree organ mucosa mucosa of biliary tract mucosa of organ of biliary tract mucosa of organ of biliary tree mucous membrane of biliary tract mucous membrane of biliary tree organ mucosa of biliary tract organ mucosa of biliary tree uberon UBERON:0004999 mucosa of biliary tree A mucosa that is part of a biliary tree [Automatically generated definition]. OBOL:automatic biliary tract mucosa OBOL:automatic biliary tract mucosa of organ OBOL:automatic biliary tract mucous membrane OBOL:automatic biliary tract organ mucosa OBOL:automatic biliary tree mucosa OBOL:automatic biliary tree mucosa of organ OBOL:automatic biliary tree mucous membrane OBOL:automatic biliary tree organ mucosa OBOL:automatic mucosa of biliary tract OBOL:automatic mucosa of organ of biliary tract OBOL:automatic mucosa of organ of biliary tree OBOL:automatic mucous membrane of biliary tract OBOL:automatic mucous membrane of biliary tree OBOL:automatic organ mucosa of biliary tract OBOL:automatic organ mucosa of biliary tree OBOL:automatic A mucosa that is part of a common bile duct [Automatically generated definition]. FMA:14688 common bile duct mucosa common bile duct mucosa of organ common bile duct mucous membrane common bile duct organ mucosa common bile ductal mucosa ductus choledochus (biliaris) mucosa ductus choledochus (biliaris) mucosa of organ ductus choledochus (biliaris) mucous membrane ductus choledochus (biliaris) organ mucosa mucosa of ductus choledochus (biliaris) mucosa of organ of common bile duct mucosa of organ of ductus choledochus (biliaris) mucous membrane of common bile duct mucous membrane of ductus choledochus (biliaris) organ mucosa of common bile duct organ mucosa of ductus choledochus (biliaris) uberon UBERON:0005000 mucosa of common bile duct A mucosa that is part of a common bile duct [Automatically generated definition]. OBOL:automatic common bile duct mucosa OBOL:automatic common bile duct mucosa of organ OBOL:automatic common bile duct mucous membrane OBOL:automatic common bile duct organ mucosa OBOL:automatic common bile ductal mucosa FMA:14688 ductus choledochus (biliaris) mucosa OBOL:automatic ductus choledochus (biliaris) mucosa of organ OBOL:automatic ductus choledochus (biliaris) mucous membrane OBOL:automatic ductus choledochus (biliaris) organ mucosa OBOL:automatic mucosa of ductus choledochus (biliaris) OBOL:automatic mucosa of organ of common bile duct OBOL:automatic mucosa of organ of ductus choledochus (biliaris) OBOL:automatic mucous membrane of common bile duct OBOL:automatic mucous membrane of ductus choledochus (biliaris) OBOL:automatic organ mucosa of common bile duct OBOL:automatic organ mucosa of ductus choledochus (biliaris) OBOL:automatic A mucosa that is part of a common hepatic duct [Automatically generated definition]. FMA:14691 common hepatic duct mucosa common hepatic duct mucosa of organ common hepatic duct mucous membrane common hepatic duct organ mucosa common hepatic ductal mucosa hepatic duct mucosa hepatic duct mucosa of organ hepatic duct mucous membrane hepatic duct organ mucosa mucosa of hepatic duct mucosa of organ of common hepatic duct mucosa of organ of hepatic duct mucous membrane of common hepatic duct mucous membrane of hepatic duct organ mucosa of common hepatic duct organ mucosa of hepatic duct uberon UBERON:0005001 mucosa of common hepatic duct A mucosa that is part of a common hepatic duct [Automatically generated definition]. OBOL:automatic common hepatic duct mucosa OBOL:automatic common hepatic duct mucosa of organ OBOL:automatic common hepatic duct mucous membrane OBOL:automatic common hepatic duct organ mucosa OBOL:automatic common hepatic ductal mucosa FMA:14691 hepatic duct mucosa OBOL:automatic hepatic duct mucosa of organ OBOL:automatic hepatic duct mucous membrane OBOL:automatic hepatic duct organ mucosa OBOL:automatic mucosa of hepatic duct OBOL:automatic mucosa of organ of common hepatic duct OBOL:automatic mucosa of organ of hepatic duct OBOL:automatic mucous membrane of common hepatic duct OBOL:automatic mucous membrane of hepatic duct OBOL:automatic organ mucosa of common hepatic duct OBOL:automatic organ mucosa of hepatic duct OBOL:automatic A mucosa that is part of a right hepatic duct [Automatically generated definition]. FMA:14692 mucosa of organ of right hepatic duct mucous membrane of right hepatic duct organ mucosa of right hepatic duct right hepatic duct mucosa right hepatic duct mucosa of organ right hepatic duct mucous membrane right hepatic duct organ mucosa right hepatic ductal mucosa uberon UBERON:0005002 mucosa of right hepatic duct A mucosa that is part of a right hepatic duct [Automatically generated definition]. OBOL:automatic mucosa of organ of right hepatic duct OBOL:automatic mucous membrane of right hepatic duct OBOL:automatic organ mucosa of right hepatic duct OBOL:automatic right hepatic duct mucosa OBOL:automatic right hepatic duct mucosa of organ OBOL:automatic right hepatic duct mucous membrane OBOL:automatic right hepatic duct organ mucosa OBOL:automatic right hepatic ductal mucosa FMA:14692 A mucosa that is part of a left hepatic duct [Automatically generated definition]. FMA:14693 left hepatic duct mucosa left hepatic duct mucosa of organ left hepatic duct mucous membrane left hepatic duct organ mucosa left hepatic ductal mucosa mucosa of organ of left hepatic duct mucous membrane of left hepatic duct organ mucosa of left hepatic duct uberon UBERON:0005003 mucosa of left hepatic duct A mucosa that is part of a left hepatic duct [Automatically generated definition]. OBOL:automatic left hepatic duct mucosa OBOL:automatic left hepatic duct mucosa of organ OBOL:automatic left hepatic duct mucous membrane OBOL:automatic left hepatic duct organ mucosa OBOL:automatic left hepatic ductal mucosa FMA:14693 mucosa of organ of left hepatic duct OBOL:automatic mucous membrane of left hepatic duct OBOL:automatic organ mucosa of left hepatic duct OBOL:automatic A mucosa that is part of a upper lip [Automatically generated definition]. FMA:59832 NCIT:C12224 SCTID:362088009 UMLS:C0226933 mucosa of organ of upper lip mucous membrane of upper lip organ mucosa of upper lip upper labial mucosa upper lip mucosa upper lip mucosa of organ upper lip mucous membrane upper lip organ mucosa uberon UBERON:0005031 mucosa of upper lip A mucosa that is part of a upper lip [Automatically generated definition]. OBOL:automatic UMLS:C0226933 ncithesaurus:Mucosa_of_the_Upper_Lip mucosa of organ of upper lip OBOL:automatic mucous membrane of upper lip OBOL:automatic organ mucosa of upper lip OBOL:automatic upper labial mucosa UBERON:cjm upper lip mucosa OBOL:automatic upper lip mucosa of organ OBOL:automatic upper lip mucous membrane OBOL:automatic upper lip organ mucosa OBOL:automatic A mucosa that is part of a lower lip [Automatically generated definition]. FMA:59833 NCIT:C12225 SCTID:362089001 UMLS:C0226939 lower labial mucosa lower lip mucosa lower lip mucosa of organ lower lip mucous membrane lower lip organ mucosa mucosa of organ of lower lip mucous membrane of lower lip organ mucosa of lower lip uberon UBERON:0005032 mucosa of lower lip A mucosa that is part of a lower lip [Automatically generated definition]. OBOL:automatic UMLS:C0226939 ncithesaurus:Mucosa_of_the_Lower_Lip lower labial mucosa UBERON:cjm lower lip mucosa OBOL:automatic lower lip mucosa of organ OBOL:automatic lower lip mucous membrane OBOL:automatic lower lip organ mucosa OBOL:automatic mucosa of organ of lower lip OBOL:automatic mucous membrane of lower lip OBOL:automatic organ mucosa of lower lip OBOL:automatic A mucosa that is part of a gallbladder [Automatically generated definition]. FMA:14662 SCTID:362196002 gall bladder mucosa gall bladder mucosa of organ gall bladder mucous membrane gall bladder organ mucosa gallbladder mucosa gallbladder mucosa of organ gallbladder mucous membrane gallbladder organ mucosa mucosa of gall bladder mucosa of organ of gall bladder mucosa of organ of gallbladder mucous membrane of gall bladder mucous membrane of gallbladder organ mucosa of gall bladder organ mucosa of gallbladder tunica mucosa (vesica biliaris) tunica mucosa vesicae biliaris uberon UBERON:0005033 mucosa of gallbladder A mucosa that is part of a gallbladder [Automatically generated definition]. OBOL:automatic gall bladder mucosa OBOL:automatic gall bladder mucosa of organ OBOL:automatic gall bladder mucous membrane OBOL:automatic gall bladder organ mucosa OBOL:automatic gallbladder mucosa OBOL:automatic gallbladder mucosa of organ OBOL:automatic gallbladder mucous membrane OBOL:automatic gallbladder organ mucosa OBOL:automatic mucosa of gall bladder OBOL:automatic mucosa of organ of gall bladder OBOL:automatic mucosa of organ of gallbladder OBOL:automatic mucous membrane of gall bladder OBOL:automatic mucous membrane of gallbladder OBOL:automatic organ mucosa of gall bladder OBOL:automatic organ mucosa of gallbladder OBOL:automatic tunica mucosa (vesica biliaris) FMA:14662 tunica mucosa vesicae biliaris FMA:14662 FMA:TA An external genitalia that is part of a female reproductive system [Automatically generated definition]. in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126] BTO:0003100 EMAPA:30984 FMA:45649 SCTID:362234008 galen:FemaleExternalGenitalia external female genital organ external genitalia of female reproductive system female external genitalia uberon organa genitalia feminina externa UBERON:0005056 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 external female genitalia An external genitalia that is part of a female reproductive system [Automatically generated definition]. OBOL:automatic external female genital organ BTO:0003100 external genitalia of female reproductive system OBOL:automatic female external genitalia FMA:45649 organa genitalia feminina externa BTO:0003100 An organ that is part of a immune system [Automatically generated definition]. immune system organ uberon UBERON:0005057 immune organ An organ that is part of a immune system [Automatically generated definition]. OBOL:automatic A gland that is part of a hemolymphoid system [Automatically generated definition]. hemopoietic or lymphoid organ EMAPA:18766 MA:0002962 hemopoietic or lymphoid gland uberon haemolymphoid system gland UBERON:0005058 hemolymphoid system gland A gland that is part of a hemolymphoid system [Automatically generated definition]. OBOL:automatic hemopoietic or lymphoid organ GO:0048534 hemopoietic or lymphoid gland http://orcid.org/0000-0002-6601-2165 haemolymphoid system gland EMAPA:18766 The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 NCIT:C34224 SCTID:361463007 UMLS:C0814992 Wikipedia:Neural_groove XAO:0000248 neuronames:1363 uberon UBERON:0005061 neural groove The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. GO:0001842 Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. Wikipedia:Neural_groove UMLS:C0814992 ncithesaurus:Neural_Groove One of the two elevated edges of the neural groove[GO,MP]. In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 SCTID:361461009 UMLS:C0814993 Wikipedia:Neural_fold XAO:0004087 neuronames:1364 medullary fold uberon UBERON:0005062 neural fold One of the two elevated edges of the neural groove[GO,MP]. GO:0001842 MP:0011256 Wikipedia:Neural_fold In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. Wikipedia:Neural_fold UMLS:C0814993 ncithesaurus:Neural_Fold medullary fold MP:0011256 Missing definition for term UBERON:0005064. Please replace it using linked reference. uberon UBERON:0005064 left ventricular trabecular myocardium GO Missing definition for term UBERON:0005064. Please replace it using linked reference. GO:0003225 Missing definition for term UBERON:0005066. Please replace it using linked reference. uberon UBERON:0005066 right ventricular trabecular myocardium GO Missing definition for term UBERON:0005066. Please replace it using linked reference. GO:0003227 A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 uberon neural tube rod UBERON:0005068 neural rod A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. GO:0014024 ZFA:0000133 An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000133 TAO ZFIN:curator neural tube rod GO:0014027 An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. hindbrain-spinal cord boundary region uberon UBERON:0005076 hindbrain-spinal cord boundary An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. OBOL:automatic A hole in a tube[GO]. AEO:0000078 EHDAA2:0004618 RETIRED_EHDAA2:0003078 uberon UBERON:0005082 tube lumen A hole in a tube[GO]. GO:0060609 An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures AEO:0000218 uberon epithelial placode UBERON:0005085 ectodermal placode An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. GO:0060788 in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures GO https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347 epithelial placode AEO:0000112 Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila EMAPA:32715 FMA:30316 musculus uberon muscle muscle element UBERON:0005090 muscle structure Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. GO:0061061 musculus FMA:30316 Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG] EHDAA2:0001841 EHDAA:484 EMAPA:16239 FMA:70318 VHOG:0000489 sinus venosus right horn uberon UBERON:0005092 right horn of sinus venosus FMA Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG] 2012-09-17 VHOG:0000489 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003 http://bgee.unil.ch/ sinus venosus right horn VHOG:0000489 A bud is a protrusion that forms from an epithelial sheet by localized folding. BTO:0001639 uberon UBERON:0005153 epithelial bud A bud is a protrusion that forms from an epithelial sheet by localized folding. GO:0060572 Any anatomical structure that is part of the reproductive system. reproductive system element reproductive system structure uberon UBERON:0005156 reproductive structure Any anatomical structure that is part of the reproductive system. http://orcid.org/0000-0002-6601-2165 An epithelial sheet bent on a linear axis. uberon UBERON:0005157 epithelial fold An epithelial sheet bent on a linear axis. GO:0060571 The functional tissue of the central nervous system consisting of neurons and glial cells. CNS parenchyma central nervous system parenchyma parenchyma of CNS parenchyma of central nervous system uberon UBERON:0005158 parenchyma of central nervous system The functional tissue of the central nervous system consisting of neurons and glial cells. CL:tm https://github.com/obophenotype/uberon/issues/8 CNS parenchyma OBOL:automatic central nervous system parenchyma OBOL:automatic parenchyma of CNS OBOL:automatic A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' AAO:0011000 CARO:0001000 FBbt:00007060 FMA:83115 multi-cell-component structure multi-cell-part structure uberon cell part cluster UBERON:0005162 multi cell part structure A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. CARO:0001000 we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' CARO FMA FBbt:00007060 multi-cell-component structure CARO:0001000 multi-cell-part structure CARO:0001000 cell part cluster FMA:83115 Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same A duct that carries bile from the liver to the small intestine.[TAO] The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG] The hepatic duct is the duct that leads from the liver to the bile duct[GO]. EHDAA2:0000741 EHDAA:3049 EMAPA:16843 FMA:71891 MA:0000357 NCIT:C32730 SCTID:245399002 UMLS:C0917710 VHOG:0000219 galen:HepaticDuct uberon UBERON:0005171 hepatic duct Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). http://orcid.org/0000-0002-6601-2165 A duct that carries bile from the liver to the small intestine.[TAO] 2012-08-14 TAO:0001100 TAO ZFIN:curator The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG] 2012-09-17 VHOG:0000219 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/hepatic+duct The hepatic duct is the duct that leads from the liver to the bile duct[GO]. GO:0061011 UMLS:C0917710 ncithesaurus:Hepatic_Duct An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 SCTID:272631008 abdomen organ uberon UBERON:0005172 abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. http://orcid.org/0000-0002-6601-2165 abdomen organ MA:0000522 An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:0000529 abdominal segment organ uberon UBERON:0005173 abdominal segment element An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. http://orcid.org/0000-0002-6601-2165 EMAPA:37062 MA:th abdominal segment organ MA:0000529 An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. EMAPA:37274 MA:0001901 back organ dorsal region organ uberon UBERON:0005174 dorsal region element An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. http://orcid.org/0000-0002-6601-2165 EMAPA:37274 MA:th back organ MA:0001901 An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:0000516 trunk organ uberon UBERON:0005177 trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. http://orcid.org/0000-0002-6601-2165 EMAPA:37270 MA:th trunk organ MA:0000516 An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:0000557 thoracic cavity organ uberon UBERON:0005178 thoracic cavity element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. http://orcid.org/0000-0002-6601-2165 EMAPA:37273 MA:th thoracic cavity organ MA:0000557 An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. EMAPA:37275 MA:0000543 pelvic element pelvis organ pelvis region organ uberon UBERON:0005179 pelvic region element An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. http://orcid.org/0000-0002-6601-2165 EMAPA:37275 MA:th pelvis organ MA:0000543 An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:0000563 uberon upper body organ UBERON:0005181 thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. http://orcid.org/0000-0002-6601-2165 EMAPA:37271 MA:th upper body organ MA:0000563 A vein that is part of a thorax [Automatically generated definition]. EMAPA:37197 MA:0002235 NCIT:C53142 SCTID:281472008 UMLS:C0226629 uberon UBERON:0005194 thoracic vein A vein that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37197 MA:th UMLS:C0226629 ncithesaurus:Thoracic_Vein An external ectoderm that is part of a optic eminence [Automatically generated definition]. EMAPA:16539 RETIRED_EHDAA2:0001311 VHOG:0000520 uberon UBERON:0005216 optic eminence surface ectoderm true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An external ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic A parenchyma that is part of a right lobe of liver [Automatically generated definition]. EHDAA2:0001010 EMAPA:18317 FMA:71657 VHOG:0000840 parenchyma of right lobe of liver uberon UBERON:0005221 liver right lobe parenchyma A parenchyma that is part of a right lobe of liver [Automatically generated definition]. OBOL:automatic parenchyma of right lobe of liver FMA:71657 A parenchyma that is part of a left lobe of liver [Automatically generated definition]. EHDAA2:0001002 EMAPA:18310 FMA:71658 VHOG:0000839 parenchyma of left lobe of liver uberon UBERON:0005222 liver left lobe parenchyma A parenchyma that is part of a left lobe of liver [Automatically generated definition]. OBOL:automatic parenchyma of left lobe of liver FMA:71658 An ectoderm that is part of a medial nasal prominence [Automatically generated definition]. EHDAA2:0001078 EMAPA:16809 FMA:312675 VHOG:0000803 uberon UBERON:0005233 medial-nasal process ectoderm An ectoderm that is part of a medial nasal prominence [Automatically generated definition]. OBOL:automatic An ectoderm that is part of a optic eminence [Automatically generated definition]. EHDAA:940 EMAPA:16539 RETIRED_EHDAA2:0001309 VHOG:0001105 uberon UBERON:0005234 optic eminence ectoderm An ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] EHDAA2:0001154 EMAPA:17078 VHOG:0000320 metencephalon basal plate uberon UBERON:0005239 basal plate metencephalon The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] 2012-09-17 VHOG:0000320 VHOG http://bgee.unil.ch/ metencephalon basal plate EHDAA2:0001154 An endocardium that is part of a interventricular septum [Automatically generated definition]. TODO - split? EHDAA2:0000886 EHDAA2:0000887 FMA:83584 VHOG:0000615 endocardium of interventricular septum uberon interventricular septum endocardial tissue UBERON:0005243 interventricular septum endocardium An endocardium that is part of a interventricular septum [Automatically generated definition]. OBOL:automatic endocardium of interventricular septum FMA:83584 interventricular septum endocardial tissue VHOG:0000615 A myocardium that is part of a bulbus cordis [Automatically generated definition]. EMAPA:36488 VHOG:0000609 uberon bulbus cordis cardiac muscle UBERON:0005248 bulbus cordis myocardium A myocardium that is part of a bulbus cordis [Automatically generated definition]. OBOL:automatic bulbus cordis cardiac muscle VHOG:0000609 A gland that is part of a stomodeum. check this VHOG:0000658 stomatodaeum gland uberon UBERON:0005250 stomatodeum gland A gland that is part of a stomodeum. OBOL:automatic stomatodaeum gland VHOG:0000658 An anatomical cavity that is part of a yolk sac [Automatically generated definition]. In mammals, the yolk sac cavity contains fluid rather than platelets in EHDAA2, there are separate primary and secondary yolk sac cavities EMAPA:16055 FMA:63942 VHOG:0000843 cavity of yolk sac yolk sac lumen uberon yolk sac space UBERON:0005251 yolk sac cavity An anatomical cavity that is part of a yolk sac [Automatically generated definition]. OBOL:automatic In mammals, the yolk sac cavity contains fluid rather than platelets ISBN:0073040584 in EHDAA2, there are separate primary and secondary yolk sac cavities EHDAA2 cavity of yolk sac FMA:63942 yolk sac space FMA:63942 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 EHDAA2:0000732 EHDAA:179 EMAPA:16098 EMAPA_RETIRED:16269 FMA:76622 TAO:0000113 VHOG:0000332 ZFA:0000113 cephalic mesenchyme uberon cranial mesenchyme desmocranium UBERON:0005253 head mesenchyme EHDAA2 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. ISBN:0683400088 MP:0011260 Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000113 TAO ZFIN:curator cephalic mesenchyme MP:0011260 cranial mesenchyme MGI:anna desmocranium FMA:76622 Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 EHDAA:377 EMAPA:16177 TAO:0000081 VHOG:0000281 ZFA:0000081 uberon trunk and cervical mesenchyme UBERON:0005256 trunk mesenchyme EHDAA2 Mesenchyme that is part of a developing trunk. OBOL:automatic trunk and cervical mesenchyme EHDAA2:0002092 The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 DHBA:10662 EHDAA2:0001207 EHDAA:5526 EMAPA:17082 HBA:9512 MA:0000205 MESH:D054024 VHOG:0000456 Wikipedia:Myelencephalon uberon myelencephalon (medulla oblongata) UBERON:0005290 myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. BTO:0000758 Wikipedia:Myelencephalon The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] 2012-09-17 VHOG:0000456 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/myelencephalon The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000456 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ MESH:D054024 https://github.com/biopragmatics/biomappings myelencephalon (medulla oblongata) DHBA:10662 A portion of tissue that is part of an embryo. CALOHA:TS-2100 portion of embryonic tissue uberon developing tissue UBERON:0005291 embryonic tissue A portion of tissue that is part of an embryo. OBOL:automatic portion of embryonic tissue OBOL:automatic Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. BTO:0003360 CALOHA:TS-2119 EFO:0001406 MAT:0000061 MIAA:0000061 extra-embryonic tissue uberon UBERON:0005292 extraembryonic tissue Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. https://orcid.org/0000-0002-6601-2165 The endothelial lining of the endocardium. FMA:83596 endocardium endothelium endothelium of endocardium uberon UBERON:0005316 endocardial endothelium The endothelial lining of the endocardium. UBERON:cjm endocardium endothelium FMA:83596 endothelium of endocardium FMA:83596 An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. BTO:0000137 pulmonary artery endothelial tube uberon UBERON:0005317 pulmonary artery endothelium An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. GO:0061155 pulmonary artery endothelial tube GO:0061155 A lamina propria that is part of a mucosa of oral region. EMAPA:26947 lamina propria of oral mucosa uberon UBERON:0005334 oral lamina propria A lamina propria that is part of a mucosa of oral region. OBOL:automatic A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. FMA:13225 Wikipedia:Ventricular_outflow_tract XAO:0004140 heart ventricle outflow tract outflow part of ventricle ventricular outflow tract uberon UBERON:0005337 outflow tract of ventricle A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. Wikipedia:Ventricular_outflow_tract heart ventricle outflow tract MP:0010224 ventricular outflow tract Wikipedia:Ventricular_outflow_tract An outflow tract that is part of a aorta. merge with LVOT? EHDAA2:0001353 EMAPA:17329 MA:0000101 VHOG:0001394 uberon UBERON:0005338 outflow tract aortic component An outflow tract that is part of a aorta. OBOL:automatic merge with RVOT? EHDAA2:0001359 EHDAA:4401 EMAPA:17330 MA:0000102 VHOG:0001395 uberon UBERON:0005339 outflow tract pulmonary component An array of photoreceptors and any supporting cells found in an eye. FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 photoreceptor array An array of photoreceptors and any supporting cells found in an eye. https://orcid.org/0000-0002-6601-2165 FBbt:00004200 A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. directing or focusing light onto light receptors lens uberon UBERON:0005389 transparent eye structure A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. http://orcid.org/0000-0002-6601-2165 One of: the common carotid artery, or its branches, the external and internal carotid arteries. This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] AAO:0010217 BTO:0000168 CALOHA:TS-0116 EFO:0000818 EHDAA:6385 EMAPA:18609 EV:0100379 FMA:70504 GAID:478 MA:0001925 MAT:0000501 MESH:D002339 NCIT:C12687 SCTID:362040006 SCTID:69105007 TAO:0000097 UMLS:C0007272 VHOG:0000266 Wikipedia:Carotid_artery ZFA:0000097 galen:CarotidArtery carotid carotid artery subdivision of common carotid artery uberon common carotid arterial subdivision UBERON:0005396 carotid artery segment FMA One of: the common carotid artery, or its branches, the external and internal carotid arteries. Wikipedia:Carotid_artery https://sourceforge.net/tracker/?func=detail&aid=3486870&group_id=76834&atid=994764 Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000097 TAO ZFIN:curator UMLS:C0007272 ncithesaurus:Carotid_Artery carotid AAO:0010217 carotid artery MA:0001925 subdivision of common carotid artery FMA:70504 common carotid arterial subdivision FMA:70504 A sex gland that is part of a female reproductive system. BTO:0000254 MA:0000383 uberon UBERON:0005398 female reproductive gland A sex gland that is part of a female reproductive system. OBOL:automatic The part of the digestive system that excludes the hepatobiliary system. the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. BTO:0000058 CALOHA:TS-0407 EHDAA2:0000110 EHDAA:514 EMAPA:16246 EV:0100056 FMA:71132 GAID:294 MA:0000323 MESH:D041981 NCIT:C12378 SCTID:373871007 UMLS:C0012240 VHOG:0000412 galen:GastrointestinalTract uberon GI tract alimentary system alimentary tract gastro-intestinal system gastroenterological system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract UBERON:0005409 alimentary part of gastrointestinal system The part of the digestive system that excludes the hepatobiliary system. http://orcid.org/0000-0002-6601-2165 The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. ncithesaurus:Gastrointestinal_System All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] 2012-09-17 VHOG:0000412 VHOG ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3 http://bgee.unil.ch/ that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. MA UMLS:C0012240 ncithesaurus:Gastrointestinal_System GI tract GAID:294 alimentary system MA:0000323 alimentary tract MA:0000323 gastro-intestinal system FMA:71132 gastroenterological system UBERON:cjm gastrointestinal (GI) tract GAID:294 gastrointestinal system FMA:71132 gastrointestinal tract FMA:71132 A limb bud that develops into a forelimb or pectoral fin. Fin bud that develops into the pectoral fin.[TAO] While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] EFO:0003430 TAO:0000141 VHOG:0001754 VHOG_RETIRED:0001259 ZFA:0000141 forelimb - pectoral fin bud uberon pectoral fin bud pectoral fin buds UBERON:0005419 at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future pectoral appendage bud A limb bud that develops into a forelimb or pectoral fin. OBOL:automatic Fin bud that develops into the pectoral fin.[TAO] 2012-08-14 TAO:0000141 TAO ZFIN:curator While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] 2012-09-17 VHOG:0001754 VHOG DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004) http://bgee.unil.ch/ forelimb - pectoral fin bud VHOG:0001754 pectoral fin bud TAO:0000141 pectoral fin buds TAO:0000141 A limb bud that develops into a hindlimb or pelvic fin. Fin bud that develops into the pelvic fin.[TAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] EFO:0003469 TAO:0001384 VHOG:0001260 ZFA:0001384 hindlimb/pelvic fin bud uberon pelvic fin bud pelvic fin buds UBERON:0005420 at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future pelvic appendage bud A limb bud that develops into a hindlimb or pelvic fin. OBOL:automatic PMID:15893975 Fin bud that develops into the pelvic fin.[TAO] 2012-08-14 TAO:0001384 TAO ZFIN:curator Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001260 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ hindlimb/pelvic fin bud VHOG:0001260 pelvic fin bud TAO:0001384 pelvic fin buds ZFA:0001384 An apical ectodermal ridge that is part of a pectoral appendage bud. An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003487 EHDAA2:0000138 EMAPA:16778 TAO:0000085 TAO:0000736 VHOG:0001064 ZFA:0000085 AER forelimb apical ectodermal ridge forelimb apical ectodermal ridge pectoral fin bud upper limb bud apical ectodermal ridge wing AER wing apical ectodermal ridge uberon aer pectoral fin apical ectodermal ridge pectoral fin apical fold pectoral fin UBERON:0005421 pectoral appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pectoral appendage bud. OBOL:automatic An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001064 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] 2012-08-14 TAO:0000085 TAO ZFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001064 VHOG DOI:10.1111/j.1440-169X.2007.00942.x http://bgee.unil.ch/ AER forelimb VHOG:0001064 apical ectodermal ridge forelimb VHOG:0001064 apical ectodermal ridge pectoral fin bud ZFA:0000085 upper limb bud apical ectodermal ridge EHDAA2:0000138 wing AER Giesha:syn wing apical ectodermal ridge aer pectoral fin TAO:0000085 apical ectodermal ridge pectoral fin TAO:0000085 apical fold pectoral fin TAO:0000085 An apical ectodermal ridge that is part of a pelvic appendage bud. An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003681 EHDAA2:0003194 EMAPA:16892 TAO:0001385 VHOG:0001066 ZFA:0001385 apical ectodermal ridge hind limb apical ectodermal ridge hindlimb lower lmb bud apical ectodermal ridge uberon AER hindlimb apical ectodermal ridge pelvic fin bud leg AER UBERON:0005422 pelvic appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pelvic appendage bud. OBOL:automatic An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001066 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] 2012-08-14 TAO:0001385 TAO ZIFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001066 VHOG DOI:10.1111/j.1440-169X.2007.00942.x http://bgee.unil.ch/ apical ectodermal ridge hind limb VHOG:0001066 apical ectodermal ridge hindlimb VHOG:0001066 lower lmb bud apical ectodermal ridge EHDAA2:0003194 AER hindlimb VHOG:0001066 apical ectodermal ridge pelvic fin bud TAO:0001385 AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 uberon developing structure developmental structure developmental tissue UBERON:0005423 developing anatomical structure FBbt:00007006 developmental tissue MIAA:0000019 Portion of tissue that is the inner layer of the optic cup and will become the neural retina. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001304 EMAPA:16675 TAO:0001071 VHOG:0000490 ZFA:0001071 future neural retina future retinal neural layer inner layer optic cup optic cup inner layer presumptive retinas uberon future NR future neural epithelium future neural layer presumptive retina UBERON:0005425 presumptive neural retina Portion of tissue that is the inner layer of the optic cup and will become the neural retina. ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000490 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ inner layer optic cup ZFA:0001071 optic cup inner layer EHDAA2:0001304 presumptive retinas ZFA:0001071 future neural epithelium EMAPA:16675 future neural layer EMAPA:16675 presumptive retina TAO:0001071 Portion of tissue that gives rise to the lens. A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals EHDAA2:0000983 EHDAA:4737 EMAPA:17163 SCTID:361510002 TAO:0002205 VHOG:0001163 ZFA:0001679 hollow lens vesicle solid lens vesicle uberon immature lens lens mass presumptive lens UBERON:0005426 lens vesicle Portion of tissue that gives rise to the lens. ZFIN:curator https://sourceforge.net/tracker/?func=detail&atid=994726&aid=3514998&group_id=76834 A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] 2012-09-17 VHOG:0001163 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/lens+vesicle (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0001163 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals ZFA hollow lens vesicle solid lens vesicle ZFA:0001679 immature lens ZFA:0001679 lens mass ZFA:0001679 ZFIN:ZDB-PUB-091023-49 presumptive lens ZFA:0001679 Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 uberon UBERON:0005427 corneal primordium ZFA Obol ZFA Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. ZFIN:ZDB-PUB-061010-3 Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) EHDAA2:0002156 EHDAA:669 TAO:0000818 VHOG:0001208 XAO:0004191 ZFA:0000818 VNC uberon enteric neural crest post-otic neural crest UBERON:0005428 vagal neural crest Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. ZFIN:curator Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] 2012-08-14 TAO:0000818 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001208 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) filemaps.com VNC XAO:0004191 post-otic neural crest ZFA:0000818 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates. the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. EHDAA2:0004145 EHDAA:9826 EMAPA:36461 FMA:71008 RETIRED_EHDAA2:0000133 SCTID:361527005 saccus aorticus uberon UBERON:0005432 aortic sac EHDAA2 EHDAA2 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates. MP:0012510 the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. http://medical-dictionary.thefreedictionary.com/aortic+sac saccus aorticus FMA:24219 SCTID:123958008 cervical region neck subdivision region of neck subdivision of neck uberon UBERON:0005434 cervical region cervical region FMA:24219 neck subdivision FMA:24219 region of neck FMA:24219 subdivision of neck FMA:24219 In anatomy, the common hepatic artery is a short blood vessel that supplies oxygenated blood to the liver, pylorus (a part of the stomach), duodenum (a part of the small intestine) and pancreas. It arises from the celiac artery and has the following branches:. EHDAA2:0000308 EHDAA:8570 EMAPA:37206 FMA:14771 MA:0003094 SCTID:244263001 Wikipedia:Common_hepatic_artery galen:CommonHepaticArtery uberon arteria hepatica communis common hepatic UBERON:0005436 common hepatic artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb In anatomy, the common hepatic artery is a short blood vessel that supplies oxygenated blood to the liver, pylorus (a part of the stomach), duodenum (a part of the small intestine) and pancreas. It arises from the celiac artery and has the following branches:. Wikipedia:Common_hepatic_artery EMAPA:37206 MA:th arteria hepatica communis Wikipedia:Common_hepatic_artery common hepatic Wikipedia:Common_hepatic_artery The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa. A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG] It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG] todo - check placement of AAO class AAO:0000194 EHDAA2:0000552 EHDAA:10629 EMAPA:18712 FMA:53154 SCTID:369439002 VHOG:0001543 Wikipedia:Foramen_rotundum uberon foramen rotundum of the skull foramen rotundum ossis sphenoidalis round foramen UBERON:0005446 foramen rotundum http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa. Wikipedia:Foramen_rotundum A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG] 2012-09-17 VHOG:0001543 VHOG http://bgee.unil.ch/ It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG] 2012-09-17 VHOG:0001543 VHOG PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976) http://bgee.unil.ch/ todo - check placement of AAO class AAO foramen rotundum of the skull Wikipedia:Foramen_rotundum foramen rotundum ossis sphenoidalis Wikipedia:Foramen_rotundum round foramen VHOG:0001543 A vitelline vein that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000971 EMAPA:16380 EMAPA:16698 FMA:70307 SCTID:361446008 uberon UBERON:0005460 left vitelline vein A vitelline vein that is in the left side of a multicellular organism. OBOL:automatic A vitelline vein that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001766 EMAPA:16381 EMAPA:16699 FMA:70306 SCTID:361445007 uberon UBERON:0005472 right vitelline vein A vitelline vein that is in the right side of a multicellular organism. OBOL:automatic A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. sulcus limitans BAMS:slim BAMS:slm neuronames:629 neural tube lateral wall sulcus limitans uberon UBERON:0005478 sulcus limitans of neural tube EHDAA2 A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. http://medical-dictionary.thefreedictionary.com/Sulcus+limitans http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube lateral wall sulcus limitans EHDAA2:0001265 The paired veins that carry blood from the yolk sac back to the embryo. One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO] Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG] check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO EMAPA:36021 FMA:70305 NCIT:C34329 RETIRED_EHDAA2:0002209 SCTID:2730004 SCTID:308832003 UMLS:C0231091 VHOG:0000401 Wikipedia:Vitelline_veins XAO:0000376 XAO:0004147 embryonic vitelline vein vascular vitelline network vena vitellina uberon omphalomesenteric vein vein of omphalomesenteric system vitelline veins UBERON:0005487 vitelline vein http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png The paired veins that carry blood from the yolk sac back to the embryo. MGI:csmith MP:0010666 One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO] XAO XAO:0004147 Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG] 2012-09-17 VHOG:0000401 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 http://bgee.unil.ch/ check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO XAO UMLS:C0231091 ncithesaurus:Vitelline_Vein embryonic vitelline vein VHOG:0000401 vascular vitelline network XAO:0004147 vena vitellina Wikipedia:Vitelline_veins omphalomesenteric vein EMAPA:16244 vitelline veins XAO:0004147 Portion of tissue on the side of the lumen of the neural tube. EHDAA2:0001257 EHDAA:2873 EHDAA:912 EMAPA:16166 TAO:0001435 VHOG:0000513 ZFA:0001435 lateral wall neural tube uberon UBERON:0005496 neural tube lateral wall Portion of tissue on the side of the lumen of the neural tube. ZFA:0001435 lateral wall neural tube ZFA:0001435 todo - epidermis? todo - track down EHDAA2 class in new release In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm. EFO:0003643 EHDAA:257 EMAPA:16074 RETIRED_EHDAA2:0001273 TAO:0001178 VHOG:0001372 XAO:0004091 ZFA:0001178 non neural ectoderm epidermal ectoderm epithelial ectoderm uberon surface ectoderm ventral ectoderm UBERON:0005497 Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). non-neural ectoderm ZFA In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] 2012-09-17 VHOG:0001372 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ non neural ectoderm ZFA:0001178 epidermal ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest epithelial ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest surface ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest ventral ectoderm ZFA:0001178 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. BTO:0006179 EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16215 FMA:321916 SCTID:361522004 TAO:0000149 Wikipedia:Primitive_heart_tube ZFA:0000149 primitive heart tube early primitive heart tube uberon UBERON:0005498 primitive heart tube ZFA Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 BTO:0006179 https://github.com/biopragmatics/biomappings primitive heart tube EMAPA:16215 early primitive heart tube EMAPA:16208 A neural tube lateral wall that is part of a rhombomere. EMAPA:32819 EMAPA:35364 uberon future hindbrain lateral wall UBERON:0005501 rhombomere lateral wall A neural tube lateral wall that is part of a rhombomere. OBOL:automatic future hindbrain lateral wall EMAPA:35364 Cranial neural crest which gives rise to the trigeminal ganglion. todo - compare ZFA and EHDAA2 representation We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003484 EHDAA2:0002083 EHDAA:667 EMAPA:16170 TAO:0000080 VHOG:0000269 ZFA:0000080 uberon UBERON:0005563 trigeminal neural crest ZFA EHDAA2 EHDAA2 Cranial neural crest which gives rise to the trigeminal ganglion. ZFA:0000080 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000269 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ Portion of tissue that gives rise to the immature gonad. Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] this is a very broad grouping class EFO:0003651 EHDAA:5927 EMAPA:17204 RETIRED_EHDAA2:0002148 TAO:0001262 WBbt:0008366 ZFA:0001262 future gonad gonadal primordium primitive gonad undifferentiated gonad uberon immature gonad UBERON:0005564 gonad primordium Obol ZFA Portion of tissue that gives rise to the immature gonad. ZFA:0001262 Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] 2012-08-14 TAO:0001262 TAO ZFIN:curator future gonad http://orcid.org/0000-0002-6601-2165 gonadal primordium ZFA:0001262 primitive gonad http://orcid.org/0000-0002-6601-2165 undifferentiated gonad ZFA:0001262 immature gonad http://orcid.org/0000-0002-6601-2165 Somite located in the head region, caudal to the otic vesicle. in humans this includes somites 1-4 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2:0003437 EMAPA:16172 XAO:0000313 occipital somite uberon cranial somite UBERON:0005594 head somite EHDAA2 EHDAA2 Somite located in the head region, caudal to the otic vesicle. PMID:11830559 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) PMID:11830559 EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2 occipital somite PMID:11830559 XAO:0000313 cranial somite XAO:0000313 A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. AAO:0011059 EFO:0002578 EMAPA:36007 XAO:0001002 uberon lateral diverticula lung diverticulum lung endoderm UBERON:0005597 lung primordium XAO XAO A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. XAO:0001002 lateral diverticula XAO:0001002 lung diverticulum AAO:3010717 lung endoderm EFO:0002578 A somite that is part of a trunk. AAO:0010385 EHDAA2:0003438 EMAPA:16184 XAO:0000314 uberon UBERON:0005598 trunk somite A somite that is part of a trunk. OBOL:automatic The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum. The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG] EHDAA2:0000416 EHDAA:3001 EMAPA:17025 MA:0001618 NCIT:C34142 UMLS:C1512038 VHOG:0000352 Wikipedia:Dorsal_mesentery uberon dorsal mesentery UBERON:0005602 dorsal mesogastrium MA EHDAA2 EHDAA2 The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum. Wikipedia:Dorsal_mesentery The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG] 2012-09-17 VHOG:0000352 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/mesogastrium UMLS:C1512038 ncithesaurus:Dorsal_Mesogastrium dorsal mesentery Wikipedia:Dorsal_mesentery EMAPA:16844 MA:0001636 VHOG:0000215 extrahepatic part of the hepatic duct hepatic duct extrahepatic part uberon UBERON:0005604 extrahepatic part of hepatic duct MA MA extrahepatic part of the hepatic duct VHOG:0000215 hepatic duct extrahepatic part MA:0001636 A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Contributes to the arch of aorta in humans EHDAA2:0000936 EHDAA:404 EMAPA:16205 MA:0000478 SCTID:361403005 VHOG:0000484 uberon UBERON:0005613 left dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000484 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 http://bgee.unil.ch/ Contributes to the arch of aorta in humans http://emedicine.medscape.com/article/899609-overview A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm lens epithelium EHDAA2:0000984 EHDAA:9059 EMAPA:17304 EMAPA:17839 FMA:70612 MA:0001302 NCIT:C33641 RETIRED_EHDAA2:0000976 SCTID:362521008 UMLS:C1182652 VHOG:0001425 lens subcapsular epithelium subcapsular lens epithelium uberon anterior epithelium of lens vesicle anterior surface of lens UBERON:0005614 lens anterior epithelium A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. http://orcid.org/0000-0002-6601-2165 UMLS:C1182652 ncithesaurus:Subcapsular_Epithelium_of_the_Lens lens subcapsular epithelium http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm subcapsular lens epithelium FMA:70612 anterior epithelium of lens vesicle EMAPA:17304 anterior surface of lens FMA:58889 Arteries which arise from the abdominal aorta and distribute to most of the intestines. includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries BTO:0000779 EHDAA2:0001123 EHDAA:4343 EMAPA:17312 MA:0002003 MESH:D008638 NCIT:C52975 SCTID:281084003 UMLS:C0025465 VHOG:0001117 Wikipedia:Mesenteric_artery XAO:0000370 uberon UBERON:0005616 mesenteric artery Arteries which arise from the abdominal aorta and distribute to most of the intestines. MESH:A07.231.114.565 Wikipedia:Mesenteric_artery UMLS:C0025465 ncithesaurus:Mesenteric_Artery A vein that returns blood from the intestines. In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein BTO:0002781 EHDAA:4442 EMAPA:17348 MA:0002177 MESH:D008642 NCIT:C53055 RETIRED_EHDAA2:0001125 SCTID:304045008 UMLS:C0025473 Wikipedia:Mesenteric_vein uberon intestinal vein UBERON:0005617 mesenteric vein A vein that returns blood from the intestines. MESH:A07.231.908.670.385 Wikipedia:Mesenteric_vein UMLS:C0025473 ncithesaurus:Mesenteric_Vein intestinal vein http://orcid.org/0000-0002-6601-2165 A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Normally regresses in humans EHDAA2:0001720 EHDAA:406 EMAPA:16206 MA:0000479 SCTID:361404004 VHOG:0000485 uberon UBERON:0005622 right dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000485 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 http://bgee.unil.ch/ Normally regresses in humans http://emedicine.medscape.com/article/899609-overview Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)] EHDAA2 is a mereological sum. EHDAA2:0004714 FMA:305915 MESH:D005321 SCTID:362840007 uberon UBERON:0005631 extraembryonic membrane https://github.com/obophenotype/uberon/wiki/Modeling-extraembryonic-membranes Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. ISBN:0073040584 EHDAA2 is a mereological sum. EHDAA2 MESH:D005321 https://github.com/biopragmatics/biomappings An epithelium that is part of a pylorus. EHDAA2:0001582 EMAPA:17633 RETIRED_EHDAA2:0001927 uberon UBERON:0005637 pyloric region epithelium An epithelium that is part of a pylorus. OBOL:automatic An epithelium that is part of a anterior chamber of eyeball. EHDAA2:0000130 uberon UBERON:0005638 anterior chamber epithelium An epithelium that is part of a anterior chamber of eyeball. OBOL:automatic An epithelium that is part of a lens vesicle. EHDAA2:0000987 EMAPA:17165 VHOG:0000532 uberon UBERON:0005656 lens vesicle epithelium An epithelium that is part of a lens vesicle. OBOL:automatic An ectoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004032 EMAPA:16762 EMAPA:16764 EMAPA:16768 RETIRED_EHDAA2:0000094 VHOG:0001095 4th pharyngeal arch ectoderm uberon UBERON:0005662 4th arch ectoderm An ectoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001095 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch ectoderm VHOG:0001095 An endoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004033 EMAPA:16765 EMAPA:16767 EMAPA:16769 RETIRED_EHDAA2:0000095 VHOG:0001092 4th pharyngeal arch endoderm uberon UBERON:0005666 4th arch endoderm An endoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001092 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch endoderm VHOG:0001092 A mesothelium that is part of a peritoneal cavity. we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood peritoneum BTO:0003156 EHDAA2:0001447 EMAPA:16139 FMA:18147 SCTID:34073007 mesothelium of peritoneal component mesothelium of peritoneum peritoneal mesothelium peritoneum mesothelium uberon UBERON:0005669 peritoneal cavity mesothelium A mesothelium that is part of a peritoneal cavity. OBOL:automatic we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood EMAPA peritoneum EMAPA:16139 mesothelium of peritoneal component EMAPA:16139 mesothelium of peritoneum FMA:18147 peritoneal mesothelium BTO:0003156 EMAPA:16139 peritoneum mesothelium FMA:18147 An endothelium that is part of a right lung. EHDAA2:0001755 uberon UBERON:0005672 right lung endothelium An endothelium that is part of a right lung. OBOL:automatic An endothelium that is part of a left lung. EHDAA2:0000961 uberon UBERON:0005673 left lung endothelium An endothelium that is part of a left lung. OBOL:automatic A dorsal mesentery that is part of a midgut. EMAPA:16722 EMAPA:17040 EMAPA:18671 RETIRED_EHDAA2:0001187 SCTID:361434009 uberon UBERON:0005685 midgut dorsal mesentery A dorsal mesentery that is part of a midgut. OBOL:automatic An anatomical cavity that is part of a lens vesicle. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] cavity of lens lens cavity EHDAA2:0000986 EMAPA:17164 VHOG:0000531 cavity of lens vesicle uberon UBERON:0005688 lens vesicle cavity An anatomical cavity that is part of a lens vesicle. OBOL:automatic (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000531 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ lens cavity EHDAA2:0000986 cavity of lens vesicle EMAPA:17164 Mesenchyme that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000096 EHDAA:1677 EMAPA:16770 FMA:295702 VHOG:0001052 4th pharyngeal arch mesenchyme uberon 4th branchial arch mesenchyme pharyngeal arch 4 mesenchyme UBERON:0005691 4th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001052 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch mesenchyme VHOG:0001052 Mesenchyme that is part of a optic eminence. EHDAA:942 EMAPA:16324 RETIRED_EHDAA2:0001310 VHOG:0001073 uberon UBERON:0005702 optic eminence mesenchyme Mesenchyme that is part of a optic eminence. OBOL:automatic A mesentery of duodenum that is part of a foregut. EHDAA2:0000564 uberon UBERON:0005711 foregut duodenum mesentery A mesentery of duodenum that is part of a foregut. OBOL:automatic A mesentery of duodenum that is part of a midgut. EHDAA2:0001193 uberon UBERON:0005712 midgut duodenum mesentery A mesentery of duodenum that is part of a midgut. OBOL:automatic A venous system that is part of a hindbrain. EHDAA2:0000776 EMAPA:18632 VHOG:0001322 uberon rhombencephalon venous system UBERON:0005720 hindbrain venous system A venous system that is part of a hindbrain. OBOL:automatic rhombencephalon venous system VHOG:0001322 BILA:0000139 uberon UBERON:0005726 chemosensory system EHDAA2:0000474 EMAPA:31862 EMAPA:31863 FMA:296719 VHOG:0000616 extra-embryonic mesoderm extraembryonic mesenchyme uberon UBERON:0005728 extraembryonic mesoderm EHDAA2 EHDAA2 A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. Embryonic region that develops into the pectoral fin bud.[TAO] TAO:0001453 ZFA:0001453 pectoral appendage field of lateral plate mesoderm pectoral fin field uberon UBERON:0005729 pectoral appendage field A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pectoral fin bud.[TAO] 2012-08-14 TAO:0001453 TAO ZFIN:curator pectoral fin field ZFA:0001453 A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. Embryonic region that develops into the pelvic fin bud.[TAO] TAO:0001454 ZFA:0001454 pelvic appendage field of lateral plate mesoderm pelvic fin field uberon UBERON:0005730 pelvic appendage field A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pelvic fin bud.[TAO] 2012-08-14 TAO:0001454 TAO ZFIN:curator pelvic fin field ZFA:0001454 A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this. limb/fin field of lateral plate mesoderm paired limb/fin field uberon UBERON:0005732 paired limb/fin field ISBN:9780878932504 ZFA-inferred A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. ISBN:9780878932504 The outermost layer of a blood vessel, composed mainly of fibrous tissue. TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]. BTO:0002010 EMAPA:36299 NCIT:C33818 SCTID:61066005 UMLS:C0225342 Wikipedia:Tunica_externa_(vessels) adventitia externa tunica adventitia tunica adventitia of vessel uberon external coat tunica adventitia vasorum tunica externa vasorum UBERON:0005734 tunica adventitia of blood vessel https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg cjm The outermost layer of a blood vessel, composed mainly of fibrous tissue. ISBN:0073040584 Wikipedia:Tunica_externa_(vessels) The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]. Wikipedia:Tunica_externa_(vessels) UMLS:C0225342 ncithesaurus:Tunica_Adventitia adventitia externa Wikipedia:Tunica_externa_(vessels) tunica adventitia Wikipedia:Tunica_externa_(vessels) tunica adventitia of vessel Wikipedia:Tunica_externa_(vessels) external coat Wikipedia:Tunica_externa_(vessels) tunica adventitia vasorum Wikipedia:Tunica_externa_(vessels) tunica externa vasorum Wikipedia:Tunica_externa_(vessels) A tunica intima that is part of a artery. EMAPA:36293 EV:0100028 FMA:14272 SCTID:40022005 galen:IntimaOfArtery arterial intima tunica interna (intima)(arteriae) uberon UBERON:0005740 tunica intima of artery A tunica intima that is part of a artery. OBOL:automatic arterial intima EV:0100028 tunica interna (intima)(arteriae) FMA:14272 An outermost connective tissue covering of an organ, vessel, or other structure[WP]. BTO:0002010 FMA:45635 MESH:D063194 SCTID:30180000 Wikipedia:Adventitia tunica advetitia tunica externa uberon UBERON:0005742 adventitia http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg An outermost connective tissue covering of an organ, vessel, or other structure[WP]. Wikipedia:Adventitia MESH:D063194 https://github.com/biopragmatics/biomappings tunica advetitia Wikipedia:Adventitia tunica externa FMA:45635 Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). foramen AAO:0010438 TAO:0001736 VHOG:0001760 ZFA:0005386 uberon UBERON:0005744 bone foramen http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. TAO:curator in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). FMA foramen ZFA:0005386 An acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 uberon UBERON:0005764 acellular membrane An acellular anatomical structure that is the bounding layer of a anatomical structure. OBOL:automatic An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 GAID:915 NCIT:C13191 SCTID:68989006 UMLS:C0004799 Wikipedia:Basement_membrane basement membrane of connective tissue membrana basalis uberon basement membrane UBERON:0005769 basement membrane of epithelium FMA An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. Wikipedia:Basement_membrane http://orcid.org/0000-0002-6601-2165 http://palaeos.com/metazoa/porifera/homoscleromorpha.html UMLS:C0004799 ncithesaurus:Basement_Membrane basement membrane of connective tissue FMA:63872 membrana basalis Wikipedia:Basement_membrane basement membrane FMA:63872 Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. FMA:13087 NCIT:C34027 SCTID:119203005 UMLS:C0506947 aortic section uberon aortic segment portion of aorta segment of aorta UBERON:0005800 section of aorta Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. ncithesaurus:Aortic_Segment UMLS:C0506947 ncithesaurus:Aortic_Segment aortic segment FMA:13087 segment of aorta FMA:13087 The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch relationship loss: part_of axial vasculature (TAO:0001073)[TAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] AAO:0011029 BTO:0004673 EHDAA:402 EMAPA:18606 SCTID:338637006 TAO:0000014 VHOG:0000264 Wikipedia:Dorsal_aorta XAO:0000051 ZFA:0000014 DA aorta dorsalis uberon aortae dorsales dorsal aorta root dorsal aortae dorsal aortic root dorsal aortæ UBERON:0005805 dorsal aorta http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. GO:0035907 https://sourceforge.net/p/geneontology/ontology-requests/8525/ Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Wikipedia:Dorsal_aorta Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000014 TAO ZFIN:curator The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch BTO:0004673 relationship loss: part_of axial vasculature (TAO:0001073)[TAO] 2012-08-14 TAO:0000014 TAO When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000264 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ DA ZFA:0000014 aorta dorsalis XAO:0000051 aortae dorsales Wikipedia:Dorsal_aorta dorsal aorta root VHOG:0000264 dorsal aortae Wikipedia:Dorsal_aorta dorsal aortic root VHOG:0000264 dorsal aortæ Wikipedia:Dorsal_aorta In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. FMA:45628 MESH:D011168 NCIT:C33344 SCTID:362063001 UMLS:C0226727 Wikipedia:Portal_venous_system portal venous system uberon UBERON:0005806 portal system In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. Wikipedia:Portal_venous_system UMLS:C0226727 ncithesaurus:Portal_Venous_System portal venous system FMA:45628 This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term BIRNLEX:2665 FMA:62420 MA:0003080 SCTID:278748001 axial part of spinal cord axial regional part of spinal cord segment of spinal cord uberon spinal neuromeres UBERON:0005844 spinal cord segment axial part of spinal cord BIRNLEX:2665 axial regional part of spinal cord BIRNLEX:2665 segment of spinal cord FMA:62420 spinal neuromeres TAO:0001332 A spinal cord segment that adjacent_to a caudal region. FMA:256635 MA:0003084 SCTID:278753006 neuronames:1656 coccygeal segment of spinal cord coccygeal segments of spinal cord [1-3] pars coccygea medullae spinalis segmenta coccygea medullae spinalis [1-3] uberon segmenta coccygea UBERON:0005845 for spinal cord segments, we treat coccygeal/caudal as synonyms - we only differentiate where bone is concerned caudal segment of spinal cord A spinal cord segment that adjacent_to a caudal region. OBOL:automatic coccygeal segment of spinal cord FMA:256635 coccygeal segments of spinal cord [1-3] FMA:256635 pars coccygea medullae spinalis FMA:256635 FMA:TA segmenta coccygea medullae spinalis [1-3] FMA:256635 FMA:TA segmenta coccygea NeuroNames:1656 A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 EHDAA:8979 mesenchyme condensation uberon UBERON:0005856 developing mesenchymal condensation AEO cjm AEO-modified-relation A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 mesenchyme condensation EMAPA:25351 Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. isa cell condensation in VSAO; has_part chondroblast in AEO AEO:0000147 EHDAA2_RETIRED:0003147 EMAPA:32731 VSAO:0000092 XAO:0004022 cartilage condensation cartilagenous condensation chondrogenic condensation uberon UBERON:0005863 cartilaginous condensation AEO AEO Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. GO:curator isa cell condensation in VSAO; has_part chondroblast in AEO VSAO cartilage condensation EMAPA:25353 cartilagenous condensation EHDAA2:0003147 chondrogenic condensation VSAO:0000092 UBERON:0008714 AEO:0000149 EHDAA2_RETIRED:0003149 pre muscle mass premuscle mass uberon UBERON:0005865 pre-muscle condensation AEO A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. AEO:0000150 EHDAA2:0003150 EMAPA:32736 pre-chondrogenic condensation precartilage condensation precartilagenous condensation prechondrogenic condensation uberon UBERON:0005866 pre-cartilage condensation AEO AEO A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. AEO:0000150 AEO:JB A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. http://dictionary.reference.com/browse/precartilage The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip. check develops_from EHDAA2:0001061 EHDAA:5871 EMAPA:17355 FMA:293051 NCIT:C34204 UMLS:C1512982 Wikipedia:Mandibular_prominence uberon mandibular process mandibular swelling prominentia mandibularis UBERON:0005867 mandibular prominence The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip. ISBN:0-683-40008-8 MP:0010939 UMLS:C1512982 ncithesaurus:Mandibular_Prominence mandibular process Wikipedia:Mandibular_prominence mandibular swelling https://orcid.org/0000-0002-6601-2165 prominentia mandibularis Wikipedia:Mandibular_prominence The paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw. EHDAA2:0001070 EHDAA:5877 EMAPA:17359 FMA:293049 NCIT:C34206 SCTID:346355001 UMLS:C1513037 Wikipedia:Maxillary_prominence embryonic maxillary process maxillary process maxillary process of embryo uberon prominentia maxilaris UBERON:0005868 maxillary prominence http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png The paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw. ISBN:0-683-40008-8 MP:0010940 UMLS:C1513037 ncithesaurus:Maxillary_Prominence maxillary process EHDAA2:0001070 prominentia maxilaris Wikipedia:Maxillary_prominence Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TODO - check An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] AAO:0010199 BTO:0004675 FMA:49187 MESH:D009778 SCTID:362618001 TAO:0001414 XAO:0003173 ZFA:0001414 neuronames:2431 basicranial region occipital part of head occipital region of head uberon back of head UBERON:0005902 occipital region Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TAO:0001414 UBERONREF:0000007 An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] 2012-06-20 AAO:0010199 AAO AAO:EJS Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] 2012-08-14 TAO:0001414 TAO TAO:MAH MESH:D009778 https://github.com/biopragmatics/biomappings basicranial region ZFA:0001414 occipital part of head FMA:49187 occipital region of head FMA:49187 back of head FMA:49187 Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]. FMA:9689 SCTID:362890006 uberon UBERON:0005906 See notes for serous membrane serous sac Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]. FMA:9689 https://github.com/obophenotype/uberon/issues/86 Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]. FMA:69065 endoderm-derived epithelium endoepithelium uberon UBERON:0005911 endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]. FMA:69065 FMA:10483 bone organ zone uberon UBERON:0005913 zone of bone organ FMA bone organ zone FMA:10483 Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 UMLS:C0222645 VSAO:0000056 Wikipedia:Axial_skeleton XAO:0004011 uberon skeleton axiale UBERON:0005944 axial skeleton plus cranial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. FMA:71221 VSAO:0000056 Wikipedia:Axial_skeleton https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000056 VSAO PSPUB:0000170 UMLS:C0222645 ncithesaurus:Axial_Skeleton skeleton axiale Wikipedia:Axial_skeleton trabecula trabecular cartilage EFO:0003677 TAO:0001321 ZFA:0001321 neurocranial trabeculae uberon UBERON:0005945 neurocranial trabecula ZFA ZFA trabecula ZFA:0001321 trabecular cartilage ZFA:0001321 neurocranial trabeculae ZFA:0001321 An outflow tract that is part of a cardiac atrium. FMA:14141 outflow part of atrium uberon UBERON:0005946 outflow tract of atrium An outflow tract that is part of a cardiac atrium. OBOL:automatic outflow part of atrium FMA:14141 Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk. infundibulum EMAPA:37926 FMA:7216 NCIT:C61368 SCTID:244379003 UMLS:C1881209 RVOT conus arteriosus (infundibulum) infundibulum of right ventricle outflow tract of right ventricle pulmonary conus right ventricle pulmonary outflow tract right ventricular outflow tract uberon arterial cone conus arteriosus pulmonary cone pulmonary conus UBERON:0005953 outflow part of right ventricle PMID:17276708 Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk. MP:0010428 infundibulum Wikipedia:Conus_arteriosus EMAPA:37926 MA:th UMLS:C1881209 ncithesaurus:Infundibulum RVOT MP:0010428 conus arteriosus (infundibulum) FMA:7216 infundibulum of right ventricle FMA:7216 MP:0010428 outflow tract of right ventricle FMA:7216 pulmonary conus FMA:7216 right ventricle pulmonary outflow tract MP:0010428 right ventricular outflow tract MP:0010428 arterial cone MP:0010428 conus arteriosus MP:0010428 pulmonary cone MP:0010428 pulmonary conus MP:0010428 Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. EMAPA:37925 FMA:9473 SCTID:264070001 Wikipedia:Aortic_vestibule LVOT Sibson vestibule aortic vestibule heart left ventricle outflow tract left ventricular outflow left ventricular outflow tract outflow tract of left ventricle vestibulum aortae uberon UBERON:0005956 outflow part of left ventricle Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. MP:0010429 EMAPA:37925 MA:th LVOT MP:0010429 Sibson vestibule MP:0010429 aortic vestibule FMA:9473 MP:0010429 heart left ventricle outflow tract MP:0010429 left ventricular outflow FMA:9473 left ventricular outflow tract HP:0011103 outflow tract of left ventricle FMA:9473 vestibulum aortae FMA:9473 FMA:TA Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA]. FMA:9550 main part of right atrium outflow tract of right atrium uberon UBERON:0005965 outflow part of right atrium Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA]. FMA:9550 FMA:FMA main part of right atrium FMA:9550 outflow tract of right atrium FMA:9550 An outflow tract of atrium that is part of a left atrium. FMA:9551 main part of left atrium outflow tract of left atrium uberon UBERON:0005966 outflow part of left atrium An outflow tract of atrium that is part of a left atrium. OBOL:automatic main part of left atrium FMA:9551 outflow tract of left atrium FMA:9551 The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium. EMAPA:37837 FMA:9236 SCTID:277693004 Wikipedia:Crista_terminalis crista terminalis atrii dextri crista terminalis cordis crista terminalis of right atrium uberon UBERON:0005979 crista terminalis The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium. MP:0010495 EMAPA:37837 MA:th crista terminalis atrii dextri FMA:9236 FMA:TA crista terminalis cordis FMA:9236 crista terminalis of right atrium FMA:9236 The laminar structure of the heart. uberon UBERON:0005983 heart layer The laminar structure of the heart. MP:0010545 Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation. TODO - change relation from part_of MESH:D003331 Wikipedia:Coronary_circulation uberon UBERON:0005985 coronary vessel Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation. MP:0010551 The supporting bundles of muscular fibers lining the walls of the atrial myocardium. EMAPA:37432 ZFA:0005810 atrial trabecula atrium myocardial trabeculae trabecula of atrium trabecular layer of atrium trabecular layer of the atrium uberon UBERON:0005988 atrium myocardial trabecula ZFA The supporting bundles of muscular fibers lining the walls of the atrial myocardium. MP:0010581 ZFA:0005810 EMAPA:37432 MA:th atrium myocardial trabeculae MP:0010581 trabecular layer of the atrium ZFA:0005810 The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve. EMAPA:37431 FMA:7136 SCTID:280151006 Wikipedia:Atrioventricular_septum membranous atrioventricular septum uberon UBERON:0005989 atrioventricular septum PMID:15797462 Wikipedia The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve. MP:0010592 EMAPA:37431 MA:th membranous atrioventricular septum FMA:7136 The paired arteries that carry blood to the yolk sac from the dorsal aorta. EHDAA2:0002208 EMAPA:16207 Wikipedia:Vitelline_arteries uberon UBERON:0006002 Development notes:; the vitelline arteries give rise to the celiac artery, superior mesenteric artery, and inferior mesenteric artery in the adult[MP:0010664] vitelline artery http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png ventral branch The paired arteries that carry blood to the yolk sac from the dorsal aorta. MP:0010664 Wikipedia:Vitelline_arteries Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] EMAPA:37883 Wikipedia:Skin_appendage body hair or bristle uberon adnexae cutis skin adnexa skin adnexal structure skin appendage UBERON:0006003 integumentary adnexa Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. http://code.google.com/p/caro2/issues/detail?id=5 http://orcid.org/0000-0002-6601-2165 the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] MP:0010678 EMAPA:37883 MA:th body hair or bristle GO:GO adnexae cutis Wikipedia:Skin_appendage skin adnexa Wikipedia:Skin_appendage skin appendage Wikipedia:Skin_appendage uberon UBERON:0006056 posterior surface of head A bone that is part of a post-anal tail. MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future. EMAPA:18042 MA:0000696 uberon tail bone tail vertebra UBERON:0006068 bone of tail A bone that is part of a post-anal tail. OBOL:automatic MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future. MA tail bone MA:0000696 tail vertebra http://orcid.org/0000-0002-6601-2165 Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this. This region is reduced in humans and corresponds to the coccyx We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud XAO:0000087 uberon post-anal caudal region post-anal tail region postsacral region tail region UBERON:0006071 caudal region Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this. http://orcid.org/0000-0002-6601-2165 We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud XAO post-anal caudal region http://orcid.org/0000-0002-6601-2165 post-anal tail region http://orcid.org/0000-0002-6601-2165 postsacral region AAO:0000082 tail region AAO:0000082 That portion of the spine comprising the cervical vertebrae. The neck area of the spine. Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO] AAO:0000092 BTO:0004148 EHDAA2:0000238 EHDAA:5051 EMAPA:17215 FMA:24138 MA:0003154 NCIT:C69313 SCTID:260488005 UMLS:C0728985 axial skeleton cervical region cervical skeleton cervical spinal column cervical spine cervical vertebrae series cervical vertebral column uberon skeletal system of neck UBERON:0006072 cervical region of vertebral column FMA That portion of the spine comprising the cervical vertebrae. The neck area of the spine. http://medical-dictionary.thefreedictionary.com/ Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO] 2012-06-20 AAO:0000092 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0728985 ncithesaurus:Cervical_Spine axial skeleton cervical region MA:0003154 cervical skeleton EHDAA2:0000238 cervical spinal column FMA:24138 cervical spine FMA:24138 cervical vertebral column FMA:24138 skeletal system of neck FMA:24138 That part of the spine comprising the thoracic vertebrae. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] AAO:0000612 BTO:0004150 EHDAA:5063 EMAPA:17396 FMA:9140 MA:0003155 NCIT:C69315 SCTID:243931006 UMLS:C0581269 axial skeleton thoracic region columna vertebralis thoracicus thoracic spine thoracic vertebrae series thoracic vertebral column uberon UBERON:0006073 thoracic region of vertebral column FMA That part of the spine comprising the thoracic vertebrae. http://medical-dictionary.thefreedictionary.com/ Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0581269 ncithesaurus:Thoracic_Spine axial skeleton thoracic region MA:0003155 columna vertebralis thoracicus FMA:9140 thoracic spine FMA:9140 thoracic vertebral column FMA:9140 Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO] in AAO, this is posterior to the caudal-sacral region AAO:0000082 EMAPA:18043 MA:0003158 axial skeleton tail region caudal skeleton caudal vertebrae series uberon caudal region postsacral region tail region UBERON:0006076 caudal region of vertebral column Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. UBERONREF:0000006 Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO] 2012-06-20 AAO:0000082 AAO AAO:Duellman_and_Trueb_1994 in AAO, this is posterior to the caudal-sacral region AAO axial skeleton tail region MA:0003158 caudal skeleton UBERONREF:0000006 caudal vertebrae series http://purl.bioontology.org/ontology/provisional/a047a2d5-418f-4d9c-ad21-ee0b7c29c29d caudal region AAO:0000082 postsacral region AAO:0000082 tail region AAO:0000082 A collection of all skeletal elements in some subdivision of the vertebral column. FMA:16201 subdivision of vertebral skeleton vertebrae series vertebral column subdivision vertebral series uberon vertebral region vertebral subdivision UBERON:0006077 subdivision of vertebral column FMA A collection of all skeletal elements in some subdivision of the vertebral column. https://orcid.org/0000-0002-6601-2165 subdivision of vertebral skeleton https://orcid.org/0000-0002-6601-2165 vertebral column subdivision FMA:16201 The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. UBERON:0005999 CALOHA:TS-2409 EHDAA2:0000136 EHDAA:2592 EMAPA:16827 VHOG:0000502 Wikipedia:Aorticopulmonary_septum aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale uberon aortic septum spiral septum UBERON:0006207 aortico-pulmonary spiral septum http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png PMID:6844926 Wikipedia The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. MP:0010650 Wikipedia:Aorticopulmonary_septum aortico-pulmonary septum Wikipedia:Aorticopulmonary_septum aorticopulmonary septum Wikipedia:Aorticopulmonary_septum septum aorticopulmonale Wikipedia:Aorticopulmonary_septum aortic septum Wikipedia:Aorticopulmonary_septum spiral septum Wikipedia:Aorticopulmonary_septum The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. EHDAA2:0000189 EHDAA:536 EMAPA:16259 FMA:313607 SCTID:361412007 VHOG:0000380 Wikipedia:Buccopharyngeal_membrane uberon oral membrane oral plate oropharyngeal membrane pharyngeal membrane UBERON:0006211 buccopharyngeal membrane http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png EHDAA2 The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. MP:0012521 oral membrane MP:0012521 oral plate MP:0012521 oropharyngeal membrane Wikipedia:Buccopharyngeal_membrane pharyngeal membrane MP:0012521 EHDAA:1267 EMAPA:16342 RETIRED_EHDAA2:0000268 uberon UBERON:0006218 common atrial chamber consider obsoleting, the ethmoid is endochondral? EHDAA2:0000456 EHDAA:8363 EMAPA:18023 FMA:312597 uberon UBERON:0006227 ethmoid bone primordium FMA AAO EHDAA2 An anatomical junctions that overlaps the foregut and midgut. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] EHDAA2:0000569 EHDAA:526 EMAPA:16363 VHOG:0000291 uberon UBERON:0006235 foregut-midgut junction An anatomical junctions that overlaps the foregut and midgut. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] 2012-09-17 VHOG:0000291 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ EHDAA2:0000577 EHDAA:9540 EMAPA:18017 FMA:312589 frontal bone primordium uberon UBERON:0006236 tetrapod frontal bone primordium frontal bone primordium EHDAA2:0000577 The embryonic precursor of the brain. The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) BAMS:Enc BTO:0004726 EFO:0003431 EHDAA:300 EHDAA:830 EMAPA:16089 FMA:312967 RETIRED_EHDAA2:0000591 TAO:0000146 ZFA:0000146 brain rudiment presumptive brain encephalon uberon embryonic brain UBERON:0006238 future brain The embryonic precursor of the brain. NLX:94995 The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) http://neurolex.org/wiki/Cumbo_terms brain rudiment TAO:0000146 presumptive brain ZFA:0000146 encephalon NLX:94995 embryonic brain BTO:0004726 A tendon that has the potential to develop into a central tendon. The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. EHDAA2:0000593 EHDAA:4118 EMAPA:25035 uberon cranial derivative of septum transversum cranial part of septum transversum UBERON:0006239 future central tendon EHDAA2 mesenchyme cranial part Wikipedia A tendon that has the potential to develop into a central tendon. OBOL:automatic cranial derivative of septum transversum http://orcid.org/0000-0002-6601-2165 cranial part of septum transversum http://orcid.org/0000-0002-6601-2165 EFO:0003438 EHDAA2:0000674 EHDAA:898 EMAPA:16092 EMAPA:16755 TAO:0000417 ZFA:0000417 presumptive spinal cord presumptive spinal cord neural keel presumptive spinal cord neural plate presumptive spinal cord neural rod uberon UBERON:0006241 future spinal cord EHDAA2 presumptive spinal cord ZFA:0000417 presumptive spinal cord neural keel TAO:0000417 presumptive spinal cord neural plate TAO:0000417 presumptive spinal cord neural rod TAO:0000417 A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. EHDAA2:0000700 EHDAA:3047 EMAPA:16713 XAO:0004205 gall bladder primordium uberon UBERON:0006242 gallbladder primordium EMAPA EHDAA2 A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. ISBN:0815318960 XAO:0004205 An anatomical junctions that overlaps the mouth and foregut. EHDAA:534 EMAPA:16258 RETIRED_EHDAA2:0001205 VHOG:0000592 uberon UBERON:0006264 mouth-foregut junction An anatomical junctions that overlaps the mouth and foregut. OBOL:automatic The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 NCIT:C34231 UMLS:C1518429 VHOG:0001212 uberon UBERON:0006267 notochordal plate EHDAA2 EHDAA2 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] 2012-09-17 VHOG:0001212 VHOG http://bgee.unil.ch/ UMLS:C1518429 ncithesaurus:Notochordal_Plate A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 EMAPA:16102 FMA:293135 NCIT:C34232 UMLS:C1518430 VHOG:0001213 uberon chordamesoderm presumptive notochord UBERON:0006268 The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process EHDAA2 A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm UMLS:C1518430 ncithesaurus:Notochordal_Process Either of two openings transmitting nerves and blood vessels to or from the orbit. EHDAA2:0001328 EHDAA:10648 EMAPA:18717 SCTID:280546005 uberon UBERON:0006271 orbital fissure Either of two openings transmitting nerves and blood vessels to or from the orbit. http://www.merriam-webster.com/medical/orbital%20fissure Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] EHDAA2:0001481 EHDAA:4128 EMAPA:17704 EMAPA:17707 SCTID:361413002 VHOG:0001505 uberon pleuroperitoneal channel UBERON:0006279 pleuroperitoneal canal EHDAA2 EHDAA2 Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. ISBN:0124020607 VHOG:0001505 Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0001505 VHOG http://bgee.unil.ch/ pleuroperitoneal channel VHOG:0001505 Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. UBERON:0010226 embryonic ventricle EHDAA2:0001531 EMAPA:16350 FMA:71006 NCIT:C34160 SCTID:361524003 TAO:0002231 Wikipedia:Embryonic_ventricle ZFA:0001719 early heart ventricle embryonic heart ventricle future heart ventricle presumptive cardiac ventricle heart tube primitive ventricle primitive ventricle of heart primordial cardiac ventricle primordial ventricle uberon UBERON:0006283 The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] future cardiac ventricle ZFA EMAPA Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. ZFA:0001719 presumptive cardiac ventricle heart tube ZFA:0001719 primitive ventricle EHDAA2:0001531 primitive ventricle of heart EMAPA:16350 primordial cardiac ventricle FMA:71006 primordial ventricle FMA:71006 A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]. check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme UBERON:0009750 EHDAA2:0001904 EHDAA:3003 EMAPA:18535 XAO:0000326 spleen mesenchyme splenic mesenchyme splenic primordium left spleen primordium uberon UBERON:0006293 spleen primordium XAO EHDAA2-modified XAO A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]. ISBN:0123747295 MP:0011263 check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme EMAPA spleen mesenchyme MP:0011263 splenic mesenchyme https://orcid.org/0000-0002-6601-2165 splenic primordium EHDAA2:0001904 left spleen primordium XAO:0000326 EHDAA:924 EMAPA:16663 RETIRED_EHDAA2:0002089 trigeminal V preganglion uberon trigeminal preganglion UBERON:0006304 See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model future trigeminal ganglion EHDAA2 trigeminal V preganglion EMAPA:16663 trigeminal preganglion EMAPA:16663 A segment of the eyeball that is filled with refractive media. BTO:0002085 EMAPA:37529 FMA:58071 MA:0002459 NCIT:C32301 SCTID:280540004 UMLS:C0459556 eye chamber eyeball chamber uberon chamber of eye UBERON:0006311 chamber of eyeball A segment of the eyeball that is filled with refractive media. http://orcid.org/0000-0002-6601-2165 EMAPA:37529 MA:th UMLS:C0459556 ncithesaurus:Chamber_of_the_Eye eye chamber MA:0002459 eyeball chamber FMA:58071 chamber of eye BTO:0002085 Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. ocular refraction MA:0001911 uberon UBERON:0006312 ocular refractive media Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. http://orcid.org/0000-0002-6601-2165 Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid BIRNLEX:20 EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 Wikipedia:Body_fluid galen:BodyFluid body fluid uberon UBERON:0006314 bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. MESH:A12.207 Wikipedia:Body_fluid EMAPA:37441 MA:th body fluid GAID:266 A nucleus of brain that is part of a brainstem. EMAPA:32790 MA:0000821 uberon brain stem nucleus UBERON:0006331 brainstem nucleus A nucleus of brain that is part of a brainstem. OBOL:automatic brain stem nucleus EMAPA:32790 2 An artery that connects two larger arteries. EMAPA:18598 MA:0001938 NCIT:C52851 UMLS:C1707451 uberon UBERON:0006347 Grouping for anterior and posterior communicating artery An artery that connects two larger arteries. ncithesaurus:Communicating_Artery UMLS:C1707451 ncithesaurus:Communicating_Artery A lobe of lung that is part of a right lung. 4 in mice, divided into 3 in human by two interlobal fissures EMAPA:35155 MA:0001791 NCIT:C48944 SCTID:272654004 UMLS:C1285106 lobe of right lung lobe of the right lung uberon UBERON:0006518 right lung lobe A lobe of lung that is part of a right lung. OBOL:automatic 4 in mice, divided into 3 in human by two interlobal fissures ISBN:0123813611 UMLS:C1285106 ncithesaurus:Lobe_of_the_Right_Lung lobe of the right lung ncithesaurus:Lobe_of_the_Right_Lung A portion of organism substance that secreted_by a zone of skin. MA:0002537 skin fluid/secretion uberon skin fluid skin substance UBERON:0006535 skin secretion A portion of organism substance that secreted_by a zone of skin. OBOL:automatic skin fluid/secretion MA:0002537 A portion of organism substance that is secreted by a female reproductive gland. MA:0002510 female reproductive system fluid/secretion uberon female reproductive system fluid female reproductive system secretion UBERON:0006537 female reproductive gland secretion A portion of organism substance that is secreted by a female reproductive gland. UBERON:cjm female reproductive system fluid/secretion MA:0002510 A portion of organism substance that secreted_by a respiratory system. EMAPA:36550 MA:0002533 NCIT:C13722 UMLS:C1514899 uberon respiratory system fluid respiratory system secretion UBERON:0006538 respiratory system fluid/secretion A portion of organism substance that secreted_by a respiratory system. OBOL:automatic UMLS:C1514899 ncithesaurus:Respiratory_System_Fluid_or_Secretion A tube that is part of a excretory system. uberon UBERON:0006555 excretory tube A tube that is part of a excretory system. OBOL:automatic The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. currently this is an extremely generic class, encompassing both protostomes and deuterostomes. 2023-04-20 branchial pharyngeal MAT:0000049 MESH:D010614 MIAA:0000049 uberon anterior part of foregut pharyngeal tube UBERON:0006562 pharynx The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. GO:0060465 Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]. FMA:85030 uberon UBERON:0006563 tunica media of pulmonary trunk Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]. FMA:85030 FMA:FMA A myocardium that is part of a left ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of aorta. EMAPA:17339 FMA:9558 MA:0002983 SCTID:362021000 left ventricular myocardium myocardium of left ventricle uberon UBERON:0006566 left ventricle myocardium A myocardium that is part of a left ventricle of a heart. http://orcid.org/0000-0002-6601-2165 Myocardium of ventricle which is continuous with the tunica media of aorta. FMA:9558 left ventricular myocardium FMA:9558 myocardium of left ventricle FMA:9558 A myocardium that is part of a right ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. EMAPA:17342 FMA:9535 MA:0002984 SCTID:362020004 myocardium of right ventricle right ventricular myocardium uberon UBERON:0006567 right ventricle myocardium A myocardium that is part of a right ventricle of a heart. http://orcid.org/0000-0002-6601-2165 Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. FMA:9535 myocardium of right ventricle FMA:9535 right ventricular myocardium FMA:9535 A trabecula carnea that is part of a heart right ventricle. FMA:7270 SCTID:192373001 trabeculae carneae (ventriculus dexter) uberon UBERON:0006570 trabecula carnea of right ventricle A trabecula carnea that is part of a heart right ventricle. OBOL:automatic trabeculae carneae (ventriculus dexter) FMA:7270 A trabecula carnea that is part of a heart left ventricle. FMA:7271 SCTID:190344008 trabeculae carneae (ventriculus sinister) uberon UBERON:0006571 trabecula carnea of left ventricle A trabecula carnea that is part of a heart left ventricle. OBOL:automatic trabeculae carneae (ventriculus sinister) FMA:7271 The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:. FMA also has FMA:29321 but it's not clear how this differs EMAPA:19159 FMA:75383 NCIT:C34245 SCTID:245445008 UMLS:C0821671 Wikipedia:Pectinate_line linea pectinata canalis analis pectinate line of anal canal uberon Hilton's 'white line' dentate line linea anocutanea recto-anal junction site of anal membrane UBERON:0006574 pectinate line http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:. Wikipedia:Pectinate_line FMA also has FMA:29321 but it's not clear how this differs FMA UMLS:C0821671 ncithesaurus:Pectinate_Line linea pectinata canalis analis FMA:75383 FMA:TA pectinate line of anal canal FMA:75383 Hilton's 'white line' EMAPA:19159 dentate line Wikipedia:Pectinate_line linea anocutanea Wikipedia:Pectinate_line recto-anal junction Wikipedia:Pectinate_line site of anal membrane EMAPA:19159 Presumptive structure of the blastula that will develop into endoderm. AAO:0000471 EFO:0003437 TAO:0000416 ZFA:0000416 uberon UBERON:0006595 presumptive endoderm Presumptive structure of the blastula that will develop into endoderm. http://orcid.org/0000-0002-6601-2165 AAO:0000468 EFO:0003439 TAO:0000568 ZFA:0000568 future blood uberon UBERON:0006596 presumptive blood Portion of embryonic tissue determined by fate mapping to become a structure. Consider merging with anlage AAO:0000479 TAO:0001116 ZFA:0001116 future structure presumptive structures uberon UBERON:0006598 presumptive structure Portion of embryonic tissue determined by fate mapping to become a structure. GOC:CVS GOC:YMB ZFA:0001116 presumptive structures ZFA:0001116 Presumptive structure of the blastula that will develop into ectoderm. AAO:0000470 EFO:0003466 TAO:0001376 XAO:0004132 ZFA:0001376 uberon presumptive epidermis UBERON:0006601 presumptive ectoderm Presumptive structure of the blastula that will develop into ectoderm. http://orcid.org/0000-0002-6601-2165 presumptive epidermis ZFA:0001376 Presumptive structure of the blastula that will develop into mesoderm. AAO:0000476 EFO:0003467 TAO:0001377 ZFA:0001377 uberon UBERON:0006603 presumptive mesoderm Presumptive structure of the blastula that will develop into mesoderm. http://orcid.org/0000-0002-6601-2165 A rigid covering that envelops an object. shell A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies) An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle. BTO:0004838 SCTID:86915006 UMLS:C0225358 Wikipedia:Muscular_layer muscular layer muscularis layer tunica muscularis uberon muscular coat muscularis muscularis externa muscularis propria transverse muscular fibers tunica externa tunica muscularis UBERON:0006660 muscular coat A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. Wikipedia:Muscular_layer An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. BTO:0004838 UMLS:C0225358 ncithesaurus:Muscle_Layer muscular layer OBOL:automatic muscularis layer FMA:45634 tunica muscularis BTO:0004838 muscular coat Wikipedia:Muscularis_externa muscularis externa BTO:0004838 muscularis propria Wikipedia:Muscularis_externa transverse muscular fibers Wikipedia:Muscularis_externa tunica externa BTO:0004838 tunica muscularis Wikipedia:Muscularis_externa The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers. In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] EMAPA:17702 FMA:58279 NCIT:C34119 SCTID:244943002 UMLS:C0230162 VHOG:0001399 Wikipedia:Central_tendon_of_diaphragm central tendon centrum tendineum centrum tendineum diaphragmatis uberon UBERON:0006670 central tendon of diaphragm VHOG definitional The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers. MGI:csmith MP:0012061 In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] 2012-09-17 VHOG:0001399 VHOG DOI:10.1016/j.resp.2006.06.003 http://bgee.unil.ch/ UMLS:C0230162 ncithesaurus:Central_Tendon_of_the_Diaphragm central tendon FMA:58279 centrum tendineum FMA:58279 centrum tendineum diaphragmatis FMA:58279 FMA:TA An anatomical boundary that adjacent_to a epithelium. FMA:70997 epithelium surface uberon UBERON:0006677 surface of epithelium An anatomical boundary that adjacent_to a epithelium. OBOL:automatic epithelium surface FMA:70997 A vein that is part of a vertebral column. EMAPA:18255 FMA:76735 MA:0002108 SCTID:181376008 Wikipedia:Spinal_veins vena spinalis uberon spinal branch UBERON:0006686 spinal vein A vein that is part of a vertebral column. OBOL:automatic vena spinalis FMA:76735 FMA:TA spinal branch FMA:76735 A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. TODO - check neural vs vertebral canal; embryonic vs adult? Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO] AAO:0000693 FMA:9680 GAID:242 MESH:D013115 NCIT:C33869 NCIT:C34221 SCTID:361746009 UMLS:C0037922 UMLS:C1522467 Wikipedia:Spinal_canal uberon c. vertebralis foramen vertebrale neural canal spinal canal spinal cavity vertebral canal UBERON:0006692 vertebral canal http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. Wikipedia:Spinal_canal http://orcid.org/0000-0002-6601-2165 Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO] 2012-06-20 AAO:0000693 AAO AAO:LAP MESH:D013115 https://github.com/biopragmatics/biomappings UMLS:C0037922 ncithesaurus:Vertebral_Canal UMLS:C1522467 ncithesaurus:Neural_Canal c. vertebralis Wikipedia:Spinal_canal foramen vertebrale AAO:0000693 neural canal AAO:0000693 spinal canal AAO:0000693 spinal cavity Wikipedia:Spinal_canal vertebral canal Wikipedia:Spinal_canal The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm. EFO:0001403 EMAPA:37835 FMA:58342 GAID:896 MESH:D016850 SCTID:63716004 Wikipedia:Corneal_limbus ZFA:0005570 cornea limbus corneal limbus corneal-scleral limbus corneoscleral junction limbus corneae sclerocorneal junction sclerocorneal limbus uberon limbus corneae UBERON:0006761 This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343 corneo-scleral junction http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm. MP:0013477 EMAPA:37835 MA:th corneal limbus FMA:58342 GAID:896 corneal-scleral limbus PMID:17051547 corneoscleral junction GAID:896 limbus corneae Wikipedia:Corneal_limbus sclerocorneal junction FMA:58342 sclerocorneal limbus GAID:896 limbus corneae Wikipedia:Corneal_limbus An epithelium that is composed primarily of secretory cells. consider splitting epithelium from epithelial tissue BTO:0002991 NCIT:C43370 NCIT:C45715 UMLS:C0682578 UMLS:C1708242 uberon UBERON:0006799 glandular epithelium An epithelium that is composed primarily of secretory cells. http://orcid.org/0000-0002-6601-2165 UMLS:C0682578 ncithesaurus:Glandular_Epithelium UMLS:C1708242 ncithesaurus:Glandular_Epithelial_Tissue Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] cushions body organs AAO:0000027 FMA:63897 SCTID:68477002 loose areolar connective tissue uberon areolar tissue loose connective tissue UBERON:0006815 areolar connective tissue FMA FMA Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. FMA:63897 Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO] 2012-06-20 AAO:0000027 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000027 AAO cushions body organs AAO loose areolar connective tissue FMA:63897 loose connective tissue AAO:0000027 The supporting bundles of muscular fibers lining the walls of the atria[MP]. Not present in any AO. Note that WP states that trabecular carnea are ventricular and 'They should not be confused with the pectinate muscles, which are present in the right and left atria only' uberon UBERON:0006828 trabecula carnea of atrium The supporting bundles of muscular fibers lining the walls of the atria[MP]. MP:0010581 A subdivision of a the reproductive tract in a female organism that is the site of embryo development. uterus FBbt:00004924 TADS:0000421 WBbt:0006760 uberon UBERON:0006834 uterus or analog A subdivision of a the reproductive tract in a female organism that is the site of embryo development. http://orcid.org/0000-0002-6601-2165 uterus FBbt:00004924 FBbt:00004924 Vein that is central to a lobule in the liver. central vein FMA:17544 NCIT:C32281 SCTID:272023004 TAO:0005168 Wikipedia:Central_veins_of_liver ZFA:0005168 terminal branch of hepatic vein terminal hepatic venule vena centralis (hepar) uberon UBERON:0006841 central vein of liver Vein that is central to a lobule in the liver. ZFA:0005168 central vein ZFA:0005168 terminal branch of hepatic vein FMA:17544 terminal hepatic venule FMA:17544 vena centralis (hepar) FMA:17544 A furrow or an incomplete tube. AEO:0000161 EHDAA2_RETIRED:0003161 uberon groove UBERON:0006846 Surface groove is modelled as immaterial - see https://github.com/obophenotype/uberon/issues/2667 for discussion surface groove https://github.com/obophenotype/uberon/issues/2667 A furrow or an incomplete tube. AEO:0000161 AEO:JB https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/4 groove AEO:0000161 The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. FBbt:00005756 WBbt:0005773 rectum uberon rectal part of digestive tract terminal section of digestive tract UBERON:0006866 terminal part of digestive tract The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. http://orcid.org/0000-0002-6601-2165 FBbt:00005756 rectum FBbt:00005756 A vasculature that is part of a organ. FMA:74612 organ vasculature set of blood vessels of organ uberon UBERON:0006876 vasculature of organ A vasculature that is part of a organ. OBOL:automatic organ vasculature FMA:74612 set of blood vessels of organ FMA:74612 A vasculature that is part of a liver. the EHDAA2 term and the FMA term may not be exact equivalents - check EHDAA2:0003454 EMAPA:35501 FMA:73748 hepatic vasculature uberon hepatic vascular element liver vascular element liver vascular system UBERON:0006877 vasculature of liver A vasculature that is part of a liver. OBOL:automatic the EHDAA2 term and the FMA term may not be exact equivalents - check EHDAA2 hepatic vasculature FMA:73748 hepatic vascular element EMAPA:35501 liver vascular element EMAPA:35501 liver vascular system EHDAA2:0003454 A head mesenchyme that develops_from a mesoderm. merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme AAO:0011051 EFO:0003337 EFO:0003603 EHDAA2:0001118 EHDAA:655 EMAPA:16099 EMAPA_RETIRED:16270 FMA:293859 TAO:0000998 VHOG:0000185 XAO:0000053 ZFA:0000998 head mesenchyme derived from mesoderm head mesenchyme from head mesoderm head mesenchyme from mesoderm mesenchyme derived from head mesoderm mesenchyme from head mesoderm uberon cranial mesoderm head mesoderm UBERON:0006904 head mesenchyme from mesoderm ZFA EHDAA2 XAO A head mesenchyme that develops_from a mesoderm. OBOL:automatic head mesenchyme from head mesoderm EHDAA2:0001118 mesenchyme derived from head mesoderm EHDAA:1057 cranial mesoderm UBERON:0005280 head mesoderm AAO:0011051 UBERON:0005280 Mesenchyme that is part of a mandibular prominence. EHDAA2:0001062 EHDAA:5861 EHDAA:5873 EMAPA:17357 mesenchyme of mandibular process mesenchyme of mandibular prominence uberon UBERON:0006905 mandibular process mesenchyme Mesenchyme that is part of a mandibular prominence. OBOL:automatic mesenchyme of mandibular process EMAPA:17357 mesenchyme of mandibular prominence https://orcid.org/0000-0002-6601-2165 An anatomical space that surrounded_by a digestive tract. BTO:0000349 EMAPA:32908 FMA:45677 digestive tract lumen gut cavity gut lumen lumen of alimentary tract lumen of digestive tract lumen of gut uberon UBERON:0006909 lumen of digestive tract An anatomical space that surrounded_by a digestive tract. OBOL:automatic digestive tract lumen https://orcid.org/0000-0002-6601-2165 gut cavity BTO:0000349 gut lumen FMA:45677 lumen of alimentary tract https://orcid.org/0000-0002-6601-2165 lumen of digestive tract https://orcid.org/0000-0002-6601-2165 lumen of gut FMA:45677 An epithelium that is part of a lip. The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] BTO:0004468 TAO:0005334 ZFA:0005334 uberon UBERON:0006913 lip epithelium An epithelium that is part of a lip. OBOL:automatic The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] 2012-08-14 TAO:0005334 TAO ZFIN:ZDB-PUB-060921-12 An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 UMLS:C0221909 Wikipedia:Squamous_epithelium uberon UBERON:0006914 squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium FBbt UMLS:C0221909 ncithesaurus:Squamous_Epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]. FMA:45563 NCIT:C13180 UMLS:C0836131 Wikipedia:Stratified_squamous_epithelium epithelium stratificatum squamosum uberon UBERON:0006915 stratified squamous epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]. FMA:45563 Wikipedia:Stratified_squamous_epithelium UMLS:C0836131 ncithesaurus:Stratified_Squamous_Epithelium epithelium stratificatum squamosum FMA:45563 A squamous epithelium that is part of a esophagus. MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass BTO:0003635 CALOHA:TS-1250 EMAPA:35324 MA:0001567 NCIT:C49222 UMLS:C1707950 uberon esophageal squamous epithelium squamous epithelium of esophagus squamous oesophageal epithelium UBERON:0006920 esophagus squamous epithelium A squamous epithelium that is part of a esophagus. OBOL:automatic MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass MA UMLS:C1707950 ncithesaurus:Esophageal_Squamous_Epithelium esophageal squamous epithelium OBOL:automatic squamous epithelium of esophagus OBOL:automatic squamous oesophageal epithelium MA:0001567 A squamous epithelium that is part of a stomach. EMAPA:35824 MA:0001611 uberon UBERON:0006921 stomach squamous epithelium A squamous epithelium that is part of a stomach. OBOL:automatic A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland. EMAPA:17623 EMAPA:35814 FMA:63458 MA:0002784 epithelium of gastric gland uberon gastric gland epithelium UBERON:0006924 stomach glandular epithelium FMA A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. ISBN:0073040584 epithelium of gastric gland FMA:63458 gastric gland epithelium FMA:63458 Any gland that is part of the digestive system. AAO:0000130 BTO:0000345 uberon digestive gland UBERON:0006925 digestive system gland Any gland that is part of the digestive system. UBERON:cjm digestive gland BTO:0000345 Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]. FMA:64800 NCIT:C13182 UMLS:C0225337 uberon UBERON:0006929 glandular columnar epithelium Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]. FMA:64800 UMLS:C0225337 ncithesaurus:Columnar_Epithelium FMA:66809 uberon UBERON:0006930 glandular cuboidal epithelium Stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. EMAPA:27167 MA:0001614 stomach glandular region glandular mucous membrane uberon UBERON:0006931 stomach glandular region mucosa Stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. http://orcid.org/0000-0002-6601-2165 stomach glandular region glandular mucous membrane EMAPA:27167 Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical CALOHA:TS-0682 FMA:62410 SCTID:309045006 uberon neuroepithelium UBERON:0006934 sensory epithelium Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. BTO:0000314 note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical FMA neuroepithelium BTO:0000314 The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. CALOHA:TS-1246 EMAPA:28880 FMA:18626 MA:0002991 NCIT:C33638 SCTID:259306002 UMLS:C0737271 Wikipedia:Stroma_of_ovary interstitial tissue of ovary ovarian stroma ovary stroma stroma of the ovary stroma ovarica uberon stroma ovarii UBERON:0006960 ovary stroma FMA The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. Wikipedia:Stroma_of_ovary UMLS:C0737271 ncithesaurus:Stroma_of_the_Ovarian_Cortex interstitial tissue of ovary FMA:18626 ovarian stroma FMA:18626 ovary stroma MA:0002991 stroma of the ovary Wikipedia:Stroma_of_ovary stroma ovarica FMA:18626 stroma ovarii Wikipedia:Stroma_of_ovary The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. EFO:0003709 TAO:0005077 ZFA:0005077 uberon UBERON:0006965 vascular cord The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. GO:0072360 ZFA:0005077 A capillary that is part of the coronary system. ZFA:0005813 heart capillary uberon UBERON:0006966 coronary capillary A capillary that is part of the coronary system. http://orcid.org/0000-0002-6601-2165 heart capillary GO:0003248 A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n. BILA:0000010 CARO:0001002 EHDAA2_RETIRED:0003192 FMA:24137 NCIT:C34022 UMLS:C1515977 uberon UBERON:0006984 Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface via morphological boundary in CARO A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n. CARO:0001002 UMLS:C1515977 ncithesaurus:Anatomic_Surface The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. consider FBbt:00005541 ! cardiogenic mesoderm review EHDAA2 placement AAO:0011021 BILA:0000051 EFO:0000315 EHDAA2:0000214 EHDAA:385 FMA:293143 SCTID:360387000 VHOG:0001641 XAO:0000235 cardiogenic splanchnopleure uberon cardiac mesoderm cardiogenic mesoderm cardiogenic region heart primordia UBERON:0007005 cardiogenic splanchnic mesoderm The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. XAO:0000235 http://www.drugs.com/dict/cardiogenic-mesoderm.html https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7 cardiogenic splanchnopleure EHDAA2:0000214 cardiac mesoderm XAO:0000235 cardiogenic mesoderm http://www.drugs.com/dict/cardiogenic-mesoderm.html cardiogenic region http://orcid.org/0000-0002-6601-2165 heart primordia XAO:0000235 Organism at the cleavage stage. BILA:0000058 uberon UBERON:0007010 cleaving embryo Organism at the cleavage stage. OBOL:automatic The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 UMLS:C1514442 future digestive tract future digestive tube future gut primitive gut uberon embryonic digestive tube primordial digestive tube primordial gut UBERON:0007026 presumptive gut The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis NCBIBook:NBK10107 UMLS:C1514442 ncithesaurus:Primordial_Gut BILA:0000142 uberon UBERON:0007037 mechanosensory system Cranial neural crest that migrates into the mandibular arch. TAO:0007064 XAO:0000024 ZFA:0007064 uberon UBERON:0007098 mandibular neural crest ZFA ZFA Cranial neural crest that migrates into the mandibular arch. ZFA:0007064 A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube heart uberon adult heart UBERON:0007100 Gene notes: Bmp, Nkx, Gata primary circulatory organ GO uses blood circulation generically to include the haemolymphatic fluid of arthropods A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. GO:0007507 dorsal tube Wikipedia:Heart heart GO:0007507 adult heart FBbt:00003154 Ganglion which is located in the trunk. EFO:0000901 MAT:0000344 MIAA:0000344 TAO:0001573 ZFA:0001573 body ganglion trunk ganglia uberon UBERON:0007134 trunk ganglion Ganglion which is located in the trunk. ZFIN:curator body ganglion MAT:0000344 trunk ganglia ZFA:0001573 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 uberon presumptive central nervous system UBERON:0007135 neural keel An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000131 TAO ZFIN:curator presumptive central nervous system ZFA:0000131 An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx). EMAPA:16748 FMA:85540 embryo tail tail of embryo uberon embryonic tail UBERON:0007144 embryonic post-anal tail An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. http://orcid.org/0000-0002-6601-2165 embryo tail FMA:85540 tail of embryo FMA:85540 embryonic tail FMA:85540 An anatomical cavity that surrounded_by a midgut. EMAPA:18377 FMA:54366 midgut lumen uberon UBERON:0007147 lumen of midgut An anatomical cavity that surrounded_by a midgut. OBOL:automatic midgut lumen FMA:54366 An anatomical cavity that surrounded_by a hindgut. EMAPA:18396 FMA:54367 hindgut lumen uberon UBERON:0007148 lumen of hindgut An anatomical cavity that surrounded_by a hindgut. OBOL:automatic hindgut lumen FMA:54367 An anatomical cavity that surrounded_by a anal canal. EMAPA:18836 FMA:17357 anal canal lumen uberon UBERON:0007158 lumen of anal canal An anatomical cavity that surrounded_by a anal canal. OBOL:automatic anal canal lumen FMA:17357 An anatomical cavity that surrounded_by a colon. EMAPA:18945 FMA:18374 SCTID:362156004 colon lumen uberon colonic lumen UBERON:0007159 lumen of colon An anatomical cavity that surrounded_by a colon. OBOL:automatic colon lumen FMA:18374 colonic lumen FMA:18374 A lamina propria that is part of a colonic mucosa. EMAPA:27395 FMA:15657 MA:0003196 SCTID:113284008 colonic lamina propria lamina propria mucosae of colon lamina propria of colonic mucosa lamina propria of colonic mucous membrane uberon UBERON:0007177 lamina propria of mucosa of colon A lamina propria that is part of a colonic mucosa. OBOL:automatic colonic lamina propria FMA:15657 lamina propria mucosae of colon FMA:15657 lamina propria of colonic mucosa FMA:15657 lamina propria of colonic mucous membrane FMA:15657 A mesothelium that is part of a serous pericardium. BTO:0003157 EMAPA:16133 FMA:18149 SCTID:67300002 mesothelium of pericardium pericardial mesothelium serous pericardium mesothelium uberon UBERON:0007188 mesothelium of serous pericardium A mesothelium that is part of a serous pericardium. OBOL:automatic mesothelium of pericardium FMA:18149 pericardial mesothelium FMA:18149 serous pericardium mesothelium FMA:18149 The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis. CALOHA:TS-0085 FMA:21426 Wikipedia:Bone_marrow#Stroma bone marrow stroma uberon UBERON:0007195 stroma of bone marrow The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis. Wikipedia:Bone_marrow#Stroma bone marrow stroma FMA:21426 The vasculature consisting of brachiocephalic arteries and veins. uberon UBERON:0007204 brachiocephalic vasculature The vasculature consisting of brachiocephalic arteries and veins. http://orcid.org/0000-0002-6601-2165 Mesenchyme that develops_from a cranial neural crest. EFO:0003572 EHDAA2:0000735 EMAPA:16169 EMAPA:16271 EMAPA_RETIRED:16271 TAO:0000787 ZFA:0000787 head mesenchyme from cranial neural crest head mesenchyme from neural crest head neural crest derived mesenchyme uberon UBERON:0007213 mesenchyme derived from head neural crest ZFA Mesenchyme that develops_from a cranial neural crest. OBOL:automatic head mesenchyme from neural crest EHDAA2:0000735 Mesenchyme that develops_from a trunk neural crest. EHDAA2:0002093 EMAPA:16182 TAO:0000999 ZFA:0000999 trunk mesenchyme from neural crest trunk neural crest derived mesenchyme uberon UBERON:0007214 mesenchyme derived from trunk neural crest Mesenchyme that develops_from a trunk neural crest. OBOL:automatic trunk mesenchyme from neural crest EHDAA2:0002093 relationship to Meckel's cartilage to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000031 EHDAA:583 EMAPA:16382 VHOG:0000510 ventral pharyngeal arch 1 uberon ventral mandibular arch ventral visceral arch 1 UBERON:0007237 1st arch mandibular component EHDAA2 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000510 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ ventral pharyngeal arch 1 VHOG:0000510 ventral mandibular arch VHOG:0000510 ventral visceral arch 1 VHOG:0000510 relationship to palatoquadrate to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000038 EHDAA:595 EMAPA:16388 VHOG:0000511 uberon UBERON:0007238 1st arch maxillary component EHDAA2 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000511 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ A tunica media that is part of a artery. EMAPA:36294 EV:0100029 FMA:14273 NCIT:C49321 SCTID:84300001 UMLS:C1710627 arterial media tunica media (arteriae) uberon UBERON:0007239 tunica media of artery A tunica media that is part of a artery. OBOL:automatic UMLS:C1710627 ncithesaurus:Venous_System_Smooth_Muscle_Tissue arterial media EV:0100029 tunica media (arteriae) FMA:14273 A tunica adventitia that is part of a artery. EMAPA:36295 EV:0100030 FMA:14274 SCTID:113261001 arterial adventitia tunica externa (adventitia)(arteriae) uberon UBERON:0007240 tunica adventitia of artery FMA A tunica adventitia that is part of a artery. OBOL:automatic arterial adventitia EV:0100030 tunica externa (adventitia)(arteriae) FMA:14274 A tunica adventitia that is part of a vein. EMAPA:36310 EV:0100034 FMA:14355 SCTID:13202006 tunica externa (adventitia)(venae) venous adventitia uberon UBERON:0007241 tunica adventitia of vein A tunica adventitia that is part of a vein. OBOL:automatic tunica externa (adventitia)(venae) FMA:14355 venous adventitia EV:0100034 A tunica intima that is part of a vein. EMAPA:36308 EV:0100032 FMA:14353 SCTID:2436009 tunica interna (intima)(venae) venous intima uberon UBERON:0007242 tunica intima of vein A tunica intima that is part of a vein. OBOL:automatic tunica interna (intima)(venae) FMA:14353 venous intima EV:0100032 A tunica media that is part of a vein. EMAPA:36309 EV:0100033 FMA:14354 SCTID:42049001 tunica media (venae) venous media uberon UBERON:0007243 tunica media of vein A tunica media that is part of a vein. OBOL:automatic tunica media (venae) FMA:14354 venous media EV:0100033 Gray matter of the central nervous system which is a collection of clustered nuclei. FMA:256381 FMA:84059 uberon cluster of neural nuclei neural nuclei nuclear complex UBERON:0007245 nuclear complex of neuraxis Gray matter of the central nervous system which is a collection of clustered nuclei. http://orcid.org/0000-0002-6601-2165 Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future. FMA:72246 SCTID:369024009 superior olivary complex nucleus uberon UBERON:0007247 nucleus of superior olivary complex Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. http://orcid.org/0000-0002-6601-2165 superior olivary complex nucleus FMA:72246 Any collection of muscles that is part of a pectoral appendage. currently defined by location rather than attachment EFO:0003540 TAO:0000563 ZFA:0000563 pectoral fin muscle pectoral fin musculature uberon UBERON:0007269 pectoral appendage musculature Any collection of muscles that is part of a pectoral appendage. OBOL:automatic pectoral fin muscle ZFA:0000563 pectoral fin musculature ZFA:0000563 Any collection of muscles that is part of a pelvic appendage. currently defined by location rather than attachment Musculature that is part of the pelvic fin.[TAO] TAO:0000258 ZFA:0000258 pelvic fin musculature uberon UBERON:0007270 pelvic appendage musculature Any collection of muscles that is part of a pelvic appendage. OBOL:automatic Musculature that is part of the pelvic fin.[TAO] 2012-08-14 TAO:0000258 TAO TAO:curator pelvic fin musculature ZFA:0000258 Any collection of muscles that is part of an appendage. currently defined by location rather than attachment TAO:0000207 ZFA:0000207 fin musculature uberon UBERON:0007271 appendage musculature Any collection of muscles that is part of an appendage. OBOL:automatic fin musculature ZFA:0000207 Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. VSAO:0005000 uberon cheiropterygium UBERON:0007272 pectoral appendage skeleton VSAO Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. VSAO:0005000 VSAO:NI cheiropterygium VSAO:0005000 VSAO:NI The collection of all skeletal elements in a pelvic appendage region. uberon UBERON:0007273 pelvic appendage skeleton VSAO The collection of all skeletal elements in a pelvic appendage region. https://orcid.org/0000-0002-6601-2165 The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. TODO - unify naming conventions The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. BAMS:HB CALOHA:TS-2118 EFO:0003440 EHDAA2:0001630 FMA:295640 TAO:0000569 Wikipedia:Rhombencephalon ZFA:0000569 presumptive rhombencephalon uberon embryonic rhombencephalon future hindbrain rhombencephalon UBERON:0007277 presumptive hindbrain XAO-abduced cjm The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. Wikipedia:Rhombencephalon The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. NPX:PDR presumptive rhombencephalon ZFA:0000569 embryonic rhombencephalon CALOHA:TS-2118 future hindbrain https://orcid.org/0000-0002-6601-2165 rhombencephalon EHDAA2:0001630 Portion of tissue that is part of the heart tube and will become the sinus venosus. TAO:0002234 ZFA:0001722 uberon UBERON:0007278 presumptive sinus venosus ZFA Portion of tissue that is part of the heart tube and will become the sinus venosus. ZFA:0001722 A presumptive structure that has the potential to develop into a endocardium. Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] TAO:0002233 ZFA:0001724 uberon UBERON:0007280 presumptive endocardium A presumptive structure that has the potential to develop into a endocardium. OBOL:automatic Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] 2012-08-14 TAO:0002233 TAO ZFIN:curator Embryonic structure that gives rise to the midbrain hindbrain boundary. EFO:0003446 TAO:0001187 XAO:0004086 ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary uberon UBERON:0007281 presumptive midbrain hindbrain boundary ZFA Embryonic structure that gives rise to the midbrain hindbrain boundary. ZFA:0001187 presumptive MHB https://orcid.org/0000-0002-6601-2165 presumptive midbrain-hindbrain boundary ZFA:0001187 A presumptive structure that has the potential to develop into a presomitic mesoderm. EFO:0003421 TAO:0000053 ZFA:0000053 uberon presumptive segmental plates UBERON:0007282 presumptive segmental plate https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 A presumptive structure that has the potential to develop into a presomitic mesoderm. OBOL:automatic presumptive segmental plates ZFA:0000053 A presumptive structure that has the potential to develop into a neural plate. consider merging Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 prospective neuroectoderm prospective vegetal ectoderm uberon UBERON:0007284 presumptive neural plate A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic Region of the gastrula which gives rise to the neural plate.[TAO] 2012-08-14 TAO:0000063 TAO ZFIN:curator prospective neuroectoderm ZFA:0000063 prospective vegetal ectoderm ZFA:0000063 The part of the blastula that has the potential to develop into a paraxial mesoderm. EFO:0003443 TAO:0000591 XAO:0004134 ZFA:0000591 future paraxial mesenchyme future paraxial mesoderm uberon UBERON:0007285 presumptive paraxial mesoderm https://github.com/obophenotype/uberon/issues/1277 The part of the blastula that has the potential to develop into a paraxial mesoderm. UBERON:cjm https://github.com/obophenotype/uberon/issues/1277 future paraxial mesenchyme UBERON:cjm A blood vessel that is part of a pectoral appendage. TAO:0005301 ZFA:0005301 pectoral fin blood vessel uberon UBERON:0007300 pectoral appendage blood vessel A blood vessel that is part of a pectoral appendage. OBOL:automatic pectoral fin blood vessel ZFA:0005301 A blood vessel that is part of a limb/fin. TAO:0005299 ZFA:0005299 fin blood vessel limb blood vessel uberon UBERON:0007301 appendage blood vessel A blood vessel that is part of a limb/fin. OBOL:automatic fin blood vessel ZFA:0005299 limb blood vessel A vasculature that is part of a pectoral appendage. TAO:0005096 ZFA:0005096 pectoral fin vasculature uberon UBERON:0007302 pectoral appendage vasculature A vasculature that is part of a pectoral appendage. OBOL:automatic pectoral fin vasculature ZFA:0005096 A vasculature that is part of a chordate pharynx. TAO:0005003 ZFA:0005003 branchial vasculature uberon UBERON:0007303 pharyngeal vasculature A vasculature that is part of a chordate pharynx. OBOL:automatic branchial vasculature ZFA:0005003 A vasculature that is part of a limb/fin. TAO:0005095 ZFA:0005095 fin vasculature uberon UBERON:0007304 appendage vasculature A vasculature that is part of a limb/fin. OBOL:automatic fin vasculature ZFA:0005095 A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans. TODO - check In mice many lobules lack islets, in contrast to other mammals including humans EMAPA:37710 FMA:16012 MA:0000721 lobulus pancreaticus pancreas lobe pancreatic lobule uberon UBERON:0007324 pancreatic lobule A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans. ISBN:0123813611 EMAPA:37710 MA:th lobulus pancreaticus FMA:16012 pancreas lobe MA:0000721 pancreatic lobule FMA:16012 A duct that collects and carries secretions of the exocrine pancreas to the intestine. this class groups together accessory (dorsal) and main (ventral) pancreatic ducts Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms EHDAA:9194 EMAPA:32952 FMA:10419 MA:0000124 MESH:D010183 SCTID:181278006 TAO:0001372 VHOG:0000254 Wikipedia:Pancreatic_duct ZFA:0001372 duct of pancreas pancreas duct uberon ductus pancreaticus UBERON:0007329 pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png ZFA MA A duct that collects and carries secretions of the exocrine pancreas to the intestine. GOC:cvs GOC:ymb Wikipedia:Pancreatic_duct https://github.com/obophenotype/uberon/issues/1250 https://orcid.org/0000-0002-2244-7917 https://orcid.org/0000-0002-6601-2165 https://orcid.org/0000-0002-9900-7880 Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000254 VHOG http://bgee.unil.ch/ These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] 2012-09-17 VHOG:0000254 VHOG DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005) http://bgee.unil.ch/ in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms EHDAA2 MESH:D010183 https://github.com/biopragmatics/biomappings duct of pancreas OBOL:accepted pancreas duct OBOL:accepted ductus pancreaticus Wikipedia:Pancreatic_duct A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones. check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton CALOHA:TS-2212 Wikipedia:Palate roof of buccal cavity roof of oral cavity uberon palate palatum primary or secondary palate UBERON:0007375 roof of mouth A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones. https://orcid.org/0000-0002-6601-2165 palatum The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. this grouping class exists primarily to align with GO - see GO:0008544. BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 WBbt:0005733 Wikipedia:Epidermis_(zoology) epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer uberon hypoderm hypodermis UBERON:0007376 outer epithelium Wikipedia:Epidermis_(zoology) The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. GO:0008544 FBbt:00004993 epidermis GO:0008544 hypoderm BTO:0000313 hypodermis GO:0008544 WBbt:0005733 Outermost layer of cells surrounding the embryo. Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm. EFO:0003425 TAO:0000086 ZFA:0000086 EVL enveloping layer uberon UBERON:0007383 enveloping layer of ectoderm Outermost layer of cells surrounding the embryo. http://orcid.org/0000-0002-6601-2165 Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000086 TAO ZFIN:curator relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] 2012-08-14 TAO:0000086 TAO EVL ZFA:0000086 enveloping layer ZFIN:ZDB-PUB-961014-576 A cartilage tissue that is part of a paired limb or fin. Cartilage which is part of one of the paired fins.[TAO] TAO:0001543 ZFA:0001543 uberon UBERON:0007389 paired limb/fin cartilage A cartilage tissue that is part of a paired limb or fin. http://orcid.org/0000-0002-6601-2165 Cartilage which is part of one of the paired fins.[TAO] 2012-08-14 TAO:0001543 TAO ZFIN:curator A cartilage tissue that is part of a pectoral appendage. Cartilage which is part of the pectoral fin.[TAO] TAO:0000257 ZFA:0000257 uberon pectoral fin cartilage UBERON:0007390 pectoral appendage cartilage tissue A cartilage tissue that is part of a pectoral appendage. OBOL:automatic Cartilage which is part of the pectoral fin.[TAO] 2012-08-14 TAO:0000257 TAO ZFIN:curator pectoral fin cartilage TAO:0000257 A cartilage tissue that is part of a pelvic appendage. Cartilage which is part of the pelvic fin.[TAO] TAO:0001459 ZFA:0001459 uberon pelvic fin cartilage UBERON:0007391 pelvic appendage cartilage tissue A cartilage tissue that is part of a pelvic appendage. OBOL:automatic Cartilage which is part of the pelvic fin.[TAO] 2012-08-14 TAO:0001459 TAO ZFIN:curator pelvic fin cartilage TAO:0001459 A nucleus of brain that spans a midbrain tegmentum. this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species UBERON:0012277 FMA:258768 ZFA:0005577 tegmental nuclei tegmental nucleus uberon UBERON:0007414 nucleus of midbrain tegmentum A nucleus of brain that spans a midbrain tegmentum. OBOL:automatic tegmental nuclei tegmental nucleus ZFA:0005577 The space within an epithelial sphere. AEO:0000079 cavity of vesicle uberon UBERON:0007473 lumen of epithelial sac The space within an epithelial sphere. AEO:JB cavity of vesicle AEO:0000079 A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified. AEO:0000081 EHDAA2:0003081 uberon UBERON:0007475 matrix-based tissue A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified. AEO:JB An epithelial tube that is open at one end only. AEO:0000115 EHDAA2:0003115 uberon UBERON:0007499 epithelial sac AEO An epithelial tube that is open at one end only. AEO:JB UBERONREF:0000001 An epithelial tube open at both ends that allows fluid flow. AEO_RETIRED:0000116 RETIRED_EHDAA2:0003116 uberon UBERON:0007500 epithelial tube open at both ends AEO An epithelial tube open at both ends that allows fluid flow. AEO:JB UBERONREF:0000001 A closed epithelium with a lumen. AEO:0000119 EHDAA2:0003119 uberon UBERON:0007503 epithelial vesicle AEO A closed epithelium with a lumen. AEO:JB A ring of smooth muscle cells whose contraction closes the opening of the ring. AEO:0000143 EHDAA2:0003143 SCTID:362915001 uberon UBERON:0007521 smooth muscle sphincter A ring of smooth muscle cells whose contraction closes the opening of the ring. AEO:JB A ring of striated muscle cells whose contraction closes the opening of the ring. AEO:0000144 EHDAA2:0003144 uberon UBERON:0007522 striated muscle sphincter A ring of striated muscle cells whose contraction closes the opening of the ring. AEO:JB Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 uberon UBERON:0007524 dense mesenchyme tissue AEO AEO Mesenchyme with little extracellular matrix. AEO:JB Mesenchymal cells that are migrating. this class will be an important part of the NC reorganization AEO:0000152 EHDAA2:0003152 uberon UBERON:0007530 migrating mesenchyme population Mesenchymal cells that are migrating. AEO:JB Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]. In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html] FMA:64798 uberon UBERON:0007592 ciliated columnar epithelium FMA Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]. FMA:64798 Epithelium bearing vibratile cilia on the free surface. uberon UBERON:0007601 ciliated epithelium Epithelium bearing vibratile cilia on the free surface. http://medical-dictionary.thefreedictionary.com/ciliated+epithelium A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 CALOHA:TS-0998 FMA:66762 synovium stratum synoviale synovial layer synovial membrane uberon synovial tissue UBERON:0007616 layer of synovial tissue BTO A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 http://www.britannica.com/EBchecked/topic/578563/synovial-tissue synovium CALOHA:TS-0998 stratum synoviale FMA:TA synovial layer FMA:66762 synovial membrane FMA:66762 synovial tissue BTO:0001338 An anatomical cavity that surrounded_by a synovial joint. FMA:11356 articular cavity (synovial joint) cavitas articularis (junctura synovialis) cavity of synovial joint uberon joint cavity synovial cavity UBERON:0007617 synovial cavity of joint An anatomical cavity that surrounded_by a synovial joint. OBOL:automatic articular cavity (synovial joint) FMA:11356 cavitas articularis (junctura synovialis) FMA:11356 cavity of synovial joint FMA:11356 joint cavity FMA:11356 synovial cavity FMA:11356 Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. GAID:907 MESH:D010857 uberon eye pigment epithelium UBERON:0007625 pigment epithelium of eye Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. MP:0005200 eye pigment epithelium MESH:A09.371.670 A neural nucleus that is part of a medulla oblongata. FMA:258772 SCTID:304943004 uberon UBERON:0007635 nucleus of medulla oblongata A neural nucleus that is part of a medulla oblongata. OBOL:automatic The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. BIRNLEX:4096 BM:V CALOHA:TS-2077 DHBA:266441713 FMA:71248 HBA:9203 MESH:D014278 UMLS:C0040999 Wikipedia:Trigeminal_nerve_nuclei neuronames:2021 trigeminal nuclei uberon nuclei trigemini UBERON:0007641 trigeminal nuclear complex http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png FMA FMA The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. Wikipedia:Trigeminal_nerve_nuclei in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. MA MESH:D014278 https://github.com/biopragmatics/biomappings UMLS:C0040999 BIRNLEX:4096 trigeminal nuclei FMA:71248 nuclei trigemini Wikipedia:Trigeminal_nerve_nuclei 2 An anatomical structure that connects two structures. junction FMA:5898 SCTID:91833003 anatomical junction uberon UBERON:0007651 anatomical junction FMA An anatomical structure that connects two structures. http://code.google.com/p/caro2/issues/detail?id=15 A sphincter that is part of an esophagus. check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here SCTID:277765007 uberon UBERON:0007652 esophageal sphincter A sphincter that is part of an esophagus. http://orcid.org/0000-0002-6601-2165 Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. field AEO:0000170 EFO:0001649 EHDAA2:0003170 FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon future organ organ field UBERON:0007688 anlage FBbt AEO FBbt Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. FBbt:00005426 http://flybase.org/reports/FBrf0178740.html FBbt:00005426 EFO:0003626 EHDAA2:0001457 EHDAA:962 EMAPA:32754 FMA:293087 TAO:0001104 ZFA:0001104 early pharyngeal arch endoderm uberon pharyngeal arch endoderm pharyngeal endoderm pharyngeal region endoderm UBERON:0007690 relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' early pharyngeal endoderm http://dev.biologists.org/content/128/22/4573.full cjm early pharyngeal arch endoderm EHDAA2:0001457 pharyngeal endoderm ZFA:0001104 pharyngeal region endoderm EHDAA2:0001456 A bone that is part of a reproductive organ. baculum uberon os penis/os clitoris UBERON:0007719 bone of reproductive organ A bone that is part of a reproductive organ. OBOL:automatic https://github.com/obophenotype/uberon/issues/1158 Wikipedia A gland that is part of a epidermis. FMA:59153 epidermal gland gland of epidermis uberon UBERON:0007771 epidermis gland A gland that is part of a epidermis. OBOL:automatic gland of epidermis FMA:59153 Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces. transudative characteristically low in protein and cellular content (unless there has been secondary concentration) FMA:12276 GAID:1195 MESH:D005122 ncithesaurus:Transudate uberon plasma ultrafiltrate UBERON:0007779 transudate Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces. http://medical-dictionary.thefreedictionary.com/transudate Any fluid produced by a serous gland. serous fluid Wikipedia:Serous_fluid serosal fluid serous gland fluid uberon UBERON:0007794 secretion of serous gland Any fluid produced by a serous gland. UBERON:cjm serosal fluid Wikipedia:Serous_fluid Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 MA:0002718 NCIT:C33854 UMLS:C0489903 uberon UBERON:0007798 vascular system MA Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. ncithesaurus:Vascular_System in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system MA UMLS:C0489903 ncithesaurus:Vascular_System Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:TS-0002 EFO:0003771 uberon abdominal adipose tissue abdominal fat intra-abdominal fat UBERON:0007808 adipose tissue of abdominal region Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 abdominal adipose tissue BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. CALOHA:TS-2356 EV:0100009 FMA:280881 MA:0000006 NCIT:C12418 SCTID:361355005 UMLS:C0460004 WikipediaCategory:Head_and_neck galen:HeadAndNeck uberon cephalic area cephalic part of animal cephalic region head and neck head or neck UBERON:0007811 craniocervical region MA The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. https://orcid.org/0000-0002-6601-2165 UMLS:C0460004 ncithesaurus:Head_and_Neck cephalic area https://github.com/obophenotype/uberon/issues/379 cephalic part of animal Wikipedia:Head cephalic region https://github.com/obophenotype/uberon/issues/379 head and neck FMA:280881 A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO] present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species) AAO:0010338 EMAPA:16748 MA:0000008 NCIT:C77663 TAO:0001117 UMLS:C0039259 XAO:0003026 ZFA:0001117 muscular postanal tail postanal tail post-anal fin tail uberon post-vent region UBERON:0007812 post-anal tail possible exception in hemichordates cjm A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. https://orcid.org/0000-0002-6601-2165 Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] 2012-06-20 AAO:0010338 AAO AAO:EJS Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO] 2012-08-14 TAO:0001117 TAO ZFIN:curator UMLS:C0039259 ncithesaurus:Tail post-anal fin tail http://purl.oboibrary.org/obo/uberon/tracker/185 post-vent region TAO:0001117 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). this encompasses non-skeletal tissue An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] UBERON:0007824 girdle girdle region EMAPA:37854 FMA:24874 VSAO:0000303 uberon fin girdle fin girdle region limb girdle limb girdle region UBERON:0007823 appendage girdle region An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] 2012-08-14 VSAO:0000303 VSAO https://orcid.org/0000-0002-6601-2165 EMAPA:37854 MA:th fin girdle fin girdle region limb girdle limb girdle region Mesentery that is located in the peritoneum. FMA:20570 TAO:0005129 XAO:0000138 ZFA:0005129 uberon UBERON:0007826 peritoneal mesentery FMA Mesentery that is located in the peritoneum. UBERON:cjm A bone that is part of a appendage girdle region. EMAPA:35379 MA:0000291 girdle bone uberon UBERON:0007828 girdle bone/zone A bone that is part of a appendage girdle region. OBOL:automatic girdle bone MA:0000291 A bone that is part of a pectoral girdle region. EMAPA:35669 MA:0000292 bone of pectoral girdle uberon UBERON:0007829 pectoral girdle bone MA A bone that is part of a pectoral girdle region. OBOL:automatic A bone element or fused bone that is part of pelvic girdle. check sacrum, coccyx (MA does NOT include these) typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone EMAPA:18028 MA:0000293 NCIT:C33287 SCTID:426214007 UMLS:C0030786 bone of pelvic girdle pelvic girdle bone uberon UBERON:0007830 pelvic girdle bone/zone MA A bone element or fused bone that is part of pelvic girdle. https://orcid.org/0000-0002-6601-2165 UMLS:C0030786 ncithesaurus:Pelvic_Bone pelvic girdle bone MA:0000293 A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons. Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO] Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO] The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG] Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. AAO:0000422 AAO:0000754 EFO:0000946 EHDAA2:0001420 FMA:24141 MAT:0000181 MIAA:0000181 NCIT:C33547 TAO:0000407 UMLS:C0427245 VHOG:0001156 VSAO:0000156 Wikipedia:Pectoral_girdle XAO:0003063 ZFA:0000407 skeletal parts of pectoral girdle skeleton of pectoral girdle uberon cingulum pectorale pectoral girdle scapular girdle UBERON:0007831 pectoral girdle skeleton http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons. Wikipedia:Pectoral_girdle Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO] 2012-08-14 TAO:0000407 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000156 VSAO https://orcid.org/0000-0002-6601-2165 Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO] 2012-06-20 AAO:0000422 AAO AAO:LAP The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG] 2012-09-17 VHOG:0001156 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18 http://bgee.unil.ch/ Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. VSAO UMLS:C0427245 ncithesaurus:Shoulder_Girdle skeletal parts of pectoral girdle https://orcid.org/0000-0002-6601-2165 skeleton of pectoral girdle https://orcid.org/0000-0002-6601-2165 cingulum pectorale Wikipedia:Pectoral_girdle pectoral girdle VSAO:0000156 scapular girdle TAO:0000407 Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts AAO:0000426 AAO:0000768 EFO:0000947 EHDAA2:0001426 EHDAA:7149 EHDAA:8324 EMAPA:18028 FMA:87592 MAT:0000182 MIAA:0000182 TAO:0000565 VHOG:0000305 VSAO:0000155 Wikipedia:Pelvis XAO:0003064 ZFA:0000565 galen:PelvicGirdle http://people.eku.edu/ritchisong/pectoralgirdles.gif pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle uberon pelvic girdle UBERON:0007832 pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png PMID:21455939 Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. VSAO:0000155 Wikipedia:Pelvis Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] 2012-06-20 AAO:0000426 AAO AAO:LAP Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] 2012-08-14 TAO:0000565 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000155 VSAO https://orcid.org/0000-0002-6601-2165 The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] 2012-09-17 VHOG:0000305 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 http://bgee.unil.ch/ Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts VSAO pelvic girdle skeleton VSAO:0000155 skeletal parts of pelvic girdle https://orcid.org/0000-0002-6601-2165 skeleton of pelvic girdle https://orcid.org/0000-0002-6601-2165 pelvic girdle VSAO:0000155 Bone element that arises as a result of intramembranous ossification. Bone element that arises as a result of intramembranous ossification.[VSAO] Intramembranous bone that forms deep in the organism.[TAO] AEO:0000085 EHDAA2:0003085 TAO:0001645 VSAO:0000023 XAO:0004014 ZFA:0001636 uberon membrane bones UBERON:0007842 membrane bone VSAO Bone element that arises as a result of intramembranous ossification. GO_REF:0000034 VSAO:0000023 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/267 Bone element that arises as a result of intramembranous ossification.[VSAO] 2012-08-14 VSAO:0000023 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Intramembranous bone that forms deep in the organism.[TAO] 2012-08-14 TAO:0001645 TAO TAO:wd membrane bones ZFA:0001636 Skeletal element that is composed of cartilage tissue and may be permanent or transient. TAO still mixes tissue and element AAO:0011130 CALOHA:TS-0118 EMAPA:32730 FMA:55107 VSAO:0000000 XAO:0004013 ZFA:0001501 cartilage organ cartilaginous element chondrogenic element uberon cartilage UBERON:0007844 cartilage element VSAO VSAO VSAO Skeletal element that is composed of cartilage tissue and may be permanent or transient. GO_REF:0000034 PSPUB:0000170 VSAO:0000000 http://dx.plos.org/10.1371/journal.pone.0051070 TAO still mixes tissue and element TAO cartilage organ FMA:55107 cartilaginous element https://orcid.org/0000-0002-6601-2165 chondrogenic element VSAO:0000000 cartilage VSAO:0000000 Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification). FMA:20103 uberon UBERON:0007845 regular connective tissue FMA Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. FMA:20103 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] FMA:64781 NCIT:C33453 SCTID:22560007 UMLS:C0225333 VSAO:0000050 Wikipedia:Dense_regular_connective_tissue XAO:0004030 dense fibrous connective tissue dense regular collagenous connective tissue dense regular collagenous tissue regular dense connective tissue typus regularis (textus connectivus collagenosus compactus) uberon UBERON:0007846 dense regular connective tissue FMA ncithesaurus Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). GO_REF:0000034 PSPUB:0000170 VSAO:0000050 http://dx.plos.org/10.1371/journal.pone.0051070 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] 2012-08-14 VSAO:0000050 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] 2012-08-29 FMA:64781 FMA UMLS:C0225333 ncithesaurus:Regular_Dense_Connective_Tissue dense fibrous connective tissue FMA:64781 dense regular collagenous connective tissue FMA:64781 dense regular collagenous tissue FMA:64781 typus regularis (textus connectivus collagenosus compactus) FMA:64781 A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 head or neck bone uberon cranial bone UBERON:0007914 bone of craniocervical region MA MA A bone that is part of a craniocervical region. OBOL:automatic EMAPA:37245 MA:th head or neck bone MA:0000569 The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. FMA:7477 NCIT:C32881 SCTID:421560006 UMLS:C0502414 Wikipedia:Irregular_bone os irregulare uberon os irregulare UBERON:0008001 irregular bone FMA The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. Wikipedia:Irregular_bone UMLS:C0502414 ncithesaurus:Irregular_Bone os irregulare Wikipedia:Irregular_bone A skeletal joint that is part of a appendage girdle region. MA:0001505 girdle joint uberon UBERON:0008114 joint of girdle MA A skeletal joint that is part of a appendage girdle region. OBOL:automatic girdle joint OBOL:automatic An anatomical surface that is part of a cartilage element. FMA:76668 cartilage surface uberon UBERON:0008115 surface of cartilage An anatomical surface that is part of a cartilage element. OBOL:automatic cartilage surface FMA:76668 A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. subclasses of this should be checked for taxonomic consistency Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity] FMA:7478 SCTID:333008005 Wikipedia:Skeletal_pneumaticity galen:PneumaticBone os pneumaticum pneumatic bone uberon hollow bone UBERON:0008193 pneumatized bone A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. http://www.medilexicon.com/medicaldictionary.php?t=11303 os pneumaticum FMA:7478 pneumatic bone FMA:7478 Any muscle organ that is part of a pectoral girdle region. EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate EMAPA:17748 FMA:37347 muscle of shoulder girdle pectoral girdle muscle uberon UBERON:0008196 muscle of pectoral girdle Any muscle organ that is part of a pectoral girdle region. OBOL:automatic EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate EMAPA muscle of shoulder girdle FMA:37347 pectoral girdle muscle FMA:37347 The part of the ventral body cavity that is within the pelvis. EMAPA:37235 FMA:9738 MA:0003089 SCTID:281903009 Wikipedia:Pelvic_cavity space of pelvic compartment uberon cavitas pelvis UBERON:0008203 pelvic cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the ventral body cavity that is within the pelvis. UBERON:cjm EMAPA:37235 MA:th space of pelvic compartment FMA:9738 cavitas pelvis Wikipedia:Pelvic_cavity Musculature system of the pharyngeal and head regions. in MA this is restricted to skeletal muscles EMAPA:37259 MA:0000571 TAO:0000328 ZFA:0000328 head or neck muscle uberon head muscles head or neck muscle UBERON:0008229 craniocervical region musculature MA MA Musculature system of the pharyngeal and head regions. ZFA:0000328 ZFA:curator in MA this is restricted to skeletal muscles MA EMAPA:37259 MA:th head or neck muscle MA:0000571 head muscles ZFA:0000328 head or neck muscle MA:0000571 Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. EMAPA:37234 FMA:24217 MA:0000028 SCTID:362666008 dorsum of thorax posterior part of thorax thoracic back thoracic part of back upper back uberon back of thorax UBERON:0008231 dorsal thoracic segment of trunk FMA MA FMA Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. FMA:24217 EMAPA:37234 MA:th dorsum of thorax FMA:24217 posterior part of thorax FMA:24217 thoracic back FMA:24217 thoracic part of back FMA:24217 upper back MA:0000028 back of thorax FMA:24217 A muscle of back that is part of a dorsal thoracic segment of trunk. EMAPA:37261 MA:0000508 SCTID:305071003 uberon UBERON:0008243 upper back muscle MA MA A muscle of back that is part of a dorsal thoracic segment of trunk. OBOL:automatic EMAPA:37261 MA:th An endothelium that is part of a heart [Automatically generated definition]. this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class. BTO:0004293 uberon cardiac endothelium UBERON:0008307 heart endothelium An endothelium that is part of a heart [Automatically generated definition]. OBOL:automatic cardiac endothelium BTO:0004293 BTO:0003122 uberon UBERON:0008339 microvascular endothelium https://github.com/obophenotype/uberon/issues/2186 An intestinal villus in the duodenum. FMA:63300 uberon UBERON:0008342 intestinal villus of duodenum An intestinal villus in the duodenum. OBOL:automatic An epithelium that is part of a duodenum. CALOHA:TS-2087 EMAPA:19078 FMA:17231 MA:0003208 SCTID:66036002 epithelium of duodenum uberon UBERON:0008346 duodenal epithelium FMA An epithelium that is part of a duodenum. OBOL:automatic epithelium of duodenum FMA:17231 A vertebral foramen that is part of a cervical vertebra. FMA:13480 SCTID:280833008 uberon UBERON:0008429 cervical vertebral foramen A vertebral foramen that is part of a cervical vertebra. OBOL:automatic A vertebral foramen that is part of a thoracic vertebra. FMA:9143 SCTID:280834002 uberon UBERON:0008432 thoracic vertebral foramen A vertebral foramen that is part of a thoracic vertebra. OBOL:automatic An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers. EHDAA2:0000444 EHDAA:42 EHDAA:75 EMAPA:16050 NCIT:C34164 UMLS:C1516906 uberon embryonic epiblast UBERON:0008780 The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5. inner cell mass derived epiblast Wikipedia An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers. MP:0003886 UMLS:C1516906 ncithesaurus:Epiblast embryonic epiblast MP:0003886 A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing EHDAA2:0000187 FMA:293041 NCIT:C34248 UMLS:C1519038 embryonic pharyngeal complex pharyngeal apparatus pharyngeal system uberon pharyngeal arch complex pharyngeal arch region pharyngeal arches and clefts pharyngeal complex UBERON:0008814 pharyngeal arch system A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. GO:0060037 GOC:dph UMLS:C1519038 ncithesaurus:Pharyngeal_Apparatus pharyngeal system GO:0060037 pharyngeal arch region EHDAA2:0000187 A head that is part of a embryo. CALOHA:TS-0246 FBbt:00000155 FMA:293011 uberon UBERON:0008816 embryonic head A head that is part of a embryo. OBOL:automatic FBbt:00000155 A brain that develops_from a neural tube. a reasoner should automatically classify all the vertebrate ontology brain classes here vertebrate brain uberon UBERON:0008823 neural tube derived brain https://github.com/obophenotype/uberon/issues/338 ZFA FMA A brain that develops_from a neural tube. OBOL:automatic https://github.com/obophenotype/uberon/issues/338 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10 The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. AAO:0011057 EHDAA2:0000740 EHDAA:1530 NCIT:C34187 UMLS:C1512407 Wikipedia:Hepatic_diverticulum XAO:0000101 liver diverticulum uberon diverticulum hepaticum UBERON:0008835 hepatic diverticulum http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png EHDAA2 caudal part EHDAA2 EHDAA2 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. MP:MP http://www.stembook.org/node/512 UMLS:C1512407 ncithesaurus:Hepatic_Diverticulum liver diverticulum XAO:0000101 diverticulum hepaticum Wikipedia:Hepatic_diverticulum BTO:0001642 uberon UBERON:0008836 liver bud cjm http://www.stembook.org/node/512 Closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals. EMAPA:16080 epamniotic cavity uberon epamniotic cavity UBERON:0008851 ectoplacental cavity Closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals. MP:0011207 http://www.medilexicon.com/medicaldictionary.php?s=epamniotic+cavity epamniotic cavity http://www.medilexicon.com/medicaldictionary.php?s=epamniotic+cavity epamniotic cavity MP:0011207 The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines. the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two FMA:14909 SCTID:362132003 gastric muscularis muscle layer of stomach muscularis externa of stomach tunica muscularis (gaster) tunica muscularis gastris uberon UBERON:0008856 stomach muscularis externa MA-abduced The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines. MP:0010779 the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two WP gastric muscularis FMA:14909 muscle layer of stomach FMA:14909 muscularis externa of stomach FMA:14909 tunica muscularis (gaster) FMA:14909 The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter. EMAPA:37944 FMA:14580 SCTID:245417002 Wikipedia:Pyloric_canal canalis pyloricus uberon canalis pyloricus UBERON:0008858 pyloric canal https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg FMA Wikipedia The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter. MP:0010791 Wikipedia:Pyloric_canal EMAPA:37944 MA:th canalis pyloricus Wikipedia:Pyloric_canal canalis pyloricus Wikipedia:Pyloric_canal The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. check relationship to pylorus vs antrum EMAPA:27211 FMA:14922 NCIT:C33431 SCTID:70710007 UMLS:C0227239 Wikipedia:Pyloric_gland glandula pylorica pyloric antrum gland pyloric gland pyloric mucuous gland uberon UBERON:0008861 pyloric gastric gland http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png MP Wikipedia:Tubular_gland The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. MP:0010797 Wikipedia:Pyloric_gland UMLS:C0227239 ncithesaurus:Pyloric_Gland glandula pylorica FMA:14922 pyloric antrum gland OBOL:automatic pyloric gland FMA:14922 Any skeletal muscle organ in the hypodermis / superficial fascia. We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this UBERON:0010934 EMAPA:18188 MA:0003140 hypodermal muscle layer hypodermis muscle layer superficial fascia muscular layer panniculus carnosus uberon UBERON:0008876 hypodermis skeletal muscle layer MP-def Any skeletal muscle organ in the hypodermis / superficial fascia. ISBN:0123813611 MP:0011157 hypodermal muscle layer MP:0011157 hypodermis muscle layer MP:0011157 panniculus carnosus MP:0011157 The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA:45621 Wikipedia:Pulmonary_circulation pulmonary circulatory system pulmonary system uberon UBERON:0008886 pulmonary vascular system Obol The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. ISBN:0073040584 Wikipedia:Pulmonary_circulation Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA FMA:45621 pulmonary circulatory system FMA:45621 pulmonary system ISBN:0073040584 Subdivision of endoskeleton derived from pharyngeal arches. Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both AAO:0010157 TAO:0001216 VHOG:0000315 VSAO:0000149 Wikipedia:Facial_skeleton XAO:0003176 ZFA:0001216 pharyngeal endoskeleton viscerocranium uberon branchial arch skeleton gill arch skeleton pharyngeal arch pharyngeal arch skeleton pharyngeal skeleton visceral cranium visceral skeletal system visceral skeleton UBERON:0008895 splanchnocranium http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg https://github.com/obophenotype/uberon/issues/83 redundant Grays PMID:11237469 Subdivision of endoskeleton derived from pharyngeal arches. ISBN:0073040584 Wikipedia:Facial_skeleton https://orcid.org/0000-0002-6601-2165 Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] 2012-08-14 TAO:0001216 TAO ZFIN:curator Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] 2012-06-20 AAO:0010157 AAO AAO:EJS The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] 2012-09-17 VHOG:0000315 VHOG http://bgee.unil.ch/ The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000315 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235 http://bgee.unil.ch/ VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. VSAO pharyngeal endoskeleton http://orcid.org/0000-0002-6601-2165 viscerocranium VHOG:0000315 Wikipedia:Viscerocranium ZFA:0001216 pharyngeal arch VSAO:0000149 pharyngeal arch skeleton ZFA:0001216 pharyngeal skeleton ZFA:0001216 visceral cranium http://orcid.org/0000-0002-6601-2165 visceral skeletal system http://orcid.org/0000-0002-6601-2165 visceral skeleton UBERONREF:0000007 Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. Intramembranous bone that forms superficially in the organism.[TAO] other AOs are not yet in sync with this classification AAO:0010769 TAO:0001590 VSAO:0000130 Wikipedia:Dermal_bone XAO:0004015 ZFA:0001590 uberon dermal bones UBERON:0008907 dermal bone wd VSAO VSAO Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. GO_REF:0000034 VSAO:0000130 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/267 Intramembranous bone that forms superficially in the organism.[TAO] 2012-08-14 TAO:0001590 TAO TAO:wd dermal bones ZFA:0001590 Bone element that is adjacent to the notochord. We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] AAO:0010777 TAO:0001639 VSAO:0000307 ZFA:0001629 perichordal bones uberon perichordal bone UBERON:0008909 perichordal bone not in VSAO ZFA Bone element that is adjacent to the notochord. GO_REF:0000034 VSAO:0000307 http://dx.plos.org/10.1371/journal.pone.0051070 Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] 2012-08-14 TAO:0001639 TAO TAO:wd perichordal bones ZFA:0001629 perichordal bone ZFA:0001629 A parenchyma that is part of a lung. EMAPA:35522 FMA:27360 MA:0003168 SCTID:201712001 respiratory portion of lung uberon parenchyma of lung pulmonary parenchyma UBERON:0008946 lung parenchyma FMA FMA A parenchyma that is part of a lung. OBOL:automatic respiratory portion of lung FMA:27360 parenchyma of lung BTO:0000763 pulmonary parenchyma EMAPA:35522 EHDAA2:0004069 NCIT:C34283 UMLS:C1514898 uberon UBERON:0008947 respiratory primordium Obol UMLS:C1514898 ncithesaurus:Respiratory_Primordium A lobe of lung that is part of a left lung. 1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure EHDAA:2981 NCIT:C48945 SCTID:272655003 UMLS:C1285107 lobe of left lung lobe of the left lung uberon UBERON:0008951 left lung lobe A lobe of lung that is part of a left lung. OBOL:automatic 1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure ISBN:0123813611 UMLS:C1285107 ncithesaurus:Lobe_of_the_Left_Lung One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed. BTO:0003634 FMA:9404 NCIT:C32536 SCTID:322749003 UMLS:C0227178 Wikipedia:Esophageal_glands esophageal gland glandulae oesophageae mucous gland of submucosa of esophagus uberon submocosal esophageal gland UBERON:0008989 submucosal esophageal gland http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed. BTO:0003634 Wikipedia:Esophageal_glands UMLS:C0227178 ncithesaurus:Esophageal_Gland esophageal gland FMA:9404 glandulae oesophageae Wikipedia:Esophageal_glands mucous gland of submucosa of esophagus FMA:9404 System pertaining to blood vessels in the brain. UBERON:0005284 BTO:0003840 EFO:0003491 EMAPA:35186 FMA:242007 FMA:61935 SCTID:362029003 TAO:0000099 ZFA:0000099 brain vasculature cerebrovascular system intracerebral vasculature uberon UBERON:0008998 vasculature of brain System pertaining to blood vessels in the brain. BTO:0003840 cerebrovascular system BTO:0003840 intracerebral vasculature FMA:61935 A zone of skin that is part of a dorsal thoracic segment of trunk. EMAPA:37280 MA:0000510 SCTID:304890003 uberon UBERON:0009015 upper back skin MA A zone of skin that is part of a dorsal thoracic segment of trunk. OBOL:automatic EMAPA:37280 MA:th Vein that drains left lung and returns blood to the heart. A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. EMAPA:37165 MA:0002207 NCIT:C48946 SCTID:304057004 UMLS:C0226670 uberon UBERON:0009030 left pulmonary vein Vein that drains left lung and returns blood to the heart. http://orcid.org/0000-0002-6601-2165 A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. ncithesaurus:Left_Pulmonary_Vein EMAPA:37165 MA:th UMLS:C0226670 ncithesaurus:Left_Pulmonary_Vein Vein that drains right lung and returns blood to the heart. A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. EMAPA:37379 MA:0002208 NCIT:C48947 SCTID:304056008 UMLS:C0226669 uberon UBERON:0009032 right pulmonary vein Vein that drains right lung and returns blood to the heart. http://orcid.org/0000-0002-6601-2165 A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. ncithesaurus:Right_Pulmonary_Vein EMAPA:37379 MA:th UMLS:C0226669 ncithesaurus:Right_Pulmonary_Vein A gonad prior to differentiating into a definitive testis or ovary. EHDAA2:0000716 NCIT:C34192 UMLS:C1512703 uberon gonad rudiment UBERON:0009117 typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] indifferent gonad A gonad prior to differentiating into a definitive testis or ovary. http://www.medterms.com/script/main/art.asp?articlekey=8981 UMLS:C1512703 ncithesaurus:Indifferent_Gonad Cranial ganglion which develops from an epibranchial placode. BTO:0006250 TAO:0001555 ZFA:0001555 epibranchial ganglia uberon UBERON:0009127 Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion ZFA NCBIBook:NBK53175 Cranial ganglion which develops from an epibranchial placode. PMID:20133851 ZFIN:curator BTO:0006250 https://github.com/biopragmatics/biomappings epibranchial ganglia ZFA:0001555 Endocardium that is part of the right atrium. EHDAA2:0000274 FMA:7281 NCIT:C102339 SCTID:3194006 VHOG:0001228 endocardium of right atrium right atrial endocardium uberon right atrium endocardial tissue UBERON:0009129 right atrium endocardium EHDAA2 EHDAA2 Endocardium that is part of the right atrium. http://orcid.org/0000-0002-6601-2165 endocardium of right atrium FMA:7281 right atrial endocardium FMA:7281 right atrium endocardial tissue VHOG:0001228 A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] UBERON:0009146 EHDAA2:0001483 EMAPA:17709 NCIT:C34256 SCTID:361429005 UMLS:C1283968 VHOG:0000757 Wikipedia:Pleuroperitoneal pleuroperitoneal fold pleuroperitoneal membranes uberon UBERON:0009133 pleuroperitoneal membrane EHDAA2 A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. Wikipedia:Pleuroperitoneal http://medical-dictionary.thefreedictionary.com/pleuroperitoneal+membrane In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000757 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ UMLS:C1283968 ncithesaurus:Pleuroperitoneal_Membrane pleuroperitoneal fold VHOG:0000757 pleuroperitoneal membranes EHDAA2:0001483 A vein that is part of a craniocervical region. EHDAA2:0004542 SCTID:32945007 craniocervical vein head and neck veins vein of head and neck uberon UBERON:0009141 craniocervical region vein A vein that is part of a craniocervical region. OBOL:automatic head and neck veins EHDAA2:0004542 Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 uberon UBERON:0009142 entire embryonic mesenchyme EHDAA2 Sum total of mesenchyme in the embryo. https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7 EMAPA:16549 RETIRED_EHDAA2:0001454 pharyngeal region uberon UBERON:0009145 pharyngeal region of foregut EHDAA2 pharyngeal region EMAPA:16549 A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0003446 EMAPA:18015 uberon UBERON:0009191 sphenoid bone pre-cartilage condensation EHDAA2 EHDAA2 EHDAA2 EHDAA2 A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A sphenoid endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001888 sphenoid bone cartilage condensation uberon UBERON:0009193 sphenoid cartilage element EHDAA2 A sphenoid endochondral element that is composed primarily of cartilage tissue. OBOL:automatic sphenoid bone cartilage condensation EHDAA2:0001888 EHDAA2:0004021 uberon UBERON:0009196 indifferent external genitalia cjm Mesenchyme that is part of a medial nasal prominence. EHDAA2:0001077 EMAPA:16810 FMA:312659 uberon UBERON:0009204 medial nasal process mesenchyme EHDAA2 Mesenchyme that is part of a medial nasal prominence. OBOL:automatic medial or lateral; in EHDAA2 also frontonasal or intermaxillary EHDAA2:0000581 EHDAA:4776 EMAPA:16680 FMA:293971 SCTID:308881001 uberon nasal placode UBERON:0009292 embryonic nasal process medial or lateral; in EHDAA2 also frontonasal or intermaxillary EHDAA2 An ectoderm that is part of a buccopharyngeal membrane. EHDAA2:0000190 EMAPA:16260 uberon UBERON:0009479 ectoderm of buccopharyngeal membrane An ectoderm that is part of a buccopharyngeal membrane. OBOL:automatic An endoderm that is part of a buccopharyngeal membrane. EHDAA2:0000191 EMAPA:16261 uberon UBERON:0009480 endoderm of buccopharyngeal membrane An endoderm that is part of a buccopharyngeal membrane. OBOL:automatic Mesenchyme that is part of a foregut-midgut junction. EHDAA2:0000570 EMAPA:16364 uberon UBERON:0009482 associated mesenchyme of foregut-midgut junction Mesenchyme that is part of a foregut-midgut junction. OBOL:automatic A mesentery that is part of a foregut-midgut junction. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0000575 EMAPA:16365 VHOG:0000430 foregut-midgut junction mesentery uberon UBERON:0009483 mesentery of foregut-midgut junction A mesentery that is part of a foregut-midgut junction. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000430 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ foregut-midgut junction mesentery VHOG:0000430 A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. EMAPA:32755 FMA:295694 branchial arch mesenchyme pharyngeal arch mesenchyme uberon UBERON:0009494 pharyngeal arch mesenchymal region EHDAA2 cjm A portion of mesenchymal tissue associated with an individual pharyngeal arch. https://orcid.org/0000-0002-6601-2165 this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. MP:0011262 branchial arch mesenchyme MP:0011262 pharyngeal arch mesenchyme https://orcid.org/0000-0002-6601-2165 An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 uberon UBERON:0009497 epithelium of foregut-midgut junction EHDAA2 EHDAA2 An epithelium that is part of a foregut-midgut junction. OBOL:automatic The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head. EHDAA2:0004109 EMAPA:16683 FMA:295821 frontonasal mesenchyme naso-frontal mesenchyme uberon UBERON:0009501 mesenchyme of fronto-nasal process The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head. MP:0011266 frontonasal mesenchyme MP:0011266 naso-frontal mesenchyme MP:0011266 Mesenchyme that is part of a developing hindgut. EHDAA2:0000780 EMAPA:16716 hindgut associated mesenchyme uberon UBERON:0009503 mesenchyme of hindgut Mesenchyme that is part of a developing hindgut. OBOL:automatic hindgut associated mesenchyme EHDAA2:0000780 An endoderm that is part of a anal region. EHDAA2:0004020 EMAPA:17177 uberon UBERON:0009521 anal membrane endodermal component An endoderm that is part of a anal region. OBOL:automatic Mesenchyme that is part of a maxillary prominence. EHDAA2:0001071 EMAPA:17361 FMA:312691 mesenchyme of maxillary process mesenchyme of maxillary prominence uberon UBERON:0009526 maxillary process mesenchyme Mesenchyme that is part of a maxillary prominence. OBOL:automatic mesenchyme of maxillary process EMAPA:17361 mesenchyme of maxillary prominence https://orcid.org/0000-0002-6601-2165 A hepatic sinusoid that is part of a left lobe of liver. EHDAA2:0001001 EMAPA:18309 VHOG:0000709 left lobe hepatic sinusoids uberon UBERON:0009548 hepatic sinusoid of left of lobe of liver A hepatic sinusoid that is part of a left lobe of liver. OBOL:automatic left lobe hepatic sinusoids VHOG:0000709 A hepatic sinusoid that is part of a right lobe of liver. EHDAA2:0001009 EMAPA:18316 VHOG:0000710 right lobe hepatic sinusoids uberon UBERON:0009549 hepatic sinusoid of right of lobe of liver A hepatic sinusoid that is part of a right lobe of liver. OBOL:automatic right lobe hepatic sinusoids VHOG:0000710 An endoderm that is part of a foregut-midgut junction. EHDAA2:0000572 EMAPA:18403 uberon UBERON:0009550 endoderm of foregut-midgut junction An endoderm that is part of a foregut-midgut junction. OBOL:automatic A submucosa that is part of a intestine. FMA:15696 submucosa of intestine uberon UBERON:0009566 intestinal submucosa FMA A submucosa that is part of a intestine. OBOL:automatic submucosa of intestine FMA:15696 Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] AAO:0000612 FMA:72066 NCIT:C92597 SCTID:281699004 thoracolumbar column thoracolumbar region of vertebral column thoracolumbar vertebrae set thoracolumbar vertebral column trunk vertebrae series trunk vertebral column uberon presacral region thoracolumbar region trunk region trunk skeleton trunk spine UBERON:0009568 trunk region of vertebral column Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions. UBERONREF:0000006 Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 thoracolumbar vertebrae set FMA:72066 presacral region AAO:0000612 thoracolumbar region AAO:0000612 trunk region AAO:0000612 FMA:25054 SCTID:22943007 region of trunk trunk subdivision uberon UBERON:0009569 subdivision of trunk region of trunk FMA:25054 trunk subdivision FMA:25054 A sulcus limitans of neural tube that is part of a future spinal cord. EHDAA2:0001265 EMAPA:17584 VHOG:0001548 spinal cord lateral wall sulcus limitans uberon UBERON:0009570 spinal cord sulcus limitans A sulcus limitans of neural tube that is part of a future spinal cord. OBOL:automatic spinal cord lateral wall sulcus limitans EHDAA2:0001265 A sulcus limitans of neural tube that is part of a future medulla oblongata. EHDAA2:0001100 EMAPA:17561 uberon UBERON:0009576 medulla oblongata sulcus limitans EHDAA2 A sulcus limitans of neural tube that is part of a future medulla oblongata. OBOL:automatic A sulcus limitans of neural tube that is part of a future metencephalon. EHDAA2:0001161 EMAPA:17567 uberon UBERON:0009577 metencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future metencephalon. OBOL:automatic A sulcus limitans of neural tube that is part of a future myelencephalon. EHDAA2:0001945 uberon UBERON:0009578 myelencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future myelencephalon. OBOL:automatic EHDAA2:0001172 EMAPA:16977 VHOG:0000910 mantle layer lateral wall midbrain midbrain lateral wall mantle layer uberon mantle layer lateral wall mesencephalon UBERON:0009581 midbrain mantle layer mantle layer lateral wall midbrain VHOG:0000910 mantle layer lateral wall mesencephalon VHOG:0000910 EMAPA:17580 VHOG:0000911 mantle layer lateral wall spinal cord spinal cord lateral wall mantle layer uberon UBERON:0009583 spinal cord mantle layer mantle layer lateral wall spinal cord VHOG:0000911 Mesenchyme that is part of a 1st arch mandibular component. UBERON:0010043 EHDAA2:0000034 EMAPA:16385 mesenchymal region of mandibular component of first pharyngeal arch mesenchyme of mandibular component uberon mandibular component mesenchyme mandibular mesenchyme UBERON:0009584 1st arch mandibular mesenchyme EMAPA Mesenchyme that is part of a 1st arch mandibular component. OBOL:automatic mesenchymal region of mandibular component of first pharyngeal arch https://orcid.org/0000-0002-6601-2165 mesenchyme of mandibular component EMAPA:16385 Mesenchyme that is part of a developing left lung. EHDAA2:0000944 EMAPA:16730 EMAPA:17654 left lung mesenchyme uberon UBERON:0009602 left lung associated mesenchyme Mesenchyme that is part of a developing left lung. OBOL:automatic left lung mesenchyme EMAPA:17654 Mesenchyme that is part of a developing right lung. EHDAA2:0001739 EMAPA:17662 right lung mesenchyme uberon UBERON:0009603 right lung associated mesenchyme Mesenchyme that is part of a developing right lung. OBOL:automatic right lung mesenchyme EMAPA:17662 A neural plate that develops_from a presumptive midbrain. TAO:0007019 ZFA:0007019 uberon UBERON:0009611 midbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive midbrain. OBOL:automatic A neural plate that develops_from a presumptive hindbrain. TAO:0007022 ZFA:0007022 uberon UBERON:0009614 hindbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive hindbrain. OBOL:automatic TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 MHB neural plate midbrain-hindbrain boundary neural plate uberon UBERON:0009615 midbrain hindbrain boundary neural plate ZFA https://github.com/obophenotype/uberon/issues/438 Bgee:AN MHB neural plate https://orcid.org/0000-0002-6601-2165 midbrain-hindbrain boundary neural plate ZFA:0007044 A presumptive structure that has the potential to develop into a midbrain. TODO - unify naming conventions BAMS:MES EFO:0003432 EHDAA2:0000615 EMAPA:16140 TAO:0000148 Wikipedia:Mesencephalon ZFA:0000148 presumptive mesencephalon uberon early midbrain future midbrain mesencephalon UBERON:0009616 presumptive midbrain ZFA ZFA A presumptive structure that has the potential to develop into a midbrain. OBOL:automatic presumptive mesencephalon ZFA:0000148 early midbrain https://orcid.org/0000-0002-6601-2165 future midbrain https://orcid.org/0000-0002-6601-2165 mesencephalon EHDAA2:0000615 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. A major contributor to neurocranium [PMID:16313393] EHDAA2:0000736 EHDAA:364 EMAPA:16171 cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme uberon somitomere somitomeric mesoderm UBERON:0009617 head paraxial mesoderm EHDAA2 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. PMID:21610022 cephalic paraxial mesenchyme https://orcid.org/0000-0002-6601-2165 cephalic paraxial mesoderm https://orcid.org/0000-0002-6601-2165 cranial paraxial mesenchyme https://orcid.org/0000-0002-6601-2165 cranial paraxial mesoderm https://orcid.org/0000-0002-6601-2165 head paraxial mesenchyme EHDAA2:0000736 https://github.com/obophenotype/uberon/issues/30 EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon trunk paraxial mesenchyme UBERON:0009618 trunk paraxial mesoderm EHDAA2 trunk and cervical paraxial mesenchyme EHDAA2:0002094 trunk paraxial mesenchyme https://github.com/obophenotype/uberon/issues/30 A somite that is part of a tail. AAO:0010383 EMAPA:16860 XAO:0003143 uberon UBERON:0009621 tail somite A somite that is part of a tail. OBOL:automatic labial artery EMAPA:37092 MA:0001987 NCIT:C52947 UMLS:C1708633 uberon UBERON:0009657 artery of lip labial artery MA:0001987 EMAPA:37092 MA:th UMLS:C1708633 ncithesaurus:Labial_Artery Nucleus located in the midbrain. SCTID:279285003 TAO:0002209 ZFA:0001665 uberon UBERON:0009661 midbrain nucleus Nucleus located in the midbrain. ZFIN:curator Nucleus located within the hindbrain. TAO:0002177 ZFA:0001658 uberon UBERON:0009662 hindbrain nucleus Nucleus located within the hindbrain. ZFIN:curator EHDAA2:0004566 EMAPA:32911 MA:0003203 uberon peritoneal cavity mesentary peritoneal mesentary UBERON:0009664 gut mesentery https://github.com/obophenotype/uberon/issues/509 EHDAA2 peritoneal cavity mesentary http://orcid.org/0000-0002-6601-2165 peritoneal mesentary http://orcid.org/0000-0002-6601-2165 An anatomical space that surrounded_by a embryonic cloaca. EHDAA2:0004586 uberon UBERON:0009669 embryonic cloacal lumen An anatomical space that surrounded_by a embryonic cloaca. OBOL:automatic An anatomical space that surrounded_by a rectum. EHDAA2:0004587 EMAPA:18388 FMA:14598 SCTID:259740004 lumen of rectum uberon UBERON:0009670 rectal lumen cjm EHDAA2 An anatomical space that surrounded_by a rectum. OBOL:automatic lumen of rectum FMA:14598 EHDAA2:0001371 uberon pancreatis dorsalis UBERON:0009708 dorsal pancreas EHDAA2 EHDAA2 EHDAA2 cjm EHDAA2:0001393 uberon pancreatis ventralis UBERON:0009709 ventral pancreas EHDAA2 EHDAA2 EHDAA2 cjm Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. EHDAA2:0002188 EMAPA:17341 FMA:9536 NCIT:C102343 SCTID:8911002 VHOG:0001235 right ventricle endocardium right ventricular endocardium uberon endocardial lining of right ventricle right ventricle endocardial tissue UBERON:0009712 endocardium of right ventricle EHDAA2 FMA Any endocardium that is part of the right ventricle of the heart. http://orcid.org/0000-0002-6601-2165 Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. FMA:9536 right ventricle endocardium VHOG:0001235 right ventricular endocardium FMA:9536 endocardial lining of right ventricle EMAPA:17341 right ventricle endocardial tissue VHOG:0001235 Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. EHDAA2:0002182 EMAPA:17338 FMA:9559 SCTID:191004004 VHOG:0001233 left ventricle endocardium left ventricular endocardium uberon endocardial lining of left ventricle left ventricle endocardial tissue UBERON:0009713 endocardium of left ventricle FMA Any endocardium that is part of the left ventricle of the heart. http://orcid.org/0000-0002-6601-2165 Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. FMA:9559 left ventricle endocardium VHOG:0001233 left ventricular endocardium FMA:9559 endocardial lining of left ventricle EMAPA:17338 left ventricle endocardial tissue VHOG:0001233 An anatomical cavity that surrounded_by a stomodeum. lumen of stomatodaeum lumen of stomodeum stomatodeal cavity uberon UBERON:0009715 stomodeal lumen An anatomical cavity that surrounded_by a stomodeum. OBOL:automatic EHDAA2:0004621 EMAPA:32754 FMA:293087 uberon pharyngeal arch endoderm UBERON:0009722 entire pharyngeal arch endoderm EHDAA2 pharyngeal arch endoderm EHDAA2:0004621 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures. decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts EHDAA2:0004162 EMAPA:36438 heart mesenchyme uberon UBERON:0009751 cardiac mesenchyme The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures. MP:0011264 heart mesenchyme EMAPA:36438 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas. EFO:0002557 EMAPA:26220 uberon UBERON:0009752 pancreas mesenchyme The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas. MP:0011265 A ganglion that is part of a abdominal segment of trunk. SCTID:280508003 uberon UBERON:0009758 abdominal ganglion A ganglion that is part of a abdominal segment of trunk. OBOL:automatic A serous sac that has the pleura and the pleural cavity as parts. despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2:0004737 FMA:9690 SCTID:361996004 uberon UBERON:0009778 pleural sac FMA FMA-abduced-lr A serous sac that has the pleura and the pleural cavity as parts. https://github.com/obophenotype/uberon/issues/86 despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2 The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinar acinus FMA:55588 Wikipedia:Acinus uberon acini UBERON:0009842 glandular acinus http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. Wikipedia:Acinus acinus FMA:55588 acini Wikipedia:Acinus An epithelium that is part of a embryonic cloaca. cloacal epithelium EHDAA2:0004585 uberon UBERON:0009846 embryonic cloacal epithelium EHDAA2 EHDAA2 An epithelium that is part of a embryonic cloaca. OBOL:automatic cloacal epithelium EHDAA2:0004585 A multicellular organism that existence_starts_and_ends_during a nematode larval stage. uberon UBERON:0009850 nematode larva A multicellular organism that existence_starts_and_ends_during a nematode larval stage. OBOL:automatic Branch or outpocketing of the digestive tract. FBbt:00100316 uberon diverticulum of gut intestinal pouch UBERON:0009854 digestive tract diverticulum Branch or outpocketing of the digestive tract. https://orcid.org/0000-0002-6601-2165 FBbt:00100316 diverticulum of gut FBbt:00100316 galen:Diverticulum pouch uberon diverticulum UBERON:0009856 sac A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach UBERON:0009034 EMAPA:35821 FMA:14558 MA:0002561 SCTID:245415005 Wikipedia:Stomach#Sections gastric zone region of stomach section of stomach uberon UBERON:0009870 zone of stomach http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. ISBN:0073040584 Wikipedia:Stomach#Sections gastric zone FMA:14558 EFO:0003704 TAO:0005041 ZFA:0005041 ALPM uberon UBERON:0009881 anterior lateral plate mesoderm ZFA ALPM ZFA:0005041 A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested in mouse has left ventricular identity[PMID:22855565] XAO:0004186 anterior heart field anterior/second heart field second heart field uberon SHF UBERON:0009889 secondary heart field GO:0003129 PMID:17276708 PMID:17276708 A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). GO:0003139 GOC:mtg_heart GOC:rl extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. PMID:17276708 In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested PMID:17276708 anterior heart field PMID:17276708 anterior/second heart field Geisha:syn NCBITaxon:8782 second heart field XAO:0004186 SHF XAO:0004186 Mesenchyme that is part of a developing face. EMAPA:35337 FMA:302884 face mesenchyme mesenchyme of face uberon UBERON:0009891 facial mesenchyme Mesenchyme that is part of a developing face. OBOL:automatic todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland) FMA:45737 NCIT:C12990 UMLS:C0921005 lobulus uberon UBERON:0009911 lobule cjm UMLS:C0921005 ncithesaurus:Lobule lobulus FMA:45737 FMA:TA A portion of an organ, such as the liver, lung, breast, or brain. FMA:45728 NCIT:C13393 UMLS:C0796494 lobus uberon UBERON:0009912 anatomical lobe cjm A portion of an organ, such as the liver, lung, breast, or brain. ncithesaurus:Lobe lobus FMA:45728 FMA:TA EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest EHDAA2 EHDAA2 A multicellular organism that existence_starts_with a post-embryonic stage. MA:0002405 postnatal organism TS28 mouse post-hatching organism post-natal organism postnatal mouse uberon UBERON:0009953 post-embryonic organism https://github.com/obophenotype/uberon/issues/667 A multicellular organism that existence_starts_with a post-embryonic stage. OBOL:automatic TS28 mouse MA:0002405 post-hatching organism https://orcid.org/0000-0002-6601-2165 post-natal organism https://orcid.org/0000-0002-6601-2165 postnatal mouse MA:0002405 Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. Includes: trigeminal, otic, lateral line and epibranchial placodes. While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) EFO:0003460 TAO:0001309 Wikipedia:Neurogenic_placodes XAO:0004620 ZFA:0001309 neurogenic placodes uberon placodae neurogenicae UBERON:0009955 neurogenic placode cjm Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. PMID:11523831 http://orcid.org/0000-0002-6601-2165 While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) NCBIBook:NBK53171 neurogenic placodes ZFA:0001309 placodae neurogenicae Wikipedia:Neurogenic_placodes An epithelium that is part of a pancreatic duct. in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this EFO:0002556 FMA:67681 pancreatic duct epithelium pancreatic ductal epithelium uberon UBERON:0009970 epithelium of pancreatic duct An epithelium that is part of a pancreatic duct. OBOL:automatic pancreatic duct epithelium FMA:67681 pancreatic ductal epithelium FMA:67681 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure CARO An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure FBbt:00100313 A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]. May be obsoleted. FMA:256381 NLXANAT:20090509 uberon set of nuclei of neuraxis UBERON:0010009 aggregate regional part of brain A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]. NLXANAT:20090509 set of nuclei of neuraxis FMA:256381 Mesenchyme that is part of a pharyngeal arch 6. EHDAA2:0004076 EMAPA:32765 FMA:318209 6th pharyngeal arch mesenchyme uberon 6th branchial arch mesenchyme pharyngeal arch 6 mesenchyme UBERON:0010031 6th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 6. OBOL:automatic An organ of the digestive tract that is capable of retaining and storing food. This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates BSA:0000123 TADS:0000172 TGMA:0001041 uberon UBERON:0010039 food storage organ An organ of the digestive tract that is capable of retaining and storing food. https://orcid.org/0000-0002-6601-2165 Mesenchyme that is part of a pharyngeal arch 1. EMAPA:16128 mesenchyme of 1st arch uberon UBERON:0010042 1st arch mesenchyme Mesenchyme that is part of a pharyngeal arch 1. OBOL:automatic mesenchyme of 1st arch EMAPA:16128 Mesenchyme that is part of a 1st arch maxillary component. EHDAA2:0000041 EMAPA:16391 mesenchyme of maxillary component uberon maxillary component mesenchyme maxillary mesenchyme UBERON:0010045 1st arch maxillary mesenchyme Mesenchyme that is part of a 1st arch maxillary component. OBOL:automatic mesenchyme of maxillary component EMAPA:16391 The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. EHDAA2:0001459 EMAPA:16550 XAO:0004524 associated mesenchyme of pharyngeal region entire branchial arch associated mesenchyme pharyngeal arch associated mesenchyme uberon UBERON:0010046 entire pharyngeal arch associated mesenchyme EHDAA2 EHDAA2 cjm The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. XAO:0004524 https://orcid.org/0000-0002-6601-2165 associated mesenchyme of pharyngeal region EMAPA:16550 entire branchial arch associated mesenchyme https://orcid.org/0000-0002-6601-2165 pharyngeal arch associated mesenchyme EHDAA2:0001459 Gland of the epithelium lining the oral cavity. The most common are the salivary glands. Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa UBERON:0003293 EHDAA2:0001327 EHDAA:2181 EMAPA:16572 EMAPA:16723 VHOG:0000652 buccal gland uberon gland of oral opening gland of oral region mouth gland oral cavity gland oral region gland UBERON:0010047 oral gland Gland of the epithelium lining the oral cavity. The most common are the salivary glands. ISBN:0073040584 Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa EHDAA2 An epithelium consisting of cuboidal epithelial cells. TODO - coordinate with CL, add cuboidal cell in NCIT this is glandular NCIT:C32415 UMLS:C0682577 Wikipedia:Cuboidal_epithelium uberon UBERON:0010077 cuboidal epithelium An epithelium consisting of cuboidal epithelial cells. Wikipedia:Cuboidal_epithelium in NCIT this is glandular NCIT UMLS:C0682577 ncithesaurus:Cuboidal_Epithelium An extrahepatic bile duct that has the potential to develop into a common hepatic duct. EHDAA2:0000595 uberon UBERON:0010081 future common hepatic duct An extrahepatic bile duct that has the potential to develop into a common hepatic duct. OBOL:automatic Mesenchyme that has the potential to develop into a dermis. check development EHDAA2:0000598 uberon UBERON:0010083 future dermis EHDAA2 EHDAA2 XAO Mesenchyme that has the potential to develop into a dermis. OBOL:automatic A structure that will develop into a diaphragm. EHDAA2:0000599 uberon UBERON:0010084 future diaphragm EHDAA2 PMID:23586979 PMID:23586979 A structure that will develop into a diaphragm. http://orcid.org/0000-0002-6601-2165 A developing anatomical structure that has the potential to develop into a metencephalon. EHDAA2:0000623 uberon UBERON:0010092 future metencephalon A developing anatomical structure that has the potential to develop into a metencephalon. OBOL:automatic A developing anatomical structure that has the potential to develop into a myelencephalon. EHDAA2:0000640 uberon UBERON:0010096 future myelencephalon A developing anatomical structure that has the potential to develop into a myelencephalon. OBOL:automatic A gray matter that has the potential to develop into a superior salivatory nucleus. EHDAA2:0004644 uberon UBERON:0010125 future superior salivatory nucleus A gray matter that has the potential to develop into a superior salivatory nucleus. OBOL:automatic Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. EHDAA2:0004528 FMA:83378 specialized conducting tissue of heart specialized muscle tissue of heart uberon UBERON:0010131 conducting tissue of heart Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. http://orcid.org/0000-0002-6601-2165 specialized conducting tissue of heart FMA:83378 specialized muscle tissue of heart FMA:83378 An epithelial sheet is a flat surface consisting of closely packed epithelial cells. uberon UBERON:0010136 epithelial sheet An epithelial sheet is a flat surface consisting of closely packed epithelial cells. GO:0002011 A mucous secretion that is produced by glands in the epidermis. uberon epidermal mucus skin mucous UBERON:0010152 skin mucus A mucous secretion that is produced by glands in the epidermis. http://orcid.org/0000-0002-6601-2165 epidermal mucus BTO:0005082 An anatomical cavity that surrounded_by a blood vessel. FMA:312610 SCTID:91747007 blood vessel lumen uberon UBERON:0010161 lumen of blood vessel An anatomical cavity that surrounded_by a blood vessel. OBOL:automatic The distal end of the tail. EMAPA:37760 MA:0002848 XAO:0004057 tail tip uberon end of tail UBERON:0010162 post-anal tail tip MA The distal end of the tail. http://orcid.org/0000-0002-6601-2165 EMAPA:37760 MA:th tail tip MA:0002848 end of tail MA:0002848 A trabecula that is part of a liver. liver trabeculae uberon hepatic trabecula UBERON:0010183 liver trabecula A trabecula that is part of a liver. GO:0060344 OBOL:automatic liver trabeculae A roughly circular bulge in a surface. requires review AEO:0000205 EHDAA2:0003250 FMA:82506 uberon UBERON:0010188 protuberance FMA A roughly circular bulge in a surface. EHDAA2:0003250 The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation. EHDAA2:0000410 EMAPA:18606 MA:0000476 paired dorsal aortae uberon UBERON:0010190 pair of dorsal aortae EHDAA2 EHDAA2 The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation. ISBN:0-914294-08-3 MP:0004787 paired dorsal aortae EHDAA2:0000410 EHDAA2:0004512 uberon UBERON:0010191 aortic system Wikipedia One of the laterally paired arteries that supply the gonads. Wikipedia:Gonadal_artery gonadal artery uberon UBERON:0010192 genital artery One of the laterally paired arteries that supply the gonads. ISBN:0073040584 Wikipedia:Gonadal_artery A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver. Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO] AAO:0010225 hepatic-portal system portal system of liver uberon UBERON:0010194 hepatic portal system A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver. ISBN:0073040584 Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO] 2012-06-20 AAO:0010225 AAO AAO:BJB hepatic-portal system AAO:0010225 An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 uberon UBERON:0010199 One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) bona-fide anatomical boundary CARO An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 A vasculature that is part of a post-anal tail. isa blood vessel in XAO TAO:0005037 XAO:0004151 ZFA:0005037 post-vent vasculature uberon tail vasculature UBERON:0010204 tail vasculature A vasculature that is part of a post-anal tail. OBOL:automatic isa blood vessel in XAO XAO post-vent vasculature ZFA:0005037 tail vasculature ZFA:0005037 Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. FMA:71005 TAO:0002228 ZFA:0001718 presumptive atrium heart tube primordial atrium primordial cardiac atrium uberon UBERON:0010227 future cardiac atrium ZFA Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. ZFA:0001718 presumptive atrium heart tube ZFA:0001718 primordial atrium FMA:71005 primordial cardiac atrium FMA:71005 The core globe-shaped component of the camera-type eye. See notes for camera-type eye FMA:12513 MIAA:0000283 SCTID:244486005 VHOG:0001616 Wikipedia:Globe_(human_eye) bulbus oculi eye globe eyeball uberon eye globe UBERON:0010230 eyeball of camera-type eye FMA The core globe-shaped component of the camera-type eye. UBERON:cjm eye globe VHOG:0001616 eyeball FMA:12513 eye globe HP:0100886 MIAA:0000283 An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged. merocrine BTO:0002324 MA:0003041 Wikipedia:Merocrine uberon UBERON:0010243 merocrine gland An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged. MGI:anna MP:0013544 Wikipedia:Merocrine Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000037 uberon UBERON:0010252 1st arch mandibular mesenchyme from neural crest inferred EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000044 uberon UBERON:0010253 1st arch maxillary mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000098 EMAPA:16772 VHOG:0000580 4th pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 4th arch neural crest derived arch 4 mesenchyme pharyngeal arch 4 mesenchyme from neural crest uberon branchial arch 4 mesenchyme from neural crest UBERON:0010256 4th arch mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000580 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch mesenchyme derived from neural crest VHOG:0000580 mesenchyme derived from neural crest of mesenchyme of 4th arch EMAPA:16772 Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. EHDAA2:0004077 neural crest derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from neural crest uberon branchial arch 6 mesenchyme from neural crest UBERON:0010257 6th arch mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a rhombencephalon neural crest. EHDAA2:0004423 uberon UBERON:0010258 mesenchyme from rhombencephalic neural crest EHDAA2 Mesenchyme that develops_from a rhombencephalon neural crest. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. EMAPA:16129 mesenchyme derived from neural crest of mesenchyme of 1st arch neural crest derived arch 1 mesenchyme pharyngeal arch 1 mesenchyme from neural crest uberon branchial arch 1 mesenchyme from neural crest UBERON:0010259 1st arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from neural crest of mesenchyme of 1st arch EMAPA:16129 Any anatomical space that is part of a vertebral column. AAO:0000700 vertebral column opening vertebral conduit uberon UBERON:0010276 space in vertebral column Any anatomical space that is part of a vertebral column. OBOL:automatic vertebral column opening AAO:0000700 Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 EHDAA2:0004375 TAO:0000761 ZFA:0000761 basal plate midbrain basal plate midbrain region uberon UBERON:0010285 midbrain basal plate EHDAA2 EHDAA2 ZFA Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. ZFA:0000761 basal plate midbrain TAO:0000761 basal plate midbrain region ZFA:0000761 Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 ZFA:0007039 uberon UBERON:0010286 midbrain neural tube ZFA Portion of neural tube that gives rise to the midbrain. ZFA:0007039 Wikipedia:Sclera#Histology uberon UBERON:0010291 layer of sclera cjm An endothelium that is part of a sclera. uberon UBERON:0010294 scleral endothelium Wikipedia An endothelium that is part of a sclera. OBOL:automatic A stroma that is part of a sclera. subsantia propria FMA:58365 NCIT:C33652 SCTID:368851004 UMLS:C1704397 scleral stroma stroma of sclera subsantia propria sclerae substantia propria sclerae uberon UBERON:0010295 substantia propria of sclera Wikipedia A stroma that is part of a sclera. OBOL:automatic UMLS:C1704397 ncithesaurus:Substantia_Propria scleral stroma FMA:58365 stroma of sclera FMA:58365 subsantia propria sclerae FMA:58365 substantia propria sclerae FMA:58365 FMA:TA Mesenchyme surrounding the developing optic cup which develops into the sclera. The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288 uberon UBERON:0010299 scleral mesenchyme Mesenchyme surrounding the developing optic cup which develops into the sclera. PMID:16496288 https://orcid.org/0000-0002-6601-2165 An epithelium that is part of a extraembryonic structure. extra-embryonic epithelium uberon UBERON:0010303 extraembryonic epithelium An epithelium that is part of a extraembryonic structure. OBOL:automatic Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus. FMA:45569 Wikipedia:Stratified_squamous_epithelium#Nonkeratinized epithelium stratificatum squamosum noncornificatum nonkeratinizing stratified squamous epithelium stratified squamous non-keratinized epithelium stratified squamous nonkeratinizing epithelium uberon UBERON:0010304 non-keratinized stratified squamous epithelium FMA Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus. FMA:45569 Wikipedia:Stratified_squamous_epithelium#Nonkeratinized epithelium stratificatum squamosum noncornificatum FMA:45569 nonkeratinizing stratified squamous epithelium FMA:45569 stratified squamous non-keratinized epithelium http://orcid.org/0000-0002-6601-2165 stratified squamous nonkeratinizing epithelium http://orcid.org/0000-0002-6601-2165 Developing anatomical structure that develops into the eyeball and associated structures. Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] TAO:0002201 ZFA:0001678 future eye uberon UBERON:0010312 immature eye definitional Developing anatomical structure that develops into the eyeball and associated structures. ZFA:0001678 Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] 2012-08-14 TAO:0002201 TAO ZFIN:curator An anatomical structure that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010313 neural crest-derived structure An anatomical structure that develops from the neural crest. https://orcid.org/0000-0002-6601-2165 An anatomical structure that has some part that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010314 structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. https://orcid.org/0000-0002-6601-2165 uberon UBERON:0010316 germ layer / neural crest A skeletal element that is part of a orbital region. uberon eye skeleton ocular skeleton skeletal element of orbital region UBERON:0010321 skeletal element of eye region A skeletal element that is part of a orbital region. OBOL:automatic Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints) that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] AAO:0000109 AAO:0000971 AAO:0010185 TAO:0000737 VSAO:0000049 XAO:0003075 ZFA:0000737 cranial skeleton osteocranium uberon cranium UBERON:0010323 cranial skeletal system Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. GO_REF:0000034 PSPUB:0000170 VSAO:0000049 http://dx.plos.org/10.1371/journal.pone.0051070 Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] 2012-06-20 AAO:0000109 AAO AAO:LAP Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] 2012-08-14 TAO:0000737 TAO ZFIN:curator cranium ZFA:0000737 Mesenchyme that is part of a limb/fin bud. uberon UBERON:0010329 paired limb/fin bud mesenchyme EHDAA2-abduced Mesenchyme that is part of a limb/fin bud. OBOL:automatic Mesenchyme that is part of a extraembryonic membrane. uberon UBERON:0010333 extraembryonic membrane mesenchyme EHDAA2-abduced Mesenchyme that is part of a extraembryonic membrane. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme. EHDAA2:0004601 uberon UBERON:0010334 maxillary process mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme. EHDAA2:0004602 uberon UBERON:0010335 maxillary process mesenchyme from head mesenchyme EHDAA2 EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. EHDAA2:0004603 uberon UBERON:0010336 mandibular process mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. EHDAA2:0004604 uberon UBERON:0010337 mandibular process mesenchyme from head mesenchyme EHDAA2 EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000043 uberon UBERON:0010338 1st arch maxillary mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000036 uberon UBERON:0010339 1st arch mandibular mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. EMAPA:16130 mesenchyme derived from head mesoderm of mesenchyme of 1st arch uberon UBERON:0010341 1st arch mesenchyme from head mesenchyme EMAPA Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 1st arch EMAPA:16130 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. EHDAA2:0000097 EMAPA:16771 head mesenchyme derived arch 4 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 4th arch pharyngeal arch 4 mesenchyme from head mesenchyme uberon branchial arch 4 mesenchyme from head mesenchyme UBERON:0010345 4th arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 4th arch EMAPA:16771 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. EHDAA2:0004078 head mesenchyme derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from head mesenchyme uberon branchial arch 6 mesenchyme from head mesenchyme UBERON:0010347 6th arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from neural crest branchial arch mesenchyme from neural crest neural crest derived arch mesenchyme uberon UBERON:0010359 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from head mesenchyme branchial arch mesenchyme from head mesenchyme head mesenchyme derived arch mesenchyme uberon UBERON:0010360 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t VSAO:0000037 Wikipedia:Endoskeleton XAO:0004026 replacement skeleton uberon UBERON:0010362 endoskeleton VSAO Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. GO_REF:0000034 PSPUB:0000170 VSAO:0000037 http://dx.plos.org/10.1371/journal.pone.0051070 An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t Wikipedia:Endoskeleton replacement skeleton VSAO:curator A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. VSAO:0000139 XAO:0004017 ZFA:0005620 endochondral replacement element uberon UBERON:0010363 endochondral element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern VSAO A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. GO_REF:0000034 PSPUB:0000170 VSAO:0000139 http://dx.plos.org/10.1371/journal.pone.0051070 endochondral replacement element VSAO:0000139 Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. exoskeleton VSAO:0000035 XAO:0004025 uberon dermal skeletal system dermoskeleton desmoskeleton UBERON:0010364 This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO dermal skeleton VSAO Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. GO_REF:0000034 PSPUB:0000170 VSAO:0000035 http://dx.plos.org/10.1371/journal.pone.0051070 exoskeleton VSAO:curator dermal skeletal system VSAO:curator dermoskeleton VSAO:curator desmoskeleton VSAO:curator The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa. FMA:75739 NCIT:C33428 lobulus pulmonis uberon UBERON:0010368 pulmonary lobule The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa. ncithesaurus:Pulmonary_Lobule lobulus pulmonis FMA:75739 FMA:TA Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 ectoderm-derived epithelium uberon UBERON:0010371 ecto-epithelium Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen') EHDAA2:0001384 FMA:79793 uberon dorsal pancreas UBERON:0010375 pancreas dorsal primordium EHDAA2 dorsal pancreas FMA:79793 Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen') EHDAA2:0001387 FMA:79794 uberon ventral pancreas UBERON:0010376 pancreas ventral primordium EHDAA2 ventral pancreas FMA:79794 Mesenchyme that develops_from a somatopleure. the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives EHDAA2:0001120 uberon UBERON:0010377 mesenchyme from somatopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a somatopleure. OBOL:automatic Mesenchyme that develops_from a splanchnopleure. EHDAA2:0001122 uberon UBERON:0010378 mesenchyme from splanchnopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a splanchnopleure. OBOL:automatic One of the branches of the splenic artery[MP]. When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia] MA:0000759 NCIT:C49775 UMLS:C1710159 Wikipedia:Trabecular_arteries uberon trabecular artery UBERON:0010399 spleen trabecular artery MP One of the branches of the splenic artery[MP]. MP:0002354 Wikipedia:Trabecular_arteries When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia] Wikipedia Wikipedia:Trabecular_arteries UMLS:C1710159 ncithesaurus:Splenic_Trabecular_Artery One of the veins that feed the splenic vein. The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia] MA:0000760 NCIT:C49779 UMLS:C1710160 Wikipedia:Trabecular_veins uberon trabecular vein UBERON:0010400 spleen trabecular vein One of the veins that feed the splenic vein. MP:0002228 Wikipedia:Trabecular_veins The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia] Wikipedia Wikipedia:Trabecular_veins UMLS:C1710160 ncithesaurus:Splenic_Trabecular_Vein trabecular vein Wikipedia:Trabecular_veins The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. EMAPA:35336 MA:0002486 eye surface eye surface region ocular surface uberon UBERON:0010409 ocular surface region The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. MP:0013754 eye surface MA:0002486 The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. FMA:76551 SCTID:280860001 Wikipedia:Ciliary_processes ciliary processes ciliary processes set processus ciliares set of ciliary processes uberon ciliary process processus ciliares UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. Wikipedia:Ciliary_processes ciliary processes FMA:76551 ciliary processes set FMA:76551 processus ciliares FMA:TA set of ciliary processes FMA:76551 ciliary process Wikipedia:Ciliary_processes processus ciliares Wikipedia:Ciliary_processes A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. In an adult mammal, most red blood cells are formed in flat bones Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment FMA:7476 NCIT:C32616 SCTID:332907008 UMLS:C0222649 Wikipedia:Flat_bone galen:FlatBone uberon os planum UBERON:0010428 Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs flat bone FMA A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. Wikipedia:Flat_bone UMLS:C0222649 ncithesaurus:Flat_Bone os planum Wikipedia:Flat_bone A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. glandular in NCIT; we consider the two NCIT terms synonymous FMA:45572 NCIT:C33419 NCIT:C49316 UMLS:C0836138 UMLS:C1514590 Wikipedia:Pseudostratified_columnar_epithelium uberon UBERON:0010498 pseudostratified columnar epithelium FMA A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. Wikipedia:Pseudostratified_columnar_epithelium http://medical-dictionary.thefreedictionary.com/pseudostratified+epithelium glandular in NCIT; we consider the two NCIT terms synonymous NCIT UMLS:C0836138 ncithesaurus:Pseudostratified_Columnar_Epithelium UMLS:C1514590 ncithesaurus:Pseudostratified_Epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. FMA:13146 NCIT:C13181 UMLS:C0506992 epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) uberon UBERON:0010499 pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. NCIT:NCIT UMLS:C0506992 ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) FMA:13146 An organ that is capable of detecting electrical stimulus. electric sense organ electroreception organ uberon UBERON:0010521 electroreceptor organ An organ that is capable of detecting electrical stimulus. http://orcid.org/0000-0002-6601-2165 Skeletal element that forms as a replacement or substitution of another element or tissue. VSAO:0000135 XAO:0004016 ZFA:0005624 uberon UBERON:0010522 replacement element VSAO cjm Skeletal element that forms as a replacement or substitution of another element or tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000135 http://dx.plos.org/10.1371/journal.pone.0051070 A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 ZFA:0005251 uberon microcirculatory vessels UBERON:0010523 microcirculatory vessel ZFA A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 ZFA:0005251 http://orcid.org/0000-0002-6601-2165 microcirculatory vessels TAO:0005251 An organ cavity that surrounded_by a bone. FMA:24021 bone organ cavity uberon UBERON:0010527 cavity of bone organ An organ cavity that surrounded_by a bone. OBOL:automatic bone organ cavity FMA:24021 FMA:24028 air space of bone uberon UBERON:0010528 pneumatic cavity of bone FMA air space of bone FMA:24028 An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) 2012-04-23T10:46:51Z EMAPA:37858 FMA:7182 VSAO:0000214 appendage complex appendage-girdle complex appendage/girdle complex girdle plus limb or fin uberon limb UBERON:0010707 appendage girdle complex An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton https://orcid.org/0000-0002-6601-2165 Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] 2012-08-14 VSAO:0000214 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] 2012-09-06 VSAO:0000214 VSAO Curator note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37858 MA:th appendage complex https://orcid.org/0000-0002-6601-2165 appendage-girdle complex https://orcid.org/0000-0002-6601-2165 appendage/girdle complex VSAO:0000214 girdle plus limb or fin https://orcid.org/0000-0002-6601-2165 limb FMA:7182 Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region) EMAPA:37860 FMA:7183 SCTID:110716002 VSAO:0000213 pectoral appendage/girdle complex pectoral girdle plus anterior limb or fin pectoral girdle plus pectoral limb or fin uberon upper limb upper limb and pectoral girdle upper limb and shoulder UBERON:0010708 pectoral complex Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. VSAO:0000213 Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO] 2012-08-14 VSAO:0000213 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37860 MA:th pectoral appendage/girdle complex VSAO:0000213 pectoral girdle plus anterior limb or fin https://orcid.org/0000-0002-6601-2165 pectoral girdle plus pectoral limb or fin https://orcid.org/0000-0002-6601-2165 upper limb FMA:7183 upper limb and pectoral girdle https://orcid.org/0000-0002-6601-2165 upper limb and shoulder https://orcid.org/0000-0002-6601-2165 Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here EMAPA:37863 FMA:7184 SCTID:416631005 VSAO:0000215 pelvic appendage/girdle complex pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin uberon lower limb lower limb and pelvic girdle lower limb and pelvis UBERON:0010709 pelvic complex Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. VSAO:0000215 Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] 2012-08-14 VSAO:0000215 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here FMA EMAPA:37863 MA:th pelvic appendage/girdle complex VSAO:0000215 pelvic girdle plus pelvic limb or fin https://orcid.org/0000-0002-6601-2165 pelvic girdle plus posterior limb or fin https://orcid.org/0000-0002-6601-2165 lower limb FMA:7184 lower limb and pelvic girdle https://orcid.org/0000-0002-6601-2165 lower limb and pelvis https://orcid.org/0000-0002-6601-2165 The subdivision of the skeleton of either the pectoral or pelvic girdle. Skeletal subdivision that is part of the appendage girdle region.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] AAO:0010686 VSAO:0000302 skeleton of girdle uberon UBERON:0010719 girdle skeleton The subdivision of the skeleton of either the pectoral or pelvic girdle. https://orcid.org/0000-0002-6601-2165 Skeletal subdivision that is part of the appendage girdle region.[VSAO] 2012-08-14 VSAO:0000302 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). EMAPA:35494 MA:0000688 uberon bone of extended limb/fin region limb bone UBERON:0010740 bone of appendage girdle complex UBERONREF:0000003 A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 bone of extended limb/fin region UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 limb bone MA:0000688 UBERONREF:0000003 A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. considering adding pectoral and pelvic complex skeleton classes note that the MA class includes girdle parts so it belongs here; EMAPA:32623 EMAPA:35933 MA:0000612 wing bone uberon bone of forelimb or pectoral fin or pectoral girdle forelimb bone UBERON:0010741 bone of pectoral complex A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 note that the MA class includes girdle parts so it belongs here; MA wing bone UBERONREF:0000003 bone of forelimb or pectoral fin or pectoral girdle UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 forelimb bone MA:0000612 UBERONREF:0000003 A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle EMAPA:32633 EMAPA:35934 MA:0000660 uberon hindlimb bone UBERON:0010742 bone of pelvic complex MA A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle MA hindlimb bone MA:0000660 UBERONREF:0000003 Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] AAO:0000218 EMAPA:32634 FMA:9622 MA:0000663 pelvic girdle and hind limb muscles pelvic girdle or hind limb muscle pelvic girdle or posterior limb muscle uberon lower limb muscle muscle of lower limb muscle of pelvic girdle and leg UBERON:0010890 pelvic complex muscle prolog Muscles of the pelvic girdle, hindlimb or pelvic fin. https://orcid.org/0000-0002-6601-2165 Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] 2012-06-20 AAO:0000218 AAO AAO:EJS pelvic girdle and hind limb muscles AAO:0000218 pelvic girdle or hind limb muscle https://orcid.org/0000-0002-6601-2165 pelvic girdle or posterior limb muscle https://orcid.org/0000-0002-6601-2165 lower limb muscle FMA:9622 muscle of lower limb FMA:9622 A muscle of a pectoral girdle, pectoral fin or anterior limb. the MA class belongs here, based on its current child classes Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] AAO:0010687 EMAPA:32624 FMA:9621 MA:0000615 pectoral girdle and fore limb muscles muscle of pectoral girdle and wing muscle of upper limb upper limb muscle uberon muscle of pectoral girdle and limb UBERON:0010891 pectoral complex muscle prolog A muscle of a pectoral girdle, pectoral fin or anterior limb. https://orcid.org/0000-0002-6601-2165 Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] 2012-06-20 AAO:0010687 AAO AAO:EJS pectoral girdle and fore limb muscles AAO:0010687 muscle of pectoral girdle and wing NCBITaxon:8782 muscle of upper limb FMA:9621 upper limb muscle FMA:9621 Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 skeletal subdivision uberon subdivision of skeleton (in vivo) UBERON:0010912 subdivision of skeleton cjm UBERONREF:0000003 VSAO Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] 2012-08-14 VSAO:0000042 incorrect VSAO VSAO:curator skeletal subdivision VSAO:0000042 subdivision of skeleton (in vivo) FMA:23879 Skeletal element that forms around the notochord and is part of the vertebral column. we include a distinct subclass for bony vertebra In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] vertebral Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage UBERON:0015005 vertebra skeletal element VHOG:0001143 VSAO:0000184 vertebra element vertebra endochondral element vertebral endochondral element uberon UBERON:0010913 vertebral element VSAO https://github.com/obophenotype/uberon/issues/82 cjm Skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/294 In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001143 VHOG DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011) http://bgee.unil.ch/ vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern vertebra endochondral element https://github.com/obophenotype/uberon/issues/82 vertebral endochondral element https://github.com/obophenotype/uberon/issues/82 Any muscle organ that is part of either the head or the neck. NCIT:C32716 UMLS:C0448281 muscle of head or neck uberon muscle of head and neck UBERON:0010959 craniocervical muscle prolog Any muscle organ that is part of either the head or the neck. http://orcid.org/0000-0002-6601-2165 UMLS:C0448281 ncithesaurus:Head_and_Neck_Muscle A cartilage element that is part of a splanchnocranium. BTO:0006051 EFO:0003689 TAO:0001460 ZFA:0001460 pharyngeal arch cartilages splanchnocranium cartilage uberon UBERON:0011004 pharyngeal arch cartilage ZFA ZFA A cartilage element that is part of a splanchnocranium. OBOL:automatic BTO:0006051 https://github.com/biopragmatics/biomappings pharyngeal arch cartilages ZFA:0001460 splanchnocranium cartilage ZFA:0001460 The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG]. Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EFO:0003659 TAO:0001272 VHOG:0000511 ZFA:0001272 dorsal visceral arch 1 upper pharyngeal jaw uberon dorsal mandibular arch dorsal pharyngeal arch 1 dorsal visceral arch 1 palatoquadrate arch upper jaw upper pharyngeal jaw UBERON:0011085 palatoquadrate arch cjm VHOG The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG]. VHOG:0000511 https://github.com/obophenotype/uberon/issues/153 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000511 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ dorsal visceral arch 1 ZFA:0001272 upper pharyngeal jaw ZFA:0001272 dorsal mandibular arch VHOG:0000511 dorsal pharyngeal arch 1 VHOG:0000511 dorsal visceral arch 1 VHOG:0000511 palatoquadrate arch VHOG:0000511 upper jaw VHOG:0000511 upper pharyngeal jaw VHOG:0000511 A skeleton of pelvic girdle that is part of a right pelvic girdle region. FMA:87593 uberon UBERON:0011090 skeleton of right pelvic girdle A skeleton of pelvic girdle that is part of a right pelvic girdle region. OBOL:automatic A skeleton of pelvic girdle that is part of a left pelvic girdle region. FMA:87594 uberon UBERON:0011091 skeleton of left pelvic girdle A skeleton of pelvic girdle that is part of a left pelvic girdle region. OBOL:automatic A pelvic girdle region that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16582 right pelvic girdle uberon UBERON:0011092 right pelvic girdle region A pelvic girdle region that is in the right side of a multicellular organism. OBOL:automatic right pelvic girdle FMA:16582 A pelvic girdle region that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16583 left pelvic girdle uberon UBERON:0011093 left pelvic girdle region A pelvic girdle region that is in the left side of a multicellular organism. OBOL:automatic left pelvic girdle FMA:16583 The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups EMAPA:32669 VHOG:0000584 vertebral cartilage condensation uberon UBERON:0011094 vertebra cartilage element The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist PMC3157150 This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups EHDAA2 vertebral cartilage condensation VHOG:0000584 The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. EMAPA:32671 VHOG:0000582 vertebral pre-cartilage condensation uberon UBERON:0011095 vertebra pre-cartilage condensation The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 vertebral pre-cartilage condensation VHOG:0000582 A synovial joint that is part of a pelvic girdle region. FMA:35173 NCIT:C32890 UMLS:C0827002 joint of pelvic girdle pelvic girdle joint uberon UBERON:0011107 synovial joint of pelvic girdle A synovial joint that is part of a pelvic girdle region. OBOL:automatic UMLS:C0827002 ncithesaurus:Joint_of_the_Pelvic_Girdle pelvic girdle joint FMA:35173 A synovial joint that is part of a pectoral girdle region. in FMA, these are part of the bony pectoral girdle FMA:35243 SCTID:303080001 joint of shoulder girdle pectoral girdle joint uberon UBERON:0011108 synovial joint of pectoral girdle A synovial joint that is part of a pectoral girdle region. OBOL:automatic in FMA, these are part of the bony pectoral girdle FMA pectoral girdle joint FMA:35243 Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint uberon UBERON:0011134 nonsynovial joint FMA Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint FMA:7491 Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. FMA:7483 uberon UBERON:0011137 axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. https://orcid.org/0000-0002-6601-2165 Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 post-cranial axial skeletal system uberon UBERON:0011138 postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA cjm Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. https://github.com/obophenotype/uberon/issues/44 https://orcid.org/0000-0002-6601-2165 axial skeletal system https://github.com/obophenotype/uberon/wiki/The-axial-skeleton Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 Wikipedia:Submucosal_glands uberon UBERON:0011148 submucosal gland perforates Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 Wikipedia:Submucosal_glands EMAPA:37970 MA:th Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 EMAPA:18022 FMA:53673 MA:0000318 Wikipedia:Facial_skeleton facial skeleton uberon facial bone ossa facialia ossa faciei viscerocranium UBERON:0011156 facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg FMA FMA Subdivision of skull that consists of the facial bones. MP:0005274 Wikipedia:Facial_skeleton http://www.bartleby.com/107/37.html https://orcid.org/0000-0002-6601-2165 facial skeleton FMA:53673 facial bone MA:0000318 ossa facialia Wikipedia:Facial_skeleton ossa faciei Wikipedia:Facial_skeleton viscerocranium MA:0000318 The skull can be divided into two: the neurocranium and the facial skeleton. FMA:54964 skull subdivision subdivision of skull uberon UBERON:0011158 primary subdivision of skull FMA The skull can be divided into two: the neurocranium and the facial skeleton. http://orcid.org/0000-0002-6601-2165 skull subdivision FMA:54964 subdivision of skull FMA:54964 uberon UBERON:0011159 primary subdivision of cranial skeletal system FMA A bone that is part of a neurocranium [Automatically generated definition]. EMAPA:35238 MA:0001478 SCTID:120229002 chondrocranium bone uberon UBERON:0011164 neurocranium bone A bone that is part of a neurocranium [Automatically generated definition]. OBOL:automatic chondrocranium bone MA:0001478 Synovial joint that articulates bones of upper and lower jaw. Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long jaw joint NCIT:C32888 craniomandibular joint uberon UBERON:0011171 joint connecting upper and lower jaws abduced Synovial joint that articulates bones of upper and lower jaw. http://evolution.berkeley.edu/evolibrary/article/evograms_05 https://orcid.org/0000-0002-6601-2165 Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long http://evolution.berkeley.edu A sphincter muscle that is part of the gastrointestinal system. NCIT:C32669 UMLS:C1517464 uberon UBERON:0011185 gastrointestinal sphincter A sphincter muscle that is part of the gastrointestinal system. OBOL:automatic UMLS:C1517464 ncithesaurus:Gastrointestinal_Sphincter A lamina propria that is part of a large intestine. FMA:15654 NCIT:C49298 UMLS:C1708644 lamina propria of mucosa of large intestine large intestinal lamina propria large intestine lamina propria uberon UBERON:0011189 lamina propria of large intestine FMA A lamina propria that is part of a large intestine. OBOL:automatic UMLS:C1708644 ncithesaurus:Large_Intestinal_Lamina_Propria lamina propria of mucosa of large intestine FMA:15654 large intestine lamina propria FMA:15654 A muscle layer that is part of a large intestine. FMA:14971 NCIT:C32927 UMLS:C0734205 muscular coat of large intestine muscular layer of large intestine muscularis externa of large intestine tunica muscularis intestini crassi uberon UBERON:0011198 muscle layer of large intestine FMA A muscle layer that is part of a large intestine. OBOL:automatic UMLS:C0734205 ncithesaurus:Large_Intestinal_Muscular_Coat muscular coat of large intestine FMA:14971 muscular layer of large intestine FMA:14971 muscularis externa of large intestine FMA:14971 tunica muscularis intestini crassi FMA:TA A muscle layer that is part of a small intestine. FMA:14932 NCIT:C33569 SCTID:362145004 UMLS:C0227269 muscular coat of small intestine muscular layer of small intestine muscularis externa of small intestine small intestine muscularis propria tunica muscularis (intestinum tenue) tunica muscularis intestini tenuis uberon UBERON:0011201 muscle layer of small intestine FMA A muscle layer that is part of a small intestine. OBOL:automatic UMLS:C0227269 ncithesaurus:Small_Intestinal_Muscular_Coat muscular coat of small intestine FMA:14932 muscular layer of small intestine FMA:14932 muscularis externa of small intestine FMA:14932 small intestine muscularis propria FMA:14932 tunica muscularis (intestinum tenue) FMA:14932 tunica muscularis intestini tenuis FMA:TA A multi cell part structure that is part of a central nervous system. FMA:83143 cell part cluster of neuraxis neuraxis layer uberon UBERON:0011215 central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. OBOL:automatic cell part cluster of neuraxis FMA:83143 neuraxis layer FMA:83143 A subdivision of an anatomical system. FBbt:00007330 FMA:67509 SCTID:91690000 uberon UBERON:0011216 organ system subdivision FBbt A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 FBbt:00007330 Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 FMA:49150 intrinsic muscle of eyeball intrinsic ocular muscle uberon UBERON:0011222 intra-ocular muscle EMAPA Muscles within the eye (bulbus oculi).[AAO] 2012-06-20 AAO:0010038 AAO AAO:EJS intrinsic ocular muscle EMAPA:18808 Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. synovium BTO:0001823 FMA:40878 Wikipedia:Synovial_sheath uberon UBERON:0011233 Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath] synovial membrane of synovial tendon sheath Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. FMA:45087 Wikipedia:Synovial_sheath synovium BTO:0001823 FMA:40877 uberon UBERON:0011234 fibrous membrane of synovial tendon sheath The most anterior region of the braincase. Provides structural support for peripheral olfactory organ. currently this is not restricted to skeletal elements, unlike UBERONREF:0000007 AAO:0000986 uberon UBERON:0011241 ethmoid region The most anterior region of the braincase. Provides structural support for peripheral olfactory organ. UBERONREF:0000007 http://palaeos.com/vertebrates/bones/braincase/ethmoid.html Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] FMA:7484 VHOG:0001666 VSAO:0000306 uberon UBERON:0011249 appendicular skeletal system https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. https://orcid.org/0000-0002-6601-2165 Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] 2012-08-14 VSAO:0000306 VSAO https://orcid.org/0000-0002-6601-2165 The part of the trunk that is in the dorsum[cjm]. In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA] EMAPA:35162 FMA:25056 MA:0000020 Wikipedia:Human_back back of trunk dorsal part of trunk dorsum of trunk trunk back uberon UBERON:0011270 dorsal trunk FMA FMA The part of the trunk that is in the dorsum[cjm]. UBERONREF:0000006 Wikipedia:Human_back back of trunk FMA:25056 dorsum of trunk FMA:25056 trunk back FMA:25056 compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' EHDAA2:0001845 uberon basal cell layer of skin outer epithelium of body UBERON:0011272 embryonic skin basal layer EHDAA2 EHDAA2 EHDAA2 outer epithelium of body Wikipathways:WP2062 A blood vasculature that is part of a head. Blood vessel part of cranial vasculature.[TAO] TAO:0005297 ZFA:0005297 cranial blood vessel set of blood vessels of head uberon cranial blood vessels UBERON:0011362 cranial blood vasculature A blood vasculature that is part of a head. OBOL:automatic Blood vessel part of cranial vasculature.[TAO] 2012-08-14 TAO:0005297 TAO ZFIN:curator cranial blood vessel ZFA:0005297 cranial blood vessels TAO:0005297 FMA:54364 SCTID:432899004 cavity of digestive tract cavity of gastrointestinal tract gastrointestinal tract lumen lumen of gastrointestinal tract uberon UBERON:0011565 lumen of gastrointestinal system gastrointestinal tract lumen FMA:54364 lumen of gastrointestinal tract FMA:54364 An anatomical cavity that is part of a esophagus. EMAPA:18380 FMA:9398 SCTID:322648002 cavity of eosophagus cavity of esophagus eosophageal cavity eosophageal lumen eosophagus lumen esophageal cavity esophageal lumen esophagus lumen uberon UBERON:0011566 lumen of esophagus FMA An anatomical cavity that is part of a esophagus. OBOL:automatic cavity of esophagus FMA:9398 esophageal cavity FMA:9398 esophageal lumen FMA:9398 esophagus lumen FMA:9398 The collection of all skeletal elements in an individual limb or fin. Skeletal subdivision that is part of the paired limb/fin.[VSAO] VSAO:0000301 limb/fin skeleton skeletal parts of limb/fin skeleton of limb/fin uberon UBERON:0011582 paired limb/fin skeleton ISBN:9780878932504 The collection of all skeletal elements in an individual limb or fin. https://orcid.org/0000-0002-6601-2165 Skeletal subdivision that is part of the paired limb/fin.[VSAO] 2012-08-14 VSAO:0000301 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 limb/fin skeleton VSAO:0000301 Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). consider obsoleting, coordinate with VSAO VSAO:0000006 XAO:0004021 uberon UBERON:0011585 cell condensation VSAO Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). GO_REF:0000034 PSPUB:0000170 VSAO:0000006 http://dx.plos.org/10.1371/journal.pone.0051070 EHDAA2:0002120 upper jaw future lip uberon UBERON:0011592 future upper lip EHDAA2 fusion fusion upper jaw future lip EHDAA2:0002120 A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. EMAPA:32905 NCIT:C114916 uberon UBERON:0011595 jaw region http://eol.org/collections/11578 EMAPA FMA-abduced ZFA-abduced A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. http://orcid.org/0000-0002-6601-2165 EHDAA2:0001020 lower jaw future lip uberon UBERON:0011596 future lower lip EHDAA2 Wikipedia:Mandibular_prominence lower jaw future lip EHDAA2:0001020 Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species). Do not manually classify under here - bones are automatically classified upper jaw bone uberon UBERON:0011597 bone of upper jaw Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species). https://orcid.org/0000-0002-6601-2165 An epithelium that develops_from a ectoderm and is part of a oral epithelium. EHDAA2:0004137 uberon UBERON:0011642 oral epithelium from ectoderm EHDAA2 EHDAA2 An epithelium that develops_from a ectoderm and is part of a oral epithelium. OBOL:automatic AAO:0000247 EFO:0003511 TAO:0000236 XAO:0003269 ZFA:0000236 mandibular muscle mandibular muscles uberon UBERON:0011648 jaw muscle mandibular muscle TAO:0000236 mandibular muscles TAO:0000236 A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem axial subdivision of organism uberon body segment main body segment UBERON:0011676 subdivision of organism along main body axis A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. https://orcid.org/0000-0002-6601-2165 A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly. thoracolumbar vertebra uberon presacral vertebra UBERON:0011677 trunk vertebra true A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly. UBERONREF:0000006 presacral vertebra http://orcid.org/0000-0002-6601-2165 A cardiovascular system that is part of a conceptus. EHDAA2:0000216 FMA:305965 NCIT:C34148 conceptus cardiovascular system uberon embryonic circulatory system fetal circulatory system UBERON:0011695 embryonic cardiovascular system A cardiovascular system that is part of a conceptus. OBOL:automatic An anatomical space that is part of a bone of lower jaw. AAO:0000273 uberon UBERON:0011772 lower jaw opening An anatomical space that is part of a bone of lower jaw. OBOL:automatic An anatomical space that is part of a bone of upper jaw. AAO:0000621 uberon UBERON:0011773 upper jaw opening An anatomical space that is part of a bone of upper jaw. OBOL:automatic A neural nucleus that is part of the spinal cord. FMA:77011 spinal cord nucleus uberon UBERON:0011777 nucleus of spinal cord A neural nucleus that is part of the spinal cord. http://orcid.org/0000-0002-6601-2165 spinal cord nucleus FMA:77011 A nerve that is part of a head. uberon cephalic nerve head nerve UBERON:0011779 nerve of head region A nerve that is part of a head. OBOL:automatic Ectodermal placode that does not develop into a component of the nervous system. uberon UBERON:0011814 non-neurogenic ectodermal placode cjm Ectodermal placode that does not develop into a component of the nervous system. PMID:11523831 http://orcid.org/0000-0002-6601-2165 An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. EHDAA2:0004149 FMA:85125 uberon AV region AV segment atrial ventricular junction atrioventricular junction atrioventricular segment UBERON:0011820 atrioventricular region An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. http://orcid.org/0000-0002-6601-2165 AV region PMID:21234997 AV segment PMID:21234997 atrial ventricular junction GO:0003294 atrioventricular junction FMA:85125 GO:0003294 atrioventricular segment PMID:21234997 Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 uberon UBERON:0011821 irregular connective tissue FMA Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] FMA:20109 NCIT:C32882 UMLS:C0738366 Wikipedia:Dense_irregular_connective_tissue irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) uberon UBERON:0011822 dense irregular connective tissue FMA Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20109 Wikipedia:Dense_irregular_connective_tissue Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] 2012-08-29 ncithesaurus:Irregular_Dense_Connective_Tissue NCIT UMLS:C0738366 ncithesaurus:Irregular_Dense_Connective_Tissue typus irregularis (textus connectivus collagenosus compactus) FMA:20109 Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] AAO:0000121 NCIT:C32450 UMLS:C1511770 Wikipedia:Dense_connective_tissue uberon UBERON:0011823 dense connective tissue Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. Wikipedia:Dense_connective_tissue Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] 2012-08-29 ncithesaurus:Dense_Connective_Tissue NCIT UMLS:C1511770 ncithesaurus:Dense_Connective_Tissue FMA:75634 SCTID:363130003 uberon UBERON:0011824 fibrous connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 NCIT:C33007 UMLS:C1253917 Wikipedia:Loose_connective_tissue textus connectivus collagenosus laxus textus connectivus laxus uberon UBERON:0011825 loose connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 UMLS:C1253917 ncithesaurus:Loose_Connective_Tissue textus connectivus collagenosus laxus FMA:19783 FMA:TA textus connectivus laxus FMA:19783 FMA:TA An acinus that is part of a exocrine gland. exocrine gland acinus uberon UBERON:0011858 acinus of exocrine gland An acinus that is part of a exocrine gland. OBOL:automatic the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NCIT:C32339 NIF_Subcellular:sao7547390221 uberon UBERON:0011860 collection of collagen fibrils ZFA the FMA class specifically refers to ureter FMA The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011861 aorta collagen fibril The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011640 The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011862 pulmonary collagen fibril The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011641 The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011863 bone collagen fibril The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011642 The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011864 tendon collagen fibril The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011643 The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011865 corneal stroma collagen fibril The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011650 A muscle layer that is part of a wall of esophagus. In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle FMA:62998 muscle coat of esophagus muscular coat of oesophagus muscular layer of oesophagus tela muscularis (oesophagus) tunica muscularis esophagi tunica muscularis oesophageae uberon UBERON:0011878 muscle layer of esophagus upper part Wikipedia:Muscular_layer A muscle layer that is part of a wall of esophagus. OBOL:automatic In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle WP muscle coat of esophagus FMA:62998 muscular coat of oesophagus FMA:62998 muscular layer of oesophagus FMA:62998 tela muscularis (oesophagus) FMA:62998 FMA:TA tunica muscularis esophagi tunica muscularis oesophageae FMA:TA Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. EMAPA:37417 SCTID:280656002 Haller tunica vascula anterior part of uveal tract anterior uveal tract anterior vascular layer of the eyeball anterior vascular tunic of the eye tunica vasculosa bulbosa ventral uveal tract uberon ciliary body and iris vasculosa oculi UBERON:0011892 anterior uvea ZFA MP lexical Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. MP:0005194 EMAPA:37417 MA:th Haller tunica vascula MP:0005194 tunica vasculosa bulbosa MP:0005194 vasculosa oculi MP:0005194 Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. The Epimysium also protects muscles from friction against other muscles and bones FMA:9726 NCIT:C32527 UMLS:C0504096 Wikipedia:Epimysium fascia of muscle organ uberon epimysia UBERON:0011899 epimysium FMA FMA Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. Wikipedia:Epimysium UMLS:C0504096 ncithesaurus:Epimysium fascia of muscle organ FMA:9726 epimysia Wikipedia:Epimysium Masses of developing blood cells attached to endothelium in the yolk sac. EHDAA2:0000177 EMAPA:16115 visceral yolk sac blood island yolk sac blood islands uberon UBERON:0011919 yolk sac blood island EHDAA2 Masses of developing blood cells attached to endothelium in the yolk sac. MP:0011204 visceral yolk sac blood island MP:0011204 yolk sac blood islands EHDAA2:0000177 A region of the stomach that is lined with glandular epithelium. as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus EMAPA:17623 MA:0001613 NCIT:C77661 SCTID:27633001 UMLS:C0227197 uberon glandular stomach UBERON:0011953 stomach glandular region A region of the stomach that is lined with glandular epithelium. http://orcid.org/0000-0002-6601-2165 UMLS:C0227197 ncithesaurus:Glandular_Stomach A hepatic vein that is part of a left lobe of liver. EMAPA:37164 FMA:14339 MA:0003032 SCTID:55188000 uberon UBERON:0011955 left hepatic vein A hepatic vein that is part of a left lobe of liver. OBOL:automatic EMAPA:37164 MA:th A hepatic vein that is part of a right lobe of liver. EMAPA:37377 FMA:14338 MA:0003034 SCTID:18135006 uberon UBERON:0011956 right hepatic vein A hepatic vein that is part of a right lobe of liver. OBOL:automatic EMAPA:37377 MA:th The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom haemocoelom schizocoelom uberon coelem coelomic cavity UBERON:0011997 coelom EHDAA2 The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. UBERON:cjm Wikipedia:Body_cavity Wikipedia:Coelom Wikipedia:Acoelomorpha enterocoelom NCBITaxon:33511 coelomic cavity EHDAA2:0004731 The cavity within a myotome. The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] EMAPA:31134 VHOG:0001283 uberon UBERON:0012054 myocoele The cavity within a myotome. http://medical-dictionary.thefreedictionary.com/myocoele The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001283 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6 http://bgee.unil.ch/ Any bone that is part of a palate. this is distinct (but not disjoint) from palatine bone EMAPA:37930 NCIT:C33248 UMLS:C1518857 palatal bone uberon UBERON:0012071 palate bone Any bone that is part of a palate. https://orcid.org/0000-0002-6601-2165 EMAPA:37930 MA:th UMLS:C1518857 ncithesaurus:Palate_Bone uberon dermatocranium, palatal series palatal series UBERON:0012072 palatal part of dermatocranium dermatocranium, palatal series ISBN:0073040584 palatal series ISBN:0073040584 Bone that forms as a replacement of another structural tissue. Bone that forms as a replacement of another structural tissue.[TAO] This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. AAO:0010768 TAO:0001637 ZFA:0001628 replacement bones uberon UBERON:0012075 replacement bone ZFA ZFA Bone that forms as a replacement of another structural tissue. ZFA:0001628 Bone that forms as a replacement of another structural tissue.[TAO] 2012-08-14 TAO:0001637 TAO TAO:wd This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. ZFA replacement bones ZFA:0001628 Anatomical system that consists of the integumental system plus all mucosae and submucosae. uberon dermatological system UBERON:0012125 dermatological-muscosal system Anatomical system that consists of the integumental system plus all mucosae and submucosae. https://github.com/obophenotype/uberon/issues/53 dermatological system OBI:MC A primordium that has the potential to develop into a stomach. EFO:0002580 NCIT:C34305 UMLS:C1514976 uberon stomach endoderm UBERON:0012172 stomach primordium A primordium that has the potential to develop into a stomach. OBOL:automatic UMLS:C1514976 ncithesaurus:Stomach_Primordium stomach endoderm EFO:0002580 A zone of skin that is part of a craniocervical region. EMAPA:37276 MA:0000574 NCIT:C12294 UMLS:C1522650 uberon UBERON:0012180 head or neck skin A zone of skin that is part of a craniocervical region. OBOL:automatic EMAPA:37276 MA:th UMLS:C1522650 ncithesaurus:Skin_of_the_Scalp_and_Neck The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. EMAPA:37180 MA:0002194 NCIT:C53062 UMLS:C1709532 uberon UBERON:0012193 phrenic vein The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. ncithesaurus:Phrenic_Vein EMAPA:37180 MA:th UMLS:C1709532 ncithesaurus:Phrenic_Vein An artery that originates from the abdominal aorta. SCTID:281470000 abdominal artery artery of abdomen uberon UBERON:0012254 abdominal aorta artery An artery that originates from the abdominal aorta. Wikipedia:Abdominal_aorta#Branches https://orcid.org/0000-0002-6601-2165 An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]. Wikipedia:Columnar_epithelium uberon UBERON:0012274 columnar epithelium An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]. Wikipedia:Columnar_epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. FMA:86452 mesoderm-derived epithelium mesoepithelium uberon UBERON:0012275 meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. OBOL:automatic One of five swellings formed during the development of the face. FMA:293103 SCTID:89066004 uberon embryonic facial process facial primordium primordium of face UBERON:0012314 embryonic facial prominence One of five swellings formed during the development of the face. http://www.indiana.edu/~anat550/hnanim/face/face.html An artery of the neck. EMAPA:37075 NCIT:C52850 UMLS:C1707349 uberon UBERON:0012320 cervical artery An artery of the neck. https://orcid.org/0000-0002-6601-2165 EMAPA:37075 MA:th UMLS:C1707349 ncithesaurus:Cervical_Artery The deep cervical artery (Profunda cervicalis) is an artery of the neck. FMA:10659 SCTID:244223002 Wikipedia:Deep_cervical_artery uberon profunda cervicalis UBERON:0012321 deep cervical artery FMA The deep cervical artery (Profunda cervicalis) is an artery of the neck. Wikipedia:Deep_cervical_artery profunda cervicalis Wikipedia:Deep_cervical_artery The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery. Unclear if MA class belongs here or in parent FMA:10664 MA:0001936 SCTID:244224008 Wikipedia:Transverse_cervical_artery uberon cervical artery cervical transverse artery descending branch of the transverse cervical transversalis artery colli transversalis colli artery transverse cervical transverse cervical vessels UBERON:0012324 transverse cervical artery The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery. Wikipedia:Transverse_cervical_artery Unclear if MA class belongs here or in parent MA cervical artery MA:0001936 Wikipedia:Transverse_cervical_artery cervical transverse artery Wikipedia:Transverse_cervical_artery descending branch of the transverse cervical Wikipedia:Transverse_cervical_artery transversalis artery colli Wikipedia:Transverse_cervical_artery transversalis colli artery Wikipedia:Transverse_cervical_artery transverse cervical Wikipedia:Transverse_cervical_artery transverse cervical vessels Wikipedia:Transverse_cervical_artery A bone element that is part of a jaw region. Do not manually classify under here - bones are automatically classified EMAPA:35453 MA:0003130 SCTID:369003004 jaw bone uberon UBERON:0012360 bone of jaw A bone element that is part of a jaw region. OBOL:automatic EHDAA2:0004588 uberon UBERON:0012361 internal anal region EHDAA2 A muscle layer that is part of an intestine. FMA:15697 intestinal muscularis propria muscularis externa of intestine uberon smooth muscle of intestine UBERON:0012367 muscle layer of intestine FMA A muscle layer that is part of an intestine. OBOL:automatic intestinal muscularis propria FMA:15697 muscularis externa of intestine FMA:15697 A layer of tissue between the muscularis and serosa. FMA:45636 NCIT:C94494 SCTID:2255006 UMLS:C0225334 Wikipedia:Subserosa uberon UBERON:0012375 Contains nerves, blood vessels, lymphatics and lymph nodes subserosa A layer of tissue between the muscularis and serosa. Wikipedia:Subserosa UMLS:C0225334 ncithesaurus:Subserosa EMAPA:37567 MA:0001802 uberon UBERON:0012416 respiratory system arterial smooth muscle EMAPA:37567 MA:th A smooth muscle tissue that is part of a respiratory system venous blood vessel. EMAPA:37586 MA:0001812 uberon UBERON:0012418 respiratory system venous smooth muscle A smooth muscle tissue that is part of a respiratory system venous blood vessel. OBOL:automatic EMAPA:37586 MA:th A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified]. a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction increases the surface area of a cell lining whilst minimizing increase in volume FMA class represents an individual microvillus. FMA:67296 MESH:D008871 NCIT:C33112 UMLS:C0026049 Wikipedia:Microvillus uberon microvilli microvillus UBERON:0012423 layer of microvilli A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified]. GO:0005902 Wikipedia:Microvillus FMA class represents an individual microvillus. FMA UMLS:C0026049 ncithesaurus:Microvillus microvilli MESH:A11.284.180.565 microvillus FMA:67296 A microvillus layer that is striated and found in the intestine. FMA class represents an individual microvillus FMA:70978 NCIT:C33634 uberon striated border UBERON:0012425 striated border microvillus layer A microvillus layer that is striated and found in the intestine. http://medical-dictionary.thefreedictionary.com/striated+border http://orcid.org/0000-0002-6601-2165 FMA class represents an individual microvillus FMA striated border FMA:70978 Blood-forming tissue, consisting of reticular fibers and cells. Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 NCIT:C13051 UMLS:C0229619 haemopoietic tissue hematopoietic tissue hemopoietic tissue textus haemopoieticus bone marrow tissue uberon UBERON:0012429 hematopoietic tissue FMA defitional Blood-forming tissue, consisting of reticular fibers and cells. http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue UMLS:C0229619 ncithesaurus:Hematopoietic_Tissue haemopoietic tissue FMA:14073 hematopoietic tissue FMA:14073 hemopoietic tissue FMA:14073 textus haemopoieticus FMA:14073 bone marrow tissue NCBITaxon:9606 The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. tunica fibrosa FMA:58102 SCTID:361318005 Wikipedia:Fibrous_tunic_of_eyeball fibrous layer of eyeball uberon corneosclera fibrous tunic UBERON:0012430 tunica fibrosa of eyeball FMA The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. Wikipedia:Fibrous_tunic_of_eyeball DOI:10.1177/0192623311409597 fibrous layer of eyeball FMA:58102 corneosclera Wikipedia:Fibrous_tunic_of_eyeball fibrous tunic Wikipedia:Fibrous_tunic_of_eyeball An anatomical space that is enclosed by a cloaca. the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ TAO:0000330 ZFA:0000330 cloaca lumen cloacal chamber uberon UBERON:0012463 cloacal lumen cjm An anatomical space that is enclosed by a cloaca. OBOL:automatic the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ ZFA cloaca lumen ZFA:0000330 cloacal chamber ZFA:0000330 The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. cloacal opening uberon cloacal orifice vent UBERON:0012464 cloacal vent The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. http://orcid.org/0000-0002-6601-2165 An anatomical space that is enclosed by a terminal part of digestive tract. includes the cloacal lumen, in species where this is present uberon UBERON:0012465 lumen of terminal part of digestive tract An anatomical space that is enclosed by a terminal part of digestive tract. OBOL:automatic EHDAA2:0000472 EMAPA:16054 VHOG:0000767 uberon extraembryonic cavities UBERON:0012466 extraembryonic cavity extraembryonic cavities EHDAA2:0000472 An anatomical space with no opening to another space or to the exterior. AEO:0000222 closed anatomical space uberon UBERON:0012467 enclosed anatomical space An anatomical space with no opening to another space or to the exterior. AEO:0000222 EHDAA2:0004589 uberon UBERON:0012469 external anal region EHDAA2 The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. FMA:24139 uberon bones of upper limb ossa membri superioris pectoral complex skeleton set of bones of upper limb skeleton of anterior limb/fin and girdle upper limb skeleton UBERON:0012475 skeleton of pectoral complex FMA The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. https://orcid.org/0000-0002-6601-2165 bones of upper limb FMA:24139 ossa membri superioris FMA:TA pectoral complex skeleton https://orcid.org/0000-0002-6601-2165 set of bones of upper limb FMA:24139 skeleton of anterior limb/fin and girdle https://orcid.org/0000-0002-6601-2165 upper limb skeleton FMA:24139 The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. FMA:24140 uberon bones of lower limb lower limb skeleton ossa membri inferioris pelvic complex skeleton set of bones of lower limb skeleton of posterior limb/fin and girdle UBERON:0012476 skeleton of pelvic complex FMA The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. https://orcid.org/0000-0002-6601-2165 bones of lower limb FMA:24140 lower limb skeleton FMA:24140 ossa membri inferioris FMA:TA pelvic complex skeleton https://orcid.org/0000-0002-6601-2165 set of bones of lower limb FMA:24140 skeleton of posterior limb/fin and girdle https://orcid.org/0000-0002-6601-2165 The posterior region of the neck, including the suboccipital region. nuchal nape BTO:0000957 FMA:24189 SCTID:182326009 SCTID:304036007 back of neck nape of neck neck back nucha nuchal region posterior cervical region posterior neck region posterior part of neck regio cervicalis posterior uberon hindneck UBERON:0012477 dorsal part of neck FMA FMA FMA The posterior region of the neck, including the suboccipital region. MP:0012723 nape BTO:0000957 back of neck FMA:24189 neck back FMA:24189 nucha FMA:24189 nuchal region FMA:24189 posterior cervical region FMA:24189 posterior neck region FMA:24189 posterior part of neck FMA:24189 regio cervicalis posterior FMA:TA A gland that is part of a cloaca. uberon UBERON:0012478 cloacal gland A gland that is part of a cloaca. OBOL:automatic A mucosa that is part of a cloaca [Automatically generated definition]. UBERON:0003349 cloaca mucosa cloaca mucosa of organ cloaca mucous membrane cloaca organ mucosa cloacal mucous membrane mucosa of cloaca mucosa of organ of cloaca mucous membrane of cloaca organ mucosa of cloaca uberon UBERON:0012480 cloacal mucosa A mucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic An epithelium that is part of a cloaca. cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 EMAPA:36070 ZFA:0005783 uberon cloacal endoderm UBERON:0012481 cloacal epithelium An epithelium that is part of a cloaca. http://orcid.org/0000-0002-6601-2165 cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 cloacal endoderm EMAPA:27577 A submucosa that is part of a cloaca [Automatically generated definition]. cloaca submucosa cloacal submucosa uberon UBERON:0012482 submucosa of cloaca A submucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic A serous membrane that is part of a cloaca [Automatically generated definition]. cloaca serosa cloaca serous membrane cloacal serosa serous membrane of cloaca visceral peritoneum of cloaca uberon UBERON:0012483 serosa of cloaca A serous membrane that is part of a cloaca [Automatically generated definition]. OBOL:automatic cloacal villi uberon UBERON:0012485 cloacal villus cloacal villi A muscular coat that is part of a cloaca. muscularis externa of cloaca uberon smooth muscle of cloaca UBERON:0012486 muscle layer of cloaca A muscular coat that is part of a cloaca. OBOL:automatic A muscular coat that is part of a duodenum. FMA:14944 SCTID:362147007 duodenal muscularis propria muscularis externa of duodenum uberon muscularis propria of duodenum smooth muscle of duodenum UBERON:0012488 muscle layer of duodenum A muscular coat that is part of a duodenum. OBOL:automatic duodenal muscularis propria FMA:14944 muscularis externa of duodenum FMA:14944 muscularis propria of duodenum https://orcid.org/0000-0002-6601-2165 smooth muscle of duodenum https://orcid.org/0000-0002-6601-2165 A muscular coat that is part of a colon. EMAPA:27383 FMA:14986 MA:0003198 SCTID:362158003 colonic muscularis propria muscular coat of colon muscular layer of colon muscularis externa of colon tunica muscularis coli uberon colon muscularis UBERON:0012489 muscle layer of colon A muscular coat that is part of a colon. OBOL:automatic colonic muscularis propria FMA:14986 muscular coat of colon FMA:14986 muscular layer of colon FMA:14986 muscularis externa of colon FMA:14986 tunica muscularis coli FMA:TA colon muscularis MA:0003198 A muscular coat that is part of a anal canal. FMA:15708 SCTID:362171000 anal canal muscularis propria anal muscularis propria muscular coat of anal canal muscular layer of anal canal muscularis externa of anal canal muscularis propria of anal canal uberon UBERON:0012490 muscle layer of anal canal A muscular coat that is part of a anal canal. OBOL:automatic anal muscularis propria FMA:15708 muscularis propria of anal canal FMA:15708 An adventitia that is part of a esophagus. FMA:63006 SCTID:85950006 adventitia of oesophagus adventitious layer of esophagus esophageal adventitia esophagus adventitia tunica adventitia (esophagus) tunica adventitia oesophageae uberon UBERON:0012504 adventitia of esophagus An adventitia that is part of a esophagus. OBOL:automatic adventitia of oesophagus FMA:63006 adventitious layer of esophagus FMA:63006 esophageal adventitia FMA:63006 esophagus adventitia FMA:63006 tunica adventitia (esophagus) FMA:63006 tunica adventitia oesophageae FMA:TA An anatomical junction that connects a stomach and connects a duodenum. FMA:17046 SCTID:264014000 uberon UBERON:0012650 gastroduodenal junction An anatomical junction that connects a stomach and connects a duodenum. OBOL:automatic A mucosa that is part of a gastroduodenal junction. BTO:0005415 gastroduodenal mucosa uberon UBERON:0012651 mucosa of gastroduodenal junction A mucosa that is part of a gastroduodenal junction. OBOL:automatic gastroduodenal mucosa BTO:0005415 A vein that is part of a abdomen. TODO mirror representation of abdominal aorta this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein SCTID:281473003 abdominal vein uberon UBERON:0013126 vein of abdomen A vein that is part of a abdomen. OBOL:automatic The part of the venous system that drains the lungs[Kardong]. Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung. Wikipedia:Pulmonary_venous_system pulmonary venous circulatory system uberon UBERON:0013127 pulmonary venous system The part of the venous system that drains the lungs[Kardong]. ISBN:0073040584 Wikipedia:Pulmonary_venous_system Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung. Wikipedia:Pulmonary_circulation A vein that drains a lip. SCTID:367664002 labial vein of face lip vein vena labialis uberon labial vein UBERON:0013136 vein of lip FMA A vein that drains a lip. OBOL:automatic lip vein OBOL:automatic vena labialis Any vein within the general circulation that transports blood back to the right atrium of the heart. FMA:66644 NCIT:C33719 SCTID:244389004 UMLS:C0447117 systemic venous tree organ part uberon UBERON:0013140 systemic vein Any vein within the general circulation that transports blood back to the right atrium of the heart. ncithesaurus:Systemic_Vein UMLS:C0447117 ncithesaurus:Systemic_Vein systemic venous tree organ part FMA:66644 A gland that is part of a foregut-midgut junction. EHDAA2:0000574 EMAPA:17065 gland of foregut-midgut junction uberon UBERON:0013158 foregut-midgut junction gland A gland that is part of a foregut-midgut junction. OBOL:automatic gland of foregut-midgut junction EMAPA:17065 The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. FMA:86279 acinus of serous gland uberon UBERON:0013232 serous acinus The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm Anatomical cavity that is the lumen of the skull and contains the brain. EMAPA:37497 FMA:9644 MA:0003061 NCIT:C77638 SCTID:264452006 UMLS:C0230041 Wikipedia:Cranial_cavity neuronames:2806 cavitas cranii uberon intracranial cavity intracranial space UBERON:0013411 cranial cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg Wikipedia Anatomical cavity that is the lumen of the skull and contains the brain. UBERON:cjm EMAPA:37497 MA:th UMLS:C0230041 ncithesaurus:Cranial_Cavity cavitas cranii FMA:9644 FMA:TA intracranial cavity Wikipedia:Cranial_cavity intracranial space Wikipedia:Cranial_cavity A blood vessel endothelium that is part of a lung [Automatically generated definition]. BTO:0004128 CALOHA:TS-0573 uberon respiratory endothelium UBERON:0013479 lung endothelium A blood vessel endothelium that is part of a lung [Automatically generated definition]. OBOL:automatic respiratory endothelium BTO:0004128 A sphincter muscle that is part of a cloaca. NCIT:C34129 UMLS:C1516658 sphincter cloacae uberon UBERON:0013501 the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938). cloacal sphincter A sphincter muscle that is part of a cloaca. OBOL:automatic UMLS:C1516658 ncithesaurus:Cloacal_Sphincter sphincter cloacae A caudal vertebra endochondral element that is composed primarily of cartilage tissue. UBERON:0013517 EHDAA2:0000260 EMAPA:18044 coccygeal vertebra cartilage element coccygeal vertebral cartilage condensation group tail vertebral cartilage condensation uberon UBERON:0013503 caudal vertebra cartilage element A caudal vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic coccygeal vertebra cartilage element http://orcid.org/0000-0002-6601-2165 coccygeal vertebral cartilage condensation group EHDAA2:0000260 tail vertebral cartilage condensation EMAPA:18044 A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation. UBERON:0013518 EMAPA:18045 coccygeal vertebra pre-cartilage condensation tail vertebral pre-cartilage condensation uberon UBERON:0013504 caudal vertebra pre-cartilage condensation A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic coccygeal vertebra pre-cartilage condensation http://orcid.org/0000-0002-6601-2165 tail vertebral pre-cartilage condensation EMAPA:18045 A cervical vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000240 cervical vertebral cartilage condensation group uberon UBERON:0013505 cervical vertebra cartilage element A cervical vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic cervical vertebral cartilage condensation group EHDAA2:0000240 A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013506 cervical vertebra pre-cartilage condensation A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0002014 thoracic vertebral cartilage condensation group uberon UBERON:0013507 thoracic vertebra cartilage element A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic thoracic vertebral cartilage condensation group EHDAA2:0002014 A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013508 thoracic vertebra pre-cartilage condensation A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic The space that surrounds an organism. external to organism outside of body uberon UBERON:0013514 space surrounding organism The space that surrounds an organism. https://orcid.org/0000-0002-6601-2165 uberon UBERON:0013522 subdivision of tube The anatomical space that is enclosed by a stomach. Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. EMAPA:18395 FMA:14585 cavity of stomach uberon gastric cavity UBERON:0013525 stomach lumen FMA The anatomical space that is enclosed by a stomach. http://orcid.org/0000-0002-6601-2165 Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. FMA:14585 cavity of stomach FMA:14585 gastric cavity FMA:14585 An epithelium that is part of a intestinal villus. FMA:63587 intestinal villus epithelium uberon villous epithelium villus epithelium UBERON:0013636 epithelium of intestinal villus FMA An epithelium that is part of a intestinal villus. OBOL:automatic intestinal villus epithelium FMA:63587 Anatomical space that is an opening in a bone of the skull. FMA:53165 SCTID:276742007 Wikipedia:Foramina_of_the_skull foramen of skull cranial conduit cranial foramen uberon foramina of the skull UBERON:0013685 foramen of skull Anatomical space that is an opening in a bone of the skull. TAO:curator http://orcid.org/0000-0002-6601-2165 foramen of skull Wikipedia:Foramina_of_the_skull cranial conduit FMA:53165 foramina of the skull Wikipedia:Foramina_of_the_skull 2 An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 foramen space uberon UBERON:0013686 anatomical conduit space FMA An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 http://orcid.org/0000-0002-6601-2165 Vascular endothelium found in blood vessels of the blood-brain-barrier. BTO:0001852 BTO:0003248 CALOHA:TS-0092 uberon cerebromicrovascular endothelium UBERON:0013694 brain endothelium Vascular endothelium found in blood vessels of the blood-brain-barrier. CALOHA:TS-0092 cerebromicrovascular endothelium CALOHA:TS-0092 Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 uberon colon endothelial cell colon endothelial cells colonic endothelial cell colonic endothelium colorectal endothelial cell colorectal endothelium UBERON:0013695 colon endothelium Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 colon endothelial cell CALOHA:TS-0162 colon endothelial cells CALOHA:TS-0162 colonic endothelial cell CALOHA:TS-0162 colonic endothelium CALOHA:TS-0162 colorectal endothelial cell CALOHA:TS-0162 colorectal endothelium CALOHA:TS-0162 Epithelium lining the exocrine pancreas. CALOHA:TS-2108 uberon epithelium of exocrine pancreas exocrine pancreas epithelial cell UBERON:0013697 exocrine pancreas epithelium Epithelium lining the exocrine pancreas. CALOHA:TS-2108 epithelium of exocrine pancreas CALOHA:TS-2108 exocrine pancreas epithelial cell CALOHA:TS-2108 Musculature of the head and neck, spine, and ribs. EHDAA2:0000159 EMAPA:18166 uberon UBERON:0013700 axial musculature Musculature of the head and neck, spine, and ribs. HP:0003327 A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. uberon UBERON:0013701 main body axis A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. https://orcid.org/0000-0002-6601-2165 The region of the organism associated with the visceral organs. Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 EMAPA:36031 FMA:231424 uberon body whole body UBERON:0013702 body proper AEO The region of the organism associated with the visceral organs. AEO:0000103 Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. FMA:231424 body AEO:0000103 whole body BTO:0001489 A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. FMA:293127 NCIT:C34230 UMLS:C1518428 uberon chordal canal UBERON:0013704 notochordal canal A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. http://medical-dictionary.thefreedictionary.com/notochordal+canal UMLS:C1518428 ncithesaurus:Notochordal_Canal Fluid contained within the notochordal canal. notochord fluid portion of notochordal fluid uberon UBERON:0013727 Distinct feature of coelocanths notochordal fluid Fluid contained within the notochordal canal. http://animaldiversity.org/accounts/Latimeria_chalumnae/ http://orcid.org/0000-0002-6601-2165 An organ component layer that is part of a integumental system. SCTID:314820002 layer of skin skin layer uberon UBERON:0013754 integumentary system layer An organ component layer that is part of a integumental system. OBOL:automatic A blood that is part of a artery. BTO:0006188 FMA:83066 arterial blood blood in artery portion of arterial blood uberon UBERON:0013755 arterial blood A blood that is part of a artery. OBOL:automatic BTO:0006188 https://github.com/biopragmatics/biomappings arterial blood FMA:83066 blood in artery FMA:83066 portion of arterial blood FMA:83066 A blood that is part of a vein. BTO:0006187 FMA:83067 blood in vein portion of venous blood venous blood uberon UBERON:0013756 venous blood A blood that is part of a vein. OBOL:automatic BTO:0006187 https://github.com/biopragmatics/biomappings blood in vein FMA:83067 portion of venous blood FMA:83067 venous blood FMA:83067 A blood that is part of a capillary. FMA:263901 NCIT:C32212 blood in capillary portion of blood in capillary portion of capillary blood uberon UBERON:0013757 capillary blood A blood that is part of a capillary. OBOL:automatic portion of blood in capillary FMA:263901 Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 SCTID:272627002 digestive organ digestive system organ uberon UBERON:0013765 digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. http://orcid.org/0000-0002-6601-2165 EMAPA:37843 MA:th Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. great vessel EMAPA:36460 SCTID:304066000 Wikipedia:Great_vessels great vessel of thorax uberon UBERON:0013768 Groupings may vary - typically pulmonary vessels and aorta and vena cavae great vessel of heart Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. Wikipedia:Great_vessels Mesenchyme that develops_from the neural crest[Automatically generated definition]. EMAPA:32735 FMA:293883 mesenchyme from neural crest neural crest derived mesenchyme neural crest mesenchyme uberon UBERON:0014387 mesenchyme derived from neural crest Mesenchyme that develops_from the neural crest[Automatically generated definition]. OBOL:automatic https://github.com/obophenotype/uberon/issues/248 Muscle that is part of the respiratory system. this class may be merged with 'respiratory system muscle'; check intercostals MESH:D012132 uberon UBERON:0014398 respiratory muscle Muscle that is part of the respiratory system. http://orcid.org/0000-0002-6601-2165 MESH:D012132 https://github.com/biopragmatics/biomappings An anatomical space that is enclosed by a sinusoid. FMA:63133 lumen of sinusoid sinusoid lumen uberon UBERON:0014399 sinusoidal space An anatomical space that is enclosed by a sinusoid. OBOL:automatic lumen of sinusoid FMA:63133 sinusoid lumen FMA:63133 A sinusoidal space that is part of a hepatic sinusoid. FMA:262090 lumen of hepatic sinusoid uberon UBERON:0014400 hepatic sinusoidal space A sinusoidal space that is part of a hepatic sinusoid. OBOL:automatic lumen of hepatic sinusoid FMA:262090 A part of the body present only in a specific gender. AEO:0000174 WBbt:0005752 gender-specific gender-specific anatomical structure sex-specific uberon UBERON:0014402 sex-specific anatomical structure A part of the body present only in a specific gender. AEO:0000174 AEO:JB gender-specific anatomical structure AEO:0000174 A part of the body present only in females. AEO:0000176 uberon UBERON:0014404 female anatomical structure A part of the body present only in females. AEO:0000176 AEO:JB Subcutaneous adipose tissue that is located in the peritoneal cavity. Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]. BTO:0004041 CALOHA:TS-2405 uberon abdominal fat intra-abdominal adipose tissue intra-abdominal fat organ fat visceral adipose tissue visceral fat UBERON:0014454 visceral abdominal adipose tissue Subcutaneous adipose tissue that is located in the peritoneal cavity. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]. BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 organ fat BTO:0004041 visceral adipose tissue BTO:0004041 visceral fat BTO:0004041 Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:TS-2406 abdominal subcutaneous adipose tissue subcutaneous abdominal fat subcutaneous fat of abdominal region uberon UBERON:0014455 subcutaneous abdominal adipose tissue Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. EHDAA2:0002013 FMA:77169 Wikipedia:Thoracic_skeleton skeleton of thorax thoracic part of axial skeleton thoracic skeleton uberon UBERON:0014477 thoracic skeleton Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. Wikipedia:Rib_cage https://orcid.org/0000-0002-6601-2165 thoracic skeleton EHDAA2:0002013 A ventral horn of spinal cord that is part of a thoracic spinal cord. BIRNLEX:1410 SCTID:367876000 UMLS:C0228632 UMLS:C1288552 thoracic spinal cord ventral horn uberon thoracic spinal cord anterior horn UBERON:0014610 thoracic spinal cord ventral horn A ventral horn of spinal cord that is part of a thoracic spinal cord. OBOL:automatic UMLS:C0228632 BIRNLEX:1410 UMLS:C1288552 BIRNLEX:1410 thoracic spinal cord ventral horn BIRNLEX:1410 thoracic spinal cord anterior horn BIRNLEX:1410 A gray matter of spinal cord that is part of a cervical spinal cord. BIRNLEX:1521 SCTID:362438009 UMLS:C0228610 cervical spinal cord gray matter uberon UBERON:0014613 cervical spinal cord gray matter A gray matter of spinal cord that is part of a cervical spinal cord. OBOL:automatic UMLS:C0228610 BIRNLEX:1521 cervical spinal cord gray matter BIRNLEX:1521 A ventral horn of spinal cord that is part of a cervical spinal cord. BIRNLEX:1680 MESH:D066151 SCTID:174363005 UMLS:C0228615 UMLS:C1278740 cervical spinal cord ventral horn uberon cervical spinal cord anterior horn UBERON:0014621 cervical spinal cord ventral horn A ventral horn of spinal cord that is part of a cervical spinal cord. OBOL:automatic MESH:D066151 https://github.com/biopragmatics/biomappings UMLS:C0228615 BIRNLEX:1680 UMLS:C1278740 BIRNLEX:1680 cervical spinal cord ventral horn BIRNLEX:1680 cervical spinal cord anterior horn BIRNLEX:1680 A gray matter of spinal cord that is part of a thoracic spinal cord. BIRNLEX:980 SCTID:362441000 UMLS:C0228627 thoracic spinal cord gray matter uberon UBERON:0014636 thoracic spinal cord gray matter A gray matter of spinal cord that is part of a thoracic spinal cord. OBOL:automatic UMLS:C0228627 BIRNLEX:980 thoracic spinal cord gray matter BIRNLEX:980 An epithelium that is part of a frontonasal prominence. EHDAA2:0004108 EMAPA:32918 uberon UBERON:0014702 frontonasal process epithelium EHDAA2 EHDAA2 An epithelium that is part of a frontonasal prominence. OBOL:automatic A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. EHDAA2:0004019 EMAPA:25040 uberon UBERON:0014703 anal membrane ectodermal component A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. OBOL:automatic An anatomical space that is enclosed by a pleuroperitoneal canal. EHDAA2:0004736 EMAPA:25034 pleuro-peritoneal canal cavity uberon UBERON:0014704 pleuroperitoneal canal lumen EHDAA2 An anatomical space that is enclosed by a pleuroperitoneal canal. OBOL:automatic pleuro-peritoneal canal cavity EMAPA:25034 A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. NCIT:C32828 UMLS:C1512857 Wikipedia:Interlobular_ducts uberon UBERON:0014716 interlobular duct A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. ncithesaurus:Interlobular_Duct The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. FMA:86278 acinus of mucuous gland mucus acinus uberon UBERON:0014717 mucous acinus The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular. SCTID:205214009 uberon intralobular ductule UBERON:0014719 intralobular duct A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular. http://www.siumed.edu/~dking2/intro/glands.htm A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory. uberon intralobular ductule UBERON:0014720 interlobar duct A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory. http://www.siumed.edu/~dking2/intro/glands.htm The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. EHDAA2:0000597 EMAPA:17703 SCTID:244668003 VHOG:0001546 Wikipedia:Crus_of_diaphragm crural diaphragm uberon crura of the diaphragm crus of the diaphragm diaphragm crura diaphragmatic crura UBERON:0014765 Classification notes: May be considered an external sphincter[PMID:8224664] crus of diaphragm PMID:23586979 PMID:23586979 The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. PMID:23586979 crural diaphragm PMID:23586979 crura of the diaphragm Wikipedia:Crus_of_diaphragm crus of the diaphragm Wikipedia:Crus_of_diaphragm diaphragm crura diaphragmatic crura Wikipedia:Crus_of_diaphragm A crus of diaphragm that is in_the_right_side_of a diaphragm. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:58286 SCTID:362690009 crus dextrum (Diaphragma) crus dextrum diaphragmatis external sphincter of esophagus right crus of diaphragm right crus of lumbar part of diaphragm uberon UBERON:0014766 right crus of diaphragm A crus of diaphragm that is in_the_right_side_of a diaphragm. OBOL:automatic crus dextrum (Diaphragma) FMA:58286 FMA:TA crus dextrum diaphragmatis FMA:58286 FMA:TA external sphincter of esophagus FMA:58286 right crus of diaphragm FMA:58286 right crus of lumbar part of diaphragm FMA:58286 A crus of diaphragm that is in_the_left_side_of a diaphragm. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:58287 SCTID:244937004 crus sinistrum (Diaphragma) crus sinistrum diaphragmatis left crus of diaphragm left crus of lumbar part of diaphragm uberon UBERON:0014767 left crus of diaphragm A crus of diaphragm that is in_the_left_side_of a diaphragm. OBOL:automatic crus sinistrum (Diaphragma) FMA:58287 FMA:TA crus sinistrum diaphragmatis FMA:58287 FMA:TA left crus of diaphragm FMA:58287 left crus of lumbar part of diaphragm FMA:58287 A neuromere that is part of the presumptive midbrain. mesomere midbrain segment segment of midbrain EHDAA2:0004352 FMA:61997 mesomere of nervous system neuromere of mesomere group uberon future mesencephalon mesomere group UBERON:0014776 midbrain neuromere A neuromere that is part of the presumptive midbrain. http://orcid.org/0000-0002-6601-2165 mesomere group EHDAA2:0004352 A neuromere that is part of the presumptive spinal cord. TAO:0001332 ZFA:0001332 spinal cord metameric segment spinal neuromeres uberon spinal cord segment UBERON:0014777 spinal neuromere A neuromere that is part of the presumptive spinal cord. http://orcid.org/0000-0002-6601-2165 spinal neuromeres TAO:0001332 spinal cord segment TAO:0001332 Any muscle organ that is part of a cloaca. uberon UBERON:0014783 cloacal muscle Any muscle organ that is part of a cloaca. OBOL:automatic Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37864 FMA:71297 muscles of lower limb musculature of lower limb musculi membri inferioris uberon UBERON:0014792 musculature of pelvic complex Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. OBOL:automatic EMAPA:37864 MA:th muscles of lower limb FMA:71297 musculature of lower limb FMA:71297 musculi membri inferioris FMA:TA Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37861 FMA:71296 muscles of upper limb musculature of upper limb musculi membri superioris set of muscles of upper limb upper limb musculature uberon UBERON:0014793 musculature of pectoral complex Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin. OBOL:automatic EMAPA:37861 MA:th muscles of upper limb FMA:71296 musculature of upper limb FMA:71296 musculi membri superioris FMA:TA set of muscles of upper limb FMA:71296 upper limb musculature FMA:71296 Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). uberon UBERON:0014794 pectoral appendage muscle prolog Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). OBOL:automatic Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). uberon UBERON:0014795 pelvic appendage muscle prolog Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). OBOL:automatic A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). skeletal muscle AAO:0011099 BTO:0001103 CALOHA:TS-0933 EFO:0000888 EHDAA:5035 EHDAA:5043 EHDAA:5978 EHDAA:5984 EMAPA:35988 EV:0100377 GAID:141 MA:0003148 MAT:0000302 MESH:D018482 MIAA:0000302 TAO:0005277 VHOG:0000319 XAO:0000174 ZFA:0005277 uberon UBERON:0014892 skeletal muscle organ, vertebrate A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). GOC:dos A portion of tissue that will develop into vasculature. EFO:0003708 TAO:0005076 ZFA:0005076 uberon UBERON:0014903 primordial vasculature A portion of tissue that will develop into vasculature. ZFA:0005076 ZFA:curator One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites. Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]. EFO:0003664 EMAPA:37389 TAO:0001285 XAO:0004075 ZFA:0001285 intersegmental vessel intersegmental vessels intersomitic blood vessel intersomitic vessels segmental vessel uberon UBERON:0014907 intersomitic vessel ZFA ZFA One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites. MGI:anna Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]. ZFA:0001285, ZFIN:ZDB-PUB-030908-4 EMAPA:37389 MA:th intersegmental vessel ZFA:0001285 intersegmental vessels ZFA:0001285 intersomitic blood vessel XAO:0004075 intersomitic vessels ZFA:0001285 segmental vessel ZFA:0001285 A vertebral endochondral element in the cervical region of the vertebral column. cervical vertebra skeletal element cervical vertebra element uberon UBERON:0015007 cervical vertebra endochondral element A vertebral endochondral element in the cervical region of the vertebral column. http://orcid.org/0000-0002-6601-2165 cervical vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern cervical vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A vertebral endochondral element in the thoracic region of the vertebral column. thoracic vertebra skeletal element thoracic vertebra element uberon UBERON:0015008 thoracic vertebra endochondral element A vertebral endochondral element in the thoracic region of the vertebral column. http://orcid.org/0000-0002-6601-2165 thoracic vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern thoracic vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A sphenoid bone or its cartilage or pre-cartilage precursor. sphenoid bone skeletal element sphenoid element uberon UBERON:0015060 sphenoid endochondral element A sphenoid bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern sphenoid bone skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern sphenoid element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern consider merging into myocardial compact layer FMA:83105 perimysial connective tissue of subepicardium subepicardial connective tissue uberon UBERON:0015128 subepicardial layer of epicardium FMA perimysial connective tissue of subepicardium FMA:83105 subepicardial connective tissue FMA:83105 Visceral intrapericardial fat contiguous with the myocardial surface. FMA:9871 SCTID:42267001 epicardial adipose tissue pericardial adipose tissue uberon UBERON:0015129 epicardial fat Visceral intrapericardial fat contiguous with the myocardial surface. DOI:10.5935/abc.20130138 A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104] the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648] ocular gland uberon orbital gland UBERON:0015152 gland of ocular region inferred A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/614 An eye consisting of multiple light-sensing organs. uberon UBERON:0015165 multi-unit eye An eye consisting of multiple light-sensing organs. PMID:21062451 http://orcid.org/0000-0002-6601-2165 present on tentacular crown PMID:21062451 present on mantle edge in arcacean Bivalvia PMID:21062451 The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species PMID:21062451 A region of somite adjacent to presomitic mesoderm. TAO:0001462 XAO:0004074 ZFA:0001462 uberon inter-somited border intersomitic boundary intersomitic fissure intersomitic junction segmental border somite boundary UBERON:0015178 somite border A region of somite adjacent to presomitic mesoderm. http://orcid.org/0000-0002-6601-2165 intersomitic junction XAO:0004074 somite boundary ZFA:0001462 Epithelium located in the intersomitic region. XAO:0004077 intersomitic epithelium intersomitic membrane uberon UBERON:0015179 somite boundary epithelium Epithelium located in the intersomitic region. XAO:0004077 XAO:EJS intersomitic epithelium XAO:0004077 intersomitic membrane XAO:0004077 An anatomical group whose component structures share a common function. AEO:0000093 FBbt:00007278 uberon UBERON:0015203 non-connected functional system An anatomical group whose component structures share a common function. AEO:0000093 AEO:JB FBC:DOS FBbt:00007278 FBbt:00007278 A non-connected functional system that is composed primarily of a gland. EHDAA2:0002223 uberon UBERON:0015204 glandular system A non-connected functional system that is composed primarily of a gland. OBOL:automatic Any structure that is placed on one side of the left-right axis of a bilaterian. This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. http://orcid.org/0000-0002-6601-2165 A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart SPD:0000130 cardiac pump heart or heart like organ circulatory vessel uberon cardiac structure UBERON:0015228 circulatory organ A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. http://orcid.org/0000-0002-6601-2165 A pancreatic lobule that is in_the_left_side_of a exocrine pancreas. EMAPA:37711 MA:0000722 uberon UBERON:0015280 pancreas left lobe A pancreatic lobule that is in_the_left_side_of a exocrine pancreas. OBOL:automatic EMAPA:37711 MA:th A pancreatic lobule that is in_the_right_side_of a exocrine pancreas. EMAPA:37712 MA:0000723 uberon UBERON:0015281 pancreas right lobe A pancreatic lobule that is in_the_right_side_of a exocrine pancreas. OBOL:automatic EMAPA:37712 MA:th A basement membrane of epithelium that is part of a respiratory system. EMAPA:37570 MA:0001815 uberon UBERON:0015329 respiratory system basement membrane MA A basement membrane of epithelium that is part of a respiratory system. OBOL:automatic EMAPA:37570 MA:th EMAPA:37597 MA:0002449 heart/pericardium uberon UBERON:0015410 heart plus pericardium MA EMAPA:37597 MA:th heart/pericardium MA:0002449 The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery. EMAPA:37217 FMA:14772 MA:0003095 SCTID:244262006 Wikipedia:Hepatic_artery_proper hepatic artery proper uberon proper hepatic UBERON:0015480 proper hepatic artery MA FMA The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery. Wikipedia:Hepatic_artery_proper EMAPA:37217 MA:th hepatic artery proper FMA:14772 proper hepatic Wikipedia:Hepatic_artery_proper A hepatic artery that is part of a left lobe of liver. EMAPA:37096 FMA:14779 MA:0003096 left branch of hepatic artery left part of hepatic artery proper ramus sinister (arteria hepatica propria) uberon UBERON:0015481 left hepatic artery FMA A hepatic artery that is part of a left lobe of liver. OBOL:automatic EMAPA:37096 MA:th left branch of hepatic artery FMA:14779 left part of hepatic artery proper FMA:14779 ramus sinister (arteria hepatica propria) FMA:14779 FMA:TA A hepatic artery that is part of a right lobe of liver. EMAPA:37376 FMA:14778 MA:0003097 ramus dexter (arteria hepatica propria) right branch of hepatic artery proper right part of hepatic artery proper uberon UBERON:0015482 right hepatic artery FMA A hepatic artery that is part of a right lobe of liver. OBOL:automatic EMAPA:37376 MA:th ramus dexter (arteria hepatica propria) FMA:14778 FMA:TA right branch of hepatic artery proper FMA:14778 right part of hepatic artery proper FMA:14778 Hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla. EMAPA:37478 MA:0003108 choledochoduodenal junction uberon UBERON:0015485 choledocho-duodenal junction Hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla. http://medical-dictionary.thefreedictionary.com/choledochoduodenal+junction EMAPA:37478 MA:th choledochoduodenal junction MA:0003108 An epithelium that is part of a anal canal. EMAPA:18835 FMA:17511 anal canal epithelium epithelium of anal canal uberon UBERON:0015716 anal canal epithelium An epithelium that is part of a anal canal. OBOL:automatic anal canal epithelium FMA:17511 epithelium of anal canal FMA:17511 FMA:62798 portion of heterogeneous tissue uberon UBERON:0015757 heterogeneous tissue FMA portion of heterogeneous tissue FMA:62798 A smooth muscle tissue that is part of a hypodermis. FMA:77862 muscle layer in fatty layer of subcutaneous tissue stratum musculosum panniculi adiposi telae subcutaneae uberon UBERON:0015783 smooth muscle layer in fatty layer of subcutaneous tissue A smooth muscle tissue that is part of a hypodermis. OBOL:automatic muscle layer in fatty layer of subcutaneous tissue FMA:77862 stratum musculosum panniculi adiposi telae subcutaneae FMA:77862 FMA:TA A blood vessel that is part of a liver. EMAPA:35498 MA:0003137 uberon hepatic blood vessel UBERON:0015796 liver blood vessel A blood vessel that is part of a liver. OBOL:automatic hepatic blood vessel EMAPA:35498 An epithelium that is part of a camera-type eye. EMAPA:35957 MA:0003162 uberon UBERON:0015808 eye epithelium An epithelium that is part of a camera-type eye. OBOL:automatic An epithelium that is part of a foregut. EMAPA:32922 MA:0003204 uberon UBERON:0015833 foregut epithelium An epithelium that is part of a foregut. OBOL:automatic A lamina propria that is part of a duodenum. EMAPA:27255 FMA:15972 MA:0003209 duodenal lamina propria lamina propria mucosae of duodenum lamina propria of duodenum uberon UBERON:0015834 duodenum lamina propria FMA A lamina propria that is part of a duodenum. OBOL:automatic duodenal lamina propria FMA:15972 lamina propria mucosae of duodenum FMA:15972 lamina propria of duodenum FMA:15972 A capillary that is part of a lung. FMA:14121 capillary of lung uberon UBERON:0016405 pulmonary capillary A capillary that is part of a lung. OBOL:automatic capillary of lung FMA:14121 A hole in the diaphragm through which the esophagus passes. FMA:58289 esophageal hiatus of diaphragm oesophageal aperture oesophageal hiatus uberon UBERON:0016458 esophageal hiatus A hole in the diaphragm through which the esophagus passes. HP:0002036 esophageal hiatus of diaphragm FMA:58289 oesophageal aperture FMA:58289 oesophageal hiatus FMA:58289 A stroma that is part of a liver. FMA:17553 hepatic stroma stroma of liver uberon UBERON:0016478 liver stroma A stroma that is part of a liver. OBOL:automatic hepatic stroma FMA:17553 stroma of liver FMA:17553 Is the sensory system for the sense of hearing. Auditory system is general anatomical term in FMA EMAPA:36002 FMA:7192 MA:0002443 NCIT:C12889 NLXANAT:090817 UMLS:C0587901 Wikipedia:Auditory_system neuronames:2888 uberon UBERON:0016490 auditory system Is the sensory system for the sense of hearing. NLXANAT:090817 Auditory system is general anatomical term in FMA FMA UMLS:C0587901 ncithesaurus:Auditory_System Luminal space of the right ventricle of the heart. EMAPA:26047 FMA:9291 right ventricle lumen right ventricular cavity uberon UBERON:0016509 cavity of right ventricle Luminal space of the right ventricle of the heart. http://orcid.org/0000-0002-6601-2165 right ventricle lumen EMAPA:26047 right ventricular cavity FMA:FMA An anatomical space that is part of a duodenum. EMAPA:19080 FMA:14589 doudenal lumen duodenal lumen uberon UBERON:0016512 lumen of duodenum An anatomical space that is part of a duodenum. OBOL:automatic doudenal lumen FMA:FMA duodenal lumen FMA:FMA Luminal space of the left atrium of the heart. EMAPA:26011 FMA:9465 left atrial cavity left atrium lumen uberon UBERON:0016513 cavity of left atrium Luminal space of the left atrium of the heart. http://orcid.org/0000-0002-6601-2165 left atrial cavity FMA:FMA left atrium lumen EMAPA:26011 Luminal space of the left ventricle of the heart. EMAPA:26038 FMA:9466 left ventricular cavity uberon UBERON:0016514 cavity of left ventricle Luminal space of the left ventricle of the heart. http://orcid.org/0000-0002-6601-2165 left ventricular cavity FMA:FMA Luminal space of the right atrium of the heart. EMAPA:26020 FMA:11359 right atrial cavity uberon UBERON:0016522 cavity of right atrium Luminal space of the right atrium of the heart. http://orcid.org/0000-0002-6601-2165 right atrial cavity FMA:FMA The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. UBERON:2001379 TAO:0001379 ZFA:0001379 uberon UBERON:0016545 pharyngeal ectoderm The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. PMID:23020903 http://orcid.org/0000-0002-6601-2165 A layer of of the central nervous system that is part of gray matter. grey matter layer FMA:83142 CNS gray matter layer CNS grey matter layer gray matter layer of neuraxis grey matter layer of neuraxis uberon UBERON:0016548 central nervous system gray matter layer A layer of of the central nervous system that is part of gray matter. http://orcid.org/0000-0002-6601-2165 gray matter layer of neuraxis FMA:83142 uberon UBERON:0016550 spinal cord column Mucus produced in the respiratory tract. NCIT:C93171 UMLS:C0225378 uberon UBERON:0016552 phlegm Mucus produced in the respiratory tract. http://orcid.org/0000-0002-6601-2165 Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm). uberon UBERON:0016553 respiratory system mucus Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm). Wikipedia:Nasal_mucus#Respiratory_system http://orcid.org/0000-0002-6601-2165 An roughly circular indentation in a surface. AEO:0000204 uberon UBERON:0016566 pit An roughly circular indentation in a surface. AEO:0000204 AEO:JB FMA:68861 Wikipedia:Rexed_laminae http://neurolex.org/wiki/Category:Rexed_spinal_cord_parcellation_scheme_region rexed lamina uberon UBERON:0016570 lamina of gray matter of spinal cord rexed lamina FMA:68861 The dorsal region of the optic cup that gives rise to the dorsal part of the retina. dorsal optic cup dorsal region of optic cup uberon UBERON:0016854 dorsal part of optic cup The dorsal region of the optic cup that gives rise to the dorsal part of the retina. http://orcid.org/0000-0002-6601-2165 dorsal optic cup http://orcid.org/0000-0002-6601-2165 dorsal region of optic cup http://orcid.org/0000-0002-6601-2165 Primordium that develops into the central nervous system. UBERON:3000469 future CNS presumptive central nervous system uberon UBERON:0016879 future central nervous system Primordium that develops into the central nervous system. http://orcid.org/0000-0002-6601-2165 Primordium that develops into the nervous system. UBERON:3000477 AAO:0000477 presumptive nervous system uberon UBERON:0016880 future nervous system Primordium that develops into the nervous system. http://orcid.org/0000-0002-6601-2165 presumptive nervous system AAO:0000477 Epithelium lining the distalmost portion of the digestive tract. BTO:0005445 WBbt:0005800 rectum epithelium uberon UBERON:0016885 epithelium of terminal part of digestive tract Epithelium lining the distalmost portion of the digestive tract. http://orcid.org/0000-0002-6601-2165 rectum epithelium BTO:0005445 Any muscle tissue of the distalmost portion of the digestive tract. rectum muscle rectum muscle structure uberon UBERON:0016886 muscle tissue of terminal part of digestive tract Any muscle tissue of the distalmost portion of the digestive tract. http://orcid.org/0000-0002-6601-2165 The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 EHDAA2:0000003 EMAPA:16042 extra-embryonic component extraembryonic component uberon UBERON:0016887 entire extraembryonic component AEO AEO The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 AEO:JB extraembryonic component AEO:0000195 An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 uberon UBERON:0016888 transitional anatomical structure AEO An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 AEO:JB A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 uberon UBERON:0017650 developing mesenchymal structure A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 AEO:JB A viscus that is part of a abdomen. FMA:32413 FMA:67355 abdominal viscera abdominal viscera set set of abdominal viscera uberon UBERON:0017672 abdominal viscera A viscus that is part of a abdomen. OBOL:automatic abdominal viscera FMA:32413 abdominal viscera set FMA:32413 set of abdominal viscera FMA:32413 A muscle layer that is part of the rectum. FMA:15035 muscular coat of rectum muscularis externa of rectum rectal muscularis propria tunica muscularis (rectum) tunica muscularis recti uberon UBERON:0018111 muscle layer of rectum A muscle layer that is part of the rectum. http://orcid.org/0000-0002-6601-2165 muscular coat of rectum FMA:15035 muscularis externa of rectum FMA:15035 rectal muscularis propria FMA:15035 tunica muscularis (rectum) FMA:15035 tunica muscularis recti FMA:TA Any portion of smooth muscle tissue that is part of the rectum. rectal smooth muscle tissue rectum smooth muscle smooth muscle of rectum uberon UBERON:0018112 rectum smooth muscle tissue Any portion of smooth muscle tissue that is part of the rectum. http://orcid.org/0000-0002-6601-2165 FMA:83521 uberon UBERON:0018135 fibrocollagenous connective tissue Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). UBERON:0015006 caudal vertebra element tail vertebra element coccygeal vertebra element coccyx vertebra element uberon UBERON:0018142 caudal vertebra endochondral element Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). http://orcid.org/0000-0002-6601-2165 A zone of skin that is part of a lower lip. FMA:24767 SCTID:281630002 lower lip skin uberon UBERON:0018150 skin of lower lip A zone of skin that is part of a lower lip. OBOL:automatic lower lip skin FMA:24767 A zone of skin that is part of a upper lip. FMA:24765 SCTID:281629007 upper lip skin uberon UBERON:0018151 skin of upper lip A zone of skin that is part of a upper lip. OBOL:automatic upper lip skin FMA:24765 A stroma that is part of a pancreas. FMA:63121 pancreatic stroma uberon UBERON:0018234 stroma of pancreas A stroma that is part of a pancreas. OBOL:automatic pancreatic stroma FMA:63121 A boundary delimiting a rhombomere. rhombomere junction uberon UBERON:0018239 rhombomere boundary A boundary delimiting a rhombomere. GO:0021654 Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104 EHDAA2:0001842 EMAPA:35578 MA:0000165 uberon UBERON:0018254 skeletal musculature MA Any portion of submucosa that lines the digestive tract. uberon UBERON:0018257 submucosa of digestive tract Any portion of submucosa that lines the digestive tract. http://orcid.org/0000-0002-6601-2165 Any organ component layer that consists of muscle tissue. NCITA class may refer to smooth muscle only FMA:45634 NCIT:C75444 UMLS:C0225358 uberon UBERON:0018260 layer of muscle tissue Any organ component layer that consists of muscle tissue. http://orcid.org/0000-0002-6601-2165 NCITA class may refer to smooth muscle only NCIT A muscular coat that is part of a digestive tract. responsible for gut movement, such as peristalsis tunica muscularis of digestive tract uberon muscular layer of digestive tract muscularis externa of digestive tract tunica externa of digestive tract UBERON:0018261 muscular coat of digestive tract A muscular coat that is part of a digestive tract. OBOL:automatic An bone foramen in the ethmoid bone. There are usually two Foramina ethmoidalia present on each side in the dog. Sometimes one is situated rostral to the other, but often it is dorsal. They are not homologous with the Foramen ethmoidale anterius and Foramen ethmoidale posterius of man. Therefore they are not listed separately.[NOMINA ANATOMICA VETERINARIA (2005)] Wikipedia:Ethmoidal_foramina ethmoidal foramen foramina ethmoidalia uberon ethmoid foramina ethmoidal foramina UBERON:0018415 Taxon nodes: In humans, refers to anterior or posterior ethmoid foramina ethmoid foramen An bone foramen in the ethmoid bone. http://orcid.org/0000-0002-6601-2165 foramina ethmoidalia ethmoid foramina ethmoidal foramina The anatomical space within the intestine. see notes in inclusivity in class 'intestine' FMA:14586 TADS:0000495 WBbt:0005791 ZFA:0005807 intestinal lumen intestine lumen uberon gut lumen UBERON:0018543 lumen of intestine The anatomical space within the intestine. http://orcid.org/0000-0002-6601-2165 intestinal lumen FMA:14586 intestine lumen ZFA:0005807 gut lumen ZFA:0005807 Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscle innervated by the trigeminal nerve muscles innervated by the trigeminal nerve uberon UBERON:0018544 trigeminal nerve muscle Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscles innervated by the trigeminal nerve MFMO:0000072 FMA:83450 ventricular cardiac muscle tissue ventricular heart muscle uberon ventricular muscle UBERON:0018649 cardiac muscle tissue of ventricle ventricular cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 ventricular heart muscle http://orcid.org/0000-0002-6601-2165 ventricular muscle http://orcid.org/0000-0002-6601-2165 An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. FMA:73747 ZFA:0005811 cardiac vasculature uberon UBERON:0018674 heart vasculature An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. ZFA:0005811 ZFA:CVS cardiac vasculature FMA:73747 uberon UBERON:0018692 dorsal side of post-anal tail A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder uberon UBERON:0018707 bladder organ A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder BTO:0000123 BTO:0002439 genital mucosa uberon UBERON:0019042 reproductive system mucosa genital mucosa BTO:0002439 Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 uberon intramuscular fat UBERON:0019143 intramuscular adipose tissue Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 intramuscular fat BTO:0004043 BTO:0004626 uberon carotid endothelium carotid epithelium UBERON:0019189 carotid artery endothelium carotid endothelium BTO:0004626 BTO:0004638 FMA:13119 SCTID:88410004 bronchial gland bronchial mucous gland peribronchial gland uberon UBERON:0019190 mucous gland of lung bronchial gland FMA:13119 bronchial mucous gland FMA:13119 peribronchial gland BTO:0004638 Any region of epithelium that is part of a skin region. BTO:0004382 uberon UBERON:0019204 skin epithelium Any region of epithelium that is part of a skin region. http://orcid.org/0000-0002-6601-2165 The part of the eye that consists of both the retina and the optic choroid. SCTID:110701000 chorioretina choroid and retina retinachoroid retinachoroidal region uberon UBERON:0019207 chorioretinal region The part of the eye that consists of both the retina and the optic choroid. UBERON:drseb http://orcid.org/0000-0002-6601-2165 DHBA:10654 FMA:268630 gray matter of the hindbrain uberon UBERON:0019263 gray matter of hindbrain gray matter of the hindbrain DHBA:HGM DHBA:10649 FMA:83913 uberon UBERON:0019267 gray matter of midbrain EMAPA:35952 MA:0003174 uberon UBERON:0019304 sensory organ epithelium An exocrine gland that is part of a integumental system. integumental exocrine gland integumental system exocrine gland uberon UBERON:0019319 exocrine gland of integumental system An exocrine gland that is part of a integumental system. GOC:dos http://orcid.org/0000-0002-6601-2165 integumental exocrine gland http://orcid.org/0000-0002-6601-2165 integumental system exocrine gland http://orcid.org/0000-0002-6601-2165 FMA:58315 uberon surface of region of wall of eyeball UBERON:0022288 surface of eyeball surface of region of wall of eyeball FMA:58315 NCIT:C33596 SCTID:282511007 uberon UBERON:0022292 splenic arteriole A portion of organism substance that is secreted by a reproductive gland. uberon genital fluid genital secretion reproductive system fluid reproductive system fluid/secretion reproductive system secretion UBERON:0022293 reproductive gland secretion A portion of organism substance that is secreted by a reproductive gland. UBERON:cjm Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer lamina layer NLX:149357 uberon UBERON:0022303 nervous system cell part layer Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. NLX:149357 lamina CUMBO:CUMBO layer CUMBO:CUMBO Serous membrane layer that is adjacent to and lines an organ. FMA:15860 visceral wall of serous membrane uberon UBERON:0022350 visceral serous membrane Serous membrane layer that is adjacent to and lines an organ. http://orcid.org/0000-0002-6601-2165 visceral wall of serous membrane FMA:15860 Serous membrane layer that lines to a body cavity. cavity lining FMA:15859 MA:0002448 parietal wall of serous membrane uberon UBERON:0022351 parietal serous membrane Serous membrane layer that lines to a body cavity. http://orcid.org/0000-0002-6601-2165 cavity lining MA:0002448 parietal wall of serous membrane FMA:15859 A specific region of the foregut into the area in which the lung will develop. SCTID:34922002 lung field uberon UBERON:0022361 lung field A specific region of the foregut into the area in which the lung will develop. GOC:dph GOC:mtg_lung An embryonic or larval epithelium that is committed to form part of the nervous system. neurepithelium AEO:0001008 BTO:0000314 EHDAA2_RETIRED:0004654 FMA:64807 embryonic neuroepithelium neuroepithelium uberon UBERON:0034705 developing neuroepithelium An embryonic or larval epithelium that is committed to form part of the nervous system. AEO:0001008 AEO:JB neurepithelium BTO:0000314 embryonic neuroepithelium http://orcid.org/0000-0002-6601-2165 neuroepithelium AEO:0001008 An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 uberon UBERON:0034706 proliferating neuroepithelium AEO An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 uberon UBERON:0034707 differentiating neuroepithelium AEO A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 DHBA:12694 EMAPA:32916 marginal zone of hindbrain uberon MZH UBERON:0034709 hindbrain marginal layer marginal zone of hindbrain DHBA:12694 MZH DHBA:12694 EHDAA2:0001267 EMAPA:17585 spinal cord lateral wall ventricular layer uberon UBERON:0034710 spinal cord ventricular layer EHDAA2 spinal cord lateral wall ventricular layer EHDAA2:0001267 Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain. uberon cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain UBERON:0034713 cranial neuron projection bundle Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain. ISBN:0471888893 http://orcid.org/0000-0002-6601-2165 cranial nerve fiber bundle http://orcid.org/0000-0002-6601-2165 cranial nerve fiber tract http://orcid.org/0000-0002-6601-2165 cranial nerve or tract http://orcid.org/0000-0002-6601-2165 neuron projection bundle from brain http://orcid.org/0000-0002-6601-2165 The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. EMAPA:37957 FMA:5866 MESH:D017776 SCTID:276145003 Wikipedia:Autonomic_nerve nervus visceralis visceral nerve uberon UBERON:0034728 autonomic nerve The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. Wikipedia:Autonomic_nerve EMAPA:37957 MA:th nervus visceralis FMA:5866 visceral nerve FMA:5866 EMAPA:37958 SCTID:181098007 uberon UBERON:0034729 sympathetic nerve EMAPA:37958 MA:th FMA:79770 NCIT:C41168 uberon UBERON:0034769 lymphomyeloid tissue FMA Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 gas in anatomical space portion of gas in anatomical space uberon UBERON:0034873 bodily gas Any substance in the body or expelled from the body that is in a gaseous state. http://orcid.org/0000-0002-6601-2165 portion of gas in anatomical space FMA:84580 Any portion of gas located in a part of the respiratory system that is composed primarily of air. FMA:84581 respiratory air respiratory system air uberon UBERON:0034874 air in respiratory system Any portion of gas located in a part of the respiratory system that is composed primarily of air. http://orcid.org/0000-0002-6601-2165 respiratory air FMA:84581 The area of axial mesoderm that develops into the prechordal plate. prechordal mesenchyme uberon UBERON:0034878 prechordal mesoderm The area of axial mesoderm that develops into the prechordal plate. MGI:anna Endocardium that is part of the left atrium. Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein. FMA:7286 SCTID:190064008 VHOG:0001226 endocardium of left atrium left atrial endocardium uberon left atrium endocardial tissue UBERON:0034903 left atrium endocardium Endocardium that is part of the left atrium. http://orcid.org/0000-0002-6601-2165 Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein. FMA:7286 endocardium of left atrium FMA:7286 left atrium endocardial tissue VHOG:0001226 lumen of gland uberon UBERON:0034905 gland lumen An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 uberon anatomical cluster UBERON:0034921 multi organ part structure CARO An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 anatomical cluster CARO:0020001 A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 uberon UBERON:0034922 cell cluster CARO A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 2 Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 FBbt:00007276 uberon UBERON:0034923 disconnected anatomical group CARO Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 FBbt:00007276 A collection of anatomical structures that are alike in terms of their morphology or developmental origin. resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected uberon UBERON:0034925 anatomical collection A collection of anatomical structures that are alike in terms of their morphology or developmental origin. http://orcid.org/0000-0002-6601-2165 A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. uberon UBERON:0034929 external soft tissue zone A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. http://orcid.org/0000-0002-6601-2165 The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. BTO:0001513 biliary system epithelium uberon biliary epithelium biliary tract epithelium UBERON:0034932 epithelium of biliary system The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. BTO:0001513 MGI:cs http://orcid.org/0000-0002-6601-2165 biliary system epithelium http://orcid.org/0000-0002-6601-2165 biliary epithelium BTO:0001513 biliary tract epithelium http://orcid.org/0000-0002-6601-2165 Any organ component layer that consists of smooth muscle tissue. uberon UBERON:0034933 layer of smooth muscle tissue Any organ component layer that consists of smooth muscle tissue. http://orcid.org/0000-0002-6601-2165 FMA:55268 organ sector organ zonal region organ zone uberon organ region with floating fiat boundary UBERON:0034944 zone of organ organ sector FMA:55268 organ zone FMA:55268 organ region with floating fiat boundary FMA:55268 Any gaseous product of an excretory process. uberon UBERON:0034945 excreted gas Any gaseous product of an excretory process. http://orcid.org/0000-0002-6601-2165 Any excreted gas that is produced by the digestive tract. FMA:78440 flatulence flatus intestinal gas uberon UBERON:0034946 In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum gas excreted from digestive tract Any excreted gas that is produced by the digestive tract. http://orcid.org/0000-0002-6601-2165 flatulence FMA:78440 flatus Wikipedia:Flatulence Any portion of gas located in a part of the respiratory system. respiratory gas respiratory system gas uberon UBERON:0034947 gas in respiratory system Any portion of gas located in a part of the respiratory system. http://orcid.org/0000-0002-6601-2165 NCIT:C25787 UMLS:C1512086 uberon duct epithelium ductal epithelium UBERON:0034969 epithelial layer of duct Mesenchyme that is part of a developing jaw [Automatically generated definition]. EMAPA:32907 EMAPA:35454 uberon UBERON:0034995 jaw mesenchyme Mesenchyme that is part of a developing jaw [Automatically generated definition]. OBOL:automatic EMAPA:32904 MA:0003220 uberon UBERON:0035037 jaw epithelium SCTID:277967008 hemorrhoidal artery uberon UBERON:0035039 rectal artery BTO:0006341 uberon UBERON:0035050 excretory duct BTO:0006341 https://github.com/biopragmatics/biomappings A post-anal tail that attaches outside the tail. uberon UBERON:0035091 extrinsic post-anal tail muscle A post-anal tail that attaches outside the tail. http://orcid.org/0000-0002-6601-2165 Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat digestive tract contents uberon ingested material entity UBERON:0035118 material entity in digestive tract Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. https://github.com/EnvironmentOntology/envo/issues/110 digestive tract contents Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 NCIT:C29667 SCTID:261060002 UMLS:C0489451 surface of body uberon UBERON:0035159 entire surface of organism Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 surface of body FMA:61695 FMA:70505 NCIT:C32552 SCTID:244216003 UMLS:C0447038 external carotid arterial subdivision subdivision of external carotid artery uberon UBERON:0035398 branch of external carotid artery external carotid arterial subdivision FMA:70505 subdivision of external carotid artery FMA:70505 Any of several arteries that arise from the aorta and supply blood to the esophagus. FMA:4149 NCIT:C32535 SCTID:56548006 UMLS:C0226294 aortic esophageal artery oesophageal artery uberon UBERON:0035539 esophageal artery FMA FMA Any of several arteries that arise from the aorta and supply blood to the esophagus. ncithesaurus:Esophageal_Artery aortic esophageal artery FMA:4149 oesophageal artery FMA:4149 FMA:51797 SCTID:149683007 ciliary vein uberon UBERON:0035546 uveal vein ciliary vein FMA:51797 SCTID:77852007 uberon UBERON:0035548 colic artery https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. FMA:225275 superficial part of circulatory system superficial vasculature dermis vasculature hypodermis vasculature uberon skin vasculature subcutaneous vasculature vasculature of skin UBERON:0035549 vasculature of integument The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. http://orcid.org/0000-0002-6601-2165 vasculature of skin FMA:225275 Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. FMA:76719 NCIT:C33666 SCTID:341382008 UMLS:C0226513 Wikipedia:Superficial_vein uberon superfical vein superficial veins superficial vessels UBERON:0035550 superficial vein Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. ncithesaurus:Superficial_Vein superfical vein Wikipedia:Superficial_vein superficial veins Wikipedia:Superficial_vein superficial vessels Wikipedia:Superficial_vein The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. deep part of circulatory system uberon UBERON:0035551 deep vasculature The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. http://orcid.org/0000-0002-6601-2165 A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. FMA:76718 NCIT:C32444 SCTID:341484008 UMLS:C0226514 Wikipedia:Deep_vein uberon deep veins deep vessels UBERON:0035552 deep vein A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. ncithesaurus:Deep_Vein deep veins Wikipedia:Deep_vein deep vessels Wikipedia:Deep_vein Any chamber of the left side of the heart. FMA:7166 SCTID:362008007 uberon UBERON:0035553 left cardiac chamber Any chamber of the left side of the heart. http://orcid.org/0000-0002-6601-2165 Any chamber of the right side of the heart. FMA:7165 SCTID:362007002 uberon UBERON:0035554 right cardiac chamber Any chamber of the right side of the heart. http://orcid.org/0000-0002-6601-2165 The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. FMA:76554 NCIT:C32574 SCTID:120612006 UMLS:C0229243 Wikipedia:Accessory_visual_structures adnexa oculi uberon accessory parts of orbital region accessory visual structures accessory visual structures set adnexal parts of orbital region appendage of eye appendages of the eye eye adnexa set of accessory visual structures structurae oculi accessoriae UBERON:0035639 ocular adnexa The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. HPO:pr UBERON:cjm http://medical-dictionary.thefreedictionary.com/ocular+adnexa https://github.com/obophenotype/uberon/issues/1132 adnexa oculi http://medical-dictionary.thefreedictionary.com/ocular+adnexa accessory visual structures FMA:76554 Wikipedia:Accessory_visual_structures accessory visual structures set FMA:76554 appendage of eye http://medical-dictionary.thefreedictionary.com/ocular+adnexa appendages of the eye http://medical-dictionary.thefreedictionary.com/ocular+adnexa set of accessory visual structures FMA:76554 structurae oculi accessoriae Wikipedia:Accessory_visual_structures EHDAA2:0004181 FMA:9464 cardiac chamber cavity heart cavity heart lumen uberon UBERON:0035763 cavity of cardiac chamber FMA cardiac chamber cavity FMA:9464 heart cavity FMA:9464 heart lumen EHDAA2:0004181 The primordial mouth region of the developing head. FMA:293105 primitive mouth primordial mouth uberon UBERON:0035804 future mouth The primordial mouth region of the developing head. MP:0003119 primitive mouth FMA:293105 A muscle layer that is part of the sigmoid colon. FMA:15028 muscularis externa of sigmoid colon muscularis propria of sigmoid colon sigmoid colon muscularis propria uberon sigmoideum muscularis tunica muscularis colon sigmoideum UBERON:0035805 muscle layer of sigmoid colon A muscle layer that is part of the sigmoid colon. https://github.com/obophenotype/uberon/issues/1162 muscularis externa of sigmoid colon FMA:15028 FMA:12241 SCTID:304404008 uberon UBERON:0035809 serous cavity The sum of epicardial and paracardial fat deposits. SCTID:42267001 ZFA:0005765 uberon UBERON:0035814 pericardial fat The sum of epicardial and paracardial fat deposits. DOI:10.5935/abc.20130138 Fat deposits in the mediastinum outside the parietal pericardium . intrathoracic fat uberon UBERON:0035815 paracardial fat Fat deposits in the mediastinum outside the parietal pericardium . DOI:10.5935/abc.20130138 intrathoracic fat DOI:10.5935/abc.20130138 Any fat deposit surrounding a visceral organ. uberon UBERON:0035818 visceral fat Any fat deposit surrounding a visceral organ. UBERON:cjm The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. FMA:12267 Wikipedia:Abdominopelvic_cavity cavitas abdominis et pelvis uberon UBERON:0035819 abdominopelvic cavity The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. UBERON:cjm cavitas abdominis et pelvis FMA:TA A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. EMAPA:16137 FMA:9908 uberon peritoneal component UBERON:0035820 peritoneal sac A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. https://github.com/obophenotype/uberon/issues/86 peritoneal component EMAPA:16137 The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. FMA:58277 SCTID:368048007 costal part of diaphragm pars costalis diaphragmatis uberon UBERON:0035831 costal diaphragm PMID:23586979 PMID:23586979 The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. PMID:23586979 costal part of diaphragm FMA:58277 pars costalis diaphragmatis FMA:TA BTO:0004378 EMAPA:37987 FMA:67473 blood vessel wall uberon vascular wall UBERON:0035965 wall of blood vessel EMAPA:37987 MA:th blood vessel wall FMA:67473 vascular wall BTO:0004378 EHDAA2:0004070 uberon UBERON:0036072 respiratory primordium epithelium EHDAA2 EHDAA2:0004071 respiratory primordium associated mesenchyme uberon UBERON:0036073 respiratory primordium mesenchyme EHDAA2 respiratory primordium associated mesenchyme EHDAA2:0004071 An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. uberon UBERON:0036146 cardiopharyngeal field An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1 https://orcid.org/0000-0003-3308-6245 FMA:83520 uberon UBERON:0036186 fibroelastic connective tissue An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 SCTID:245429006 uberon rectosigmoid region UBERON:0036214 rectosigmoid junction An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 https://github.com/obophenotype/uberon/issues/1319 https://www.cdc.gov/cancer/npcr/pdf/abstracting/colon.pdf rectosigmoid region NCIT:C54188 Material anatomical entity that forms the outermost boundary of an anatomical structure. AAO:0010270 ZFA:0005594 uberon UBERON:0036215 anatomical surface region Material anatomical entity that forms the outermost boundary of an anatomical structure. https://github.com/obophenotype/uberon/issues/1324 A bodily fluid that is located in the coelom. he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid] BTO:0001708 uberon UBERON:0036217 coelomic fluid A bodily fluid that is located in the coelom. PMID:10874572 https://github.com/obophenotype/uberon/issues/1326 Any gland that is part os the respiratory system. uberon UBERON:0036225 respiratory system gland Any gland that is part os the respiratory system. UBERON:cjm A notochord that has persisted beyond the embryonic stage. uberon UBERON:0036242 post-embryonic notochord A notochord that has persisted beyond the embryonic stage. UBERON:cjm A transudate found in the serous sac. serous fluid FMA:20932 serous sac fluid uberon UBERON:0036244 secretion of serous membrane A transudate found in the serous sac. FMA:20932 serous fluid FMA:20932 FMA:53133 cranial orifice skull orifice uberon UBERON:0036253 orifice of skull cranial orifice FMA:53133 skull orifice FMA:53133 The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. FMA:52972 SCTID:280243001 Wikipedia:Zygomaticotemporal_nerve ramus zygomaticotemporalis (Nervus zygomaticus) ramus zygomaticotemporalis nervus zygomatici zygomaticotemporal branch of zygomatic nerve uberon zygomaticotemporal zygomaticotemporal branch UBERON:0036264 zygomaticotemporal nerve The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. Wikipedia:Zygomaticotemporal_nerve ramus zygomaticotemporalis (Nervus zygomaticus) FMA:52972 ramus zygomaticotemporalis nervus zygomatici FMA:TA zygomaticotemporal branch of zygomatic nerve FMA:52972 zygomaticotemporal Wikipedia:Zygomaticotemporal_nerve zygomaticotemporal branch Wikipedia:Zygomaticotemporal_nerve SCTID:13152008 uberon UBERON:0036268 pelvic vein Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall uberon UBERON:0036285 wall of left ventricle FMA FMA Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall FMA:9556 Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 right ventricular wall uberon UBERON:0036286 wall of right ventricle FMA FMA Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 right ventricular wall FMA:9533 FMA:9560 uberon UBERON:0036288 anterior wall of left ventricle FMA Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 uberon UBERON:0036289 anterior wall of right ventricle Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 FMA:87177 uberon UBERON:0036290 myocardium of anterior wall of left ventricle FMA:260877 uberon UBERON:0036291 myocardium of anterior wall of right ventricle A mucosa that is part of a lip region [Automatically generated definition]. NCIT:C12226 labial mucosa uberon UBERON:0036294 mucosa of lip A mucosa that is part of a lip region [Automatically generated definition]. OBOL:automatic labial mucosa UBERON:cjm FMA:225251 SCTID:297287005 uberon UBERON:0036301 vasculature of spleen FMA uberon UBERON:0036302 vasculature of central nervous system plus retina FMA:259905 uberon UBERON:0036303 vasculature of central nervous system FMA:14657 gallbladder wall uberon UBERON:0036343 wall of gallbladder FMA gallbladder wall FMA:14657 FMA:15089 brachiocephalic arterial wall uberon UBERON:0036351 wall of brachiocephalic artery FMA FMA brachiocephalic arterial wall FMA:15089 FMA:15090 subclavian arterial wall uberon UBERON:0036352 wall of subclavian artery FMA FMA subclavian arterial wall FMA:15090 FMA:15704 anal canal wall uberon UBERON:0036362 wall of anal canal FMA anal canal wall FMA:15704 FMA:18211 pulmonary arterial wall uberon UBERON:0036422 wall of pulmonary artery FMA FMA pulmonary arterial wall FMA:18211 FMA:231590 uberon UBERON:0036553 wall of synovial tendon sheath FMA FMA FMA:58098 eyeball wall uberon UBERON:0036925 wall of eyeball FMA FMA eyeball wall FMA:58098 FMA:63144 orbit wall uberon UBERON:0037089 wall of orbit FMA FMA orbit wall FMA:63144 FMA:66284 common carotid arterial wall uberon UBERON:0037094 wall of common carotid artery FMA FMA common carotid arterial wall FMA:66284 Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall uberon UBERON:0037144 wall of heart FMA FMA FMA FMA Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall FMA:7274 An artery that supplies oxygenated blood to the cystic duct. FMA:14835 cholecystic artery uberon UBERON:0039222 cystic artery https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA Wikipedia An artery that supplies oxygenated blood to the cystic duct. http://orcid.org/0000-0002-6601-2165 https://en.wikipedia.org/wiki/Cystic_artery cholecystic artery FMA:14835 FMA:15395 uberon UBERON:0039228 sigmoid vein FMA FMA:70471 uberon UBERON:0039261 pancreatic artery Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament. FMA:14342 uberon UBERON:0039856 right ovarian vein FMA FMA Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament. FMA:14342 Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament. FMA:14347 uberon UBERON:0039857 left ovarian vein FMA Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament. FMA:14347 A zone of skin that is part of the face. 2012-02-05T05:23:01Z EMAPA:36657 FMA:24758 NCIT:C33561 SCTID:361703006 UMLS:C0222084 face skin uberon facial skin UBERON:1000021 skin of face A zone of skin that is part of the face. UBERON:EJS https://github.com/obophenotype/uberon/issues/34 UMLS:C0222084 ncithesaurus:Skin_of_the_Face face skin EMAPA:36657 FMA:24758 A parenchyma that is part of a spleen. FMA:16029 splenic parenchyma uberon UBERON:1000024 parenchyma of spleen A parenchyma that is part of a spleen. OBOL:automatic splenic parenchyma FMA:16029 An anatomical junction between two parts of the digestive tract. 2021-02-05T11:19:31Z uberon UBERON:1100000 digestive tract junction An anatomical junction between two parts of the digestive tract. https://orcid.org/0000-0002-7073-9172 This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0001073 uberon UBERON:2001073 axial vasculature This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/tao.owl Cartilage which is part of the axial skeleton. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0001457 uberon UBERON:2001457 postcranial axial cartilage Cartilage which is part of the axial skeleton. ZFIN:curator This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/tao.owl Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse. the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA]. fenestrated blood vessel endothelium FMA:63196 NCIT:C32595 TAO:0005260 UMLS:C1179615 Wikipedia:Capillary#Types ZFA:0005260 fenestrated capillary vessel uberon UBERON:2005260 fenestrated capillary FMA ZFA Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse. Wikipedia:Capillary#Types Wikipedia:Fenestra_(histology) fenestrated blood vessel endothelium ZFA:0005260 UMLS:C1179615 ncithesaurus:Fenestrated_Capillary fenestrated capillary vessel FMA:63196 Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0007013 uberon UBERON:2007013 preplacodal ectoderm Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. ZFIN:curator This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/tao.owl Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000961 Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 external integument structure Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Dermal, epidermal, glandular and pigment structures of the external head integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000972 head external integument structure Dermal, epidermal, glandular and pigment structures of the external head integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Dermal, epidermal, glandular and pigment structures of the body integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000977 body external integument structure Dermal, epidermal, glandular and pigment structures of the body integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Dermal, epidermal, glandular and pigment structures of the tail integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000982 tail external integument structure Dermal, epidermal, glandular and pigment structures of the tail integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Blood vessels in respiratory skin. Modified from the original AAO source This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3010200 vasculature of respiratory integument Blood vessels in respiratory skin. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl An anatomical surface that is part of a bone. bone surface uberon UBERON:4200230 surface of bone An anatomical surface that is part of a bone. PHENOSCAPE FBbt:00000004 uberon UBERON:6000004 panarthropod head FBbt:00000004 Any head that is part of some larva. FBbt:00001730 uberon UBERON:6001730 insect larval head Any head that is part of some larva. FBC:auto_generated_definition FBbt:00001730 Any sense organ that is part of some larva. FBbt:00002639 larval sense organ uberon UBERON:6002639 insect larval sense organ Any sense organ that is part of some larva. FBC:auto_generated_definition FBbt:00002639 Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727). FBbt:00007240 larval sensillum uberon UBERON:6007240 insect embryonic/larval sensillum Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727). FBC:auto_generated_definition FBbt:00007240 Any sensillum (UBERON:6007152) that is part of some larval head (UBERON:6001730). FBbt:00007242 larval head sensillum uberon UBERON:6007242 insect embryonic/larval head sensillum Any sensillum (UBERON:6007152) that is part of some larval head (UBERON:6001730). FBC:auto_generated_definition FBbt:00007242 Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730). FBbt:00007280 larval head sense organ uberon UBERON:6007280 insect embryonic/larval head sense organ Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730). FBC:auto_generated_definition FBbt:00007280 Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. uberon UBERON:8000006 left side of back Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. https://microbiomedb.org/ Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. uberon UBERON:8000007 right side of back Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. https://microbiomedb.org/ A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles. Purkinje fibre network uberon UBERON:8000009 Purkinje fiber network https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 https://github.com/obophenotype/uberon/issues/1785 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9791-0064 A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles. PMID:26786210 Purkinje fibre network PMID:26786210 Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the 'bare area of the liver') and a smaller area where the liver and gallbladder are in direct contact. serosa of liver tunica serosa hepatis uberon UBERON:8400021 liver serosa Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the 'bare area of the liver') and a smaller area where the liver and gallbladder are in direct contact. https://medical-dictionary.thefreedictionary.com/serosa+of+liver https://orcid.org/0000-0002-0449-2730 serosa of liver FMA:15811 tunica serosa hepatis https://medical-dictionary.thefreedictionary.com/serosa+of+liver Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson. hepatic subserosa subserosal tissue of liver subserous layer of liver tela subserosa (hepar) tela subserosa hepatis uberon UBERON:8400023 liver subserosa Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson. FMA:15812 https://medical-dictionary.thefreedictionary.com/subserosa+of+liver https://orcid.org/0000-0002-0449-2730 tela subserosa (hepar) FMA:15821 tela subserosa hepatis https://medical-dictionary.thefreedictionary.com/subserosa+of+liver Venule of villus of small intestine. venule of small intestine uberon UBERON:8410001 small intestine venule Venule of villus of small intestine. https://orcid.org/0000-0003-4183-8865 Arteriole of villus of small intestine. arteriole of small intestine arteriole of villus of small intestine small intestine villus arteriole uberon UBERON:8410004 small intestine arteriole Arteriole of villus of small intestine. http://orcid.org/0000-0003-4183-8865 A venule that is located in the anorectum. anorectum venule uberon UBERON:8410008 venule of anorectum A venule that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 An arteriole that is located in the anorectum. anorectum arteriole uberon UBERON:8410009 arteriole of anorectum An arteriole that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 An arteriole located in the colon. uberon UBERON:8410015 arteriole of colon An arteriole located in the colon. http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865 An anatomical junction between two parts of the intestine. junction of intestine uberon UBERON:8410024 intestinal junction An anatomical junction between two parts of the intestine. https://orcid.org/0000-0002-7073-9172 A venule located in the colon. uberon UBERON:8410048 venule of colon A venule located in the colon. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum. anorectal anorectal canal uberon UBERON:8410050 anorectum A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. DOI:10.1007/978-3-319-26938-2_8 DOI:10.1148/rg.2015150037 PMID:29742860 http://orcid.org/0000-0002-6826-8770 http://orcid.org/0000-0003-3440-1876 A capillary that is part of the anorectum. blood vessel capillary of anorectum uberon UBERON:8410056 capillary of anorectum A capillary that is part of the anorectum. http://orcid.org/0000-0003-3440-1876 A capillary that is part of the colon. blood vessel capillary of colon uberon UBERON:8410057 capillary of colon A capillary that is part of the colon. http://orcid.org/0000-0003-3440-1876 A capillary that is part of a small intestine. 2021-12-21T15:14:31Z blood vessel capillary of small intestine small intestine capillary uberon UBERON:8410068 capillary of small intestine A capillary that is part of a small intestine. http://orcid.org/0000-0003-3440-1876 A submucosal gland found in a respiratory tract. 2022-03-24T14:21:59Z EFO:0010666 respiratory tract submucosal gland submucosal gland of respiratory tract uberon UBERON:8410077 airway submucosal gland A submucosal gland found in a respiratory tract. http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865 Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins. microvascular http://orcid.org/0000-0002-2825-0621 microvasculature microvessel uberon UBERON:8410081 blood microvessel https://github.com/obophenotype/uberon/issues/2186 Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins. Wikipedia:Microcirculation http://orcid.org/0000-0002-7073-9172 Collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain the neurotransmitter norepinephrine (noradrenalin). uberon UBERON:8440015 noradrenergic cell groups Collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain the neurotransmitter norepinephrine (noradrenalin). WikipediaVersioned:Noradrenergic_cell_groups&oldid=965992184 An anatomical system that eliminates waste products that arise as a result of metabolic activity. http://orcid.org/0000-0002-6095-8718 2022-05-25T18:21:29Z BTO:0006338 uberon UBERON:8450002 excretory system An anatomical system that eliminates waste products that arise as a result of metabolic activity. GO:0007588 BTO:0006338 https://github.com/biopragmatics/biomappings A capillary that is part of the brain. 2022-06-24T09:28:31Z uberon UBERON:8480001 capillary of brain A capillary that is part of the brain. https://orcid.org/0000-0002-0819-0473 A portion of smooth muscle tissue that is part of the thoracic aorta. 2022-06-24T09:30:54Z uberon UBERON:8480002 thoracic aorta smooth muscle tissue A portion of smooth muscle tissue that is part of the thoracic aorta. https://orcid.org/0000-0002-0819-0473 A zone of skin that is above the clavicle zone in the pectoral girdle region. 2022-08-29T14:17:12Z uberon UBERON:8480025 skin of clavicle region A zone of skin that is above the clavicle zone in the pectoral girdle region. https://orcid.org/0000-0002-0819-0473 A zone of skin that is above the iliac crest in the pelvic girdle bone/zone. 2022-08-29T14:19:16Z skin of posterior iliac crest region uberon UBERON:8480026 skin of iliac crest region A zone of skin that is above the iliac crest in the pelvic girdle bone/zone. https://orcid.org/0000-0002-0819-0473 A zone of skin that is part of the external genitalia. 2022-08-30T06:55:06Z uberon UBERON:8480029 skin of external genitalia A zone of skin that is part of the external genitalia. https://orcid.org/0000-0002-0819-0473 A zone of skin part of some gonad. 2023-08-29T10:24:24Z uberon UBERON:8480074 skin of gonad A zone of skin part of some gonad. https://orcid.org/0000-0002-0819-0473 A muscle tissue that is associated with soft internal organs (viscera). 2023-02-16T10:17:46Z visceral muscle uberon UBERON:8600004 It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. visceral muscle tissue A muscle tissue that is associated with soft internal organs (viscera). BTO:0002780 CLAO:0001295 visceral muscle BTO:0002780 It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. FBbt:00005070 https://en.wikipedia.org/wiki/Smooth_muscle PMID:8720463 A striated muscle tissue that is associated with soft internal organs (viscera). 2023-02-16T10:34:43Z striated visceral muscle tissue uberon UBERON:8600006 visceral striated muscle tissue A striated muscle tissue that is associated with soft internal organs (viscera). PMID:8720463 https://pressbooks.pub/rbtallitsch/chapter/chapter-6-muscle-tissue/ A spherical or tubular structure in a submucosal gland that produces and secretes mucus and other substances into the ducts leading to the surface epithelium. 2023-05-02T08:57:27Z uberon UBERON:8600012 submucosal gland acinus A spherical or tubular structure in a submucosal gland that produces and secretes mucus and other substances into the ducts leading to the surface epithelium. PMID:17394068 PMID:17707699 PMID:25648514 PMID:30864819 A discrete anatomical unit of the lung that is composed of a segmental bronchus and the lung tissue supplied by that bronchus. A bronchopulmonary segment exhibits a pyramidal shape, with its apex pointing towards the center of the lung and its base toward the pleural surface. 2023-07-20T12:43:29Z lung segment uberon UBERON:8600017 A bronchopulmonary segment is surrounded by connective tissue septa, which are continuous with the pleural surface and prevent air collateralization between segments somewhat. In humans, the right lung has ten bronchopulmonary segments and eight or nine bronchopulmonary segments in the left lung. bronchopulmonary segment A discrete anatomical unit of the lung that is composed of a segmental bronchus and the lung tissue supplied by that bronchus. A bronchopulmonary segment exhibits a pyramidal shape, with its apex pointing towards the center of the lung and its base toward the pleural surface. FMA:7312 PMID:18271171 PMID:33620799 doi:10.1016/j.mpaic.2008.09.022 lung segment PMID:33620799 A bronchopulmonary segment is surrounded by connective tissue septa, which are continuous with the pleural surface and prevent air collateralization between segments somewhat. In humans, the right lung has ten bronchopulmonary segments and eight or nine bronchopulmonary segments in the left lung. PMID:18271171 doi:10.1016/j.mpaic.2008.09.022 A venule that is part of a lung and drains oxygenated blood from pulmonary capillaries. A pulmonary venule merges into a pulmonary vein branch that runs in the pulmonary interlobular septa. 2023-10-24T11:26:27Z uberon UBERON:8600024 pulmonary venule A venule that is part of a lung and drains oxygenated blood from pulmonary capillaries. A pulmonary venule merges into a pulmonary vein branch that runs in the pulmonary interlobular septa. PMID:22283705 PMID:30247823 A unit of measurement is a standardized quantity of a physical quality. James Malone Jie Zheng Tomasz Adamusiak http://www.ebi.ac.uk/efo/EFO_0001446 MO:3 NCIt:C44278 NCIt:C68553 NIFSTD:birnlex_2015 SNOMEDCT:258666001 "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] unit length unit A unit which is a standard measure of the distance between two points. "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time derived unit "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] time unit "A unit which is a standard measure of the flow of electric charge." [Wikipedia:Wikipedia] electric current unit temperature unit temperature derived unit "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] temperature unit substance unit "A unit which is a standardised quantity of an element or compound with uniform composition." [Wikipedia:Wikipedia] substance unit "A unit which is a standard measure of the wavelength-weighted power emitted by a light source in a particular direction." [Wikipedia:Wikipedia] luminous intensity unit A "An electric current unit which is equal to the constant current which, if maintained in two straight parallel conductors of infinite length, of negligible circular cross-section, and placed 1 m apart in vacuum, would produce between these conductors a force equal to 2 x 10^[-7] newton per meter of length." [BIPM:BIPM, NIST:NIST] ampere K "A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST] kelvin mol "A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12." [BIPM:BIPM, NIST:NIST] mole cd "A luminous intensity unit which equal to the luminous intensity, in a given direction, of a source that emits monochromatic radiation of frequency 540 x 1012 hertz and that has a radiant intensity in that direction of 1/683 watt per steradian." [BIPM:BIPM, NIST:NIST] candela picometre pm "A length unit which is equal to 10^[-12] m." [NIST:NIST] picometer fg "A mass unit which is equal to 10^[-15] g." [NIST:NIST] femtogram ms "A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST] millisecond us "A time unit which is equal to one millionth of a second or 10^[-6] s." [NIST:NIST] microsecond ps "A time unit which is equal to 10^[-12] s." [NIST:NIST] picosecond mA "An electric current unit current which is equal to one thousandth of an ampere or 10^[-3] A." [UOC:GVG] milliampere uA "An electric current unit current which is equal to one millionth of an ampere or 10^[-6] A." [UOC:GVG] microampere mmol "A substance unit equal to a thousandth of a mol or 10^[-3] mol." [NIST:NIST] millimole fmol "A substance unit equal to 10^[-15] mol." [NIST:NIST] femtomole amol "A substance unit equal to 10^[-18] mol." [NIST:NIST] attomole "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST] base unit A derived unit is a unit which is derived from base units. A unit which is derived from base units. James Malone http://www.ebi.ac.uk/efo/EFO_0001692 UO_0000046 derived unit prefix "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG] area unit "A unit which is a standard measure of the rate of change of velocity in either speed or direction." [Wikipedia:Wikipedia] acceleration unit "A unit which is a standard measure of the rate of angular movement about an axis; the angle rotated in a given time." [Wikipedia:Wikipedia] angular velocity unit "A unit which is a standard measure of the rate of change of angular velocity." [Wikipedia:Wikipedia] angular acceleration unit concentration unit "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG] concentration unit mass per unit volume "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG] mass density unit "A unit which is a standard measure of the luminous intensity impinging on a given area." [Wikipedia:Wikipedia] luminance unit mass per unit area unit "A density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia] area density unit "A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia] molar mass unit "A unit which is a standard measure of the volume of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia] molar volume unit "A unit which is a standard measure of the quantity of motion measured by the product of mass and velocity." [Wikipedia:Wikipedia] momentum unit "A unit which is a standard measure of the number of rotations in a given time." [NIST:NIST] rotational frequency unit "A unit which is a standard measure of the volume of a given mass of substance (the reciprocal of density)." [Wikipedia:Wikipedia] specific volume unit "A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity." [Wikipedia:Wikipedia] speed/velocity unit "A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution." [UOC:GVG] unit of molarity "A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG] unit of molality m "A unit of concentration which expresses a concentration of a solution of 1 mole per kilogram of solvent (mol/kg)." [UOC:GVG] molal mm "A molality unit which is equal to one thousandth of a molal or 10^[-3] m." [UOC:GVG] millimolal um "A molality unit which is equal to one millionth of a molal or 10^[-6] m." [UOC:GVG] micromolal nm "A molality unit which is equal to one thousandth of one millionth of a molal or 10^[-9] m." [UOC:GVG] nanomolal pm "A molality unit which is equal to 10^[-12] m." [UOC:GVG] picomolal fM "A unit of molarity which is equal to 10^[-15] M." [UOC:GVG] femtomolar "A unit of concentration which highlights the chemical nature of salts." [Wikipedia:Wikipedia] unit of normality N "A unit of concentration which is one gram equivalent of a solute per liter of solution. A gram equivalent weight or equivalent is a measure of the reactive capacity of a given molecule." [Wikipedia:Wikipedia] normal (x) chi "A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia] mole fraction m/s^[2] metre per second per second "An acceleration unit which is equal to the acceleration an object changing its velocity by 1meter/s over a time period that equals one second." [NIST:NIST] meter per second per second alpha rad/s^[2] "An angular unit acceleration which is equal to the angular acceleration of an object changing its angular velocity by 1rad/s over a time period that equals one second." [NIST:NIST] radian per second per second rad/s "An angular unit velocity which is equal to about 9.54930 rpm (revolutions per minute)." [NIST:NIST] radian per second m^[2] square metre "An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST] square meter cm^[2] square centimetre "An area unit which is equal to one ten thousandth of a square meter or 10^[-4] m^[2]." [NIST:NIST] square centimeter mm^[2] square millimetre "An area unit which is equal to one millionth of a square meter or 10^[-6] m^[2]." [NIST:NIST] square millimeter kg/m^[3] kilogram per cubic metre "A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters." [UOC:GVG] kilogram per cubic meter g/cm^[3] gram per cubic centimetre "A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters." [UOC:GVG] gram per cubic centimeter candela per square metre cd/m^[2] "A luminance unit which is equal to a luminous intensity of one candela radiating from a surface whose area is one square meter." [NIST:NIST] candela per square meter kg/m^[2] kilogram per square metre "An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared." [NIST:NIST] kilogram per square meter kg/mol "A molar mass unit which is equal to one kilogram of mass of one mole of chemical element or chemical compound." [NIST:NIST] kilogram per mole g/mol "A molar mass unit which is equal to one gram of mass of one mole of chemical element or chemical compound." [NIST:NIST] gram per mole cubic metre per mole m^[3]/mol "A molar volume unit which is equal to 1 cubic meter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST] cubic meter per mole cm^[3]/mol cubic centimetre per mole "A molar volume unit which is equal to 1 cubic centimeter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST] cubic centimeter per mole kg.m/s kilogram metre per second "A momentum unit which is equal to the momentum of a one kilogram mass object with a speed of one meter per second." [NIST:NIST] kilogram meter per second 1/s one turn per second "A rotational frequency unit which is equal to the number complete turn in a period of time that equals to 1 second." [NIST:NIST] turns per second cubic metre per kilogram m^[3]/kg "A specific volume unit which is equal to one cubic meter volume occupied by one kilogram of a particular substance." [NIST:NIST] cubic meter per kilogram m/s metre per second "A speed/velocity unit which is equal to the speed of an object traveling 1 meter distance in one second." [NIST:NIST] meter per second volume unit "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] volume unit cubic metre m^[3] "A volume unit which is equal to the volume of a cube with edges one meter in length. One cubic meter equals to 1000 liters." [NIST:NIST] cubic meter femtolitre fl "A volume unit which is equal to 10^[-15] L." [NIST:NIST] femtoliter frequency unit "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST] frequency unit "A unit which is a standard measure of the force is applied when a mass is accelerated." [NIST:NIST] force unit N "A force unit which is equal to the force required to cause an acceleration of 1m/s2 of a mass of 1 Kg in the direction of the force." [NIST:NIST] newton "A unit which is a standard measure of the force applied to a given area." [NIST:NIST] pressure unit Pa "A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST] pascal "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST] energy unit J "An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST] joule "A unit which is a standard measure power or the rate of doing work." [NIST:NIST] power unit W "A power unit which is equal to the power used when work is done at the rate of 1 joule per second." [NIST:NIST] watt "A unit which is a standard measure of the luminous flux incident on a unit area." [Wikipedia:Wikipedia] illuminance unit lx "An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 m^[2]." [NIST:NIST] lux "A unit which is a standard measure of the flow of radiant energy." [Wikipedia:Wikipedia] luminous flux unit lm "A luminous flux unit which is equal to the luminous flux emitted into 1 steradian by a point source of 1 candela." [NIST:NIST] lumen "A unit which is a standard measure of the amount of the action of a catalyst." [NIST:NIST] catalytic activity unit kat "A catalytic unit activity which is equal to the activity of a catalyst in moles per second, such as the amount of an enzyme needed to transform one mole of substrate per second." [NIST:NIST] katal "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] angle unit "A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia] plane angle unit rad "A plane angle unit which is equal to the angle subtended at the center of a circle by an arc equal in length to the radius of the circle, approximately 57 degrees 17 minutes and 44.6 seconds." [NIST:NIST] radian "A unit which is a standard measure of the angle formed by three or more planes intersecting at a common point." [Wikipedia:Wikipedia] solid angle unit sr "A solid angle unit which is equal to the solid angle subtended at the center of a sphere by an area on the surface of the sphere that is equal to the radius squared." [NIST:NIST] steradian A derived unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source. A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source. "A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source." [OCRBS:OCRBS] radiation unit "A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance." [DEFRA:DEFRA] activity (of a radionuclide) unit A derived unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue. A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue. "A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue." [DEFRA:DEFRA] absorbed dose unit "A unit which is a standard measure of the expression of dose in terms of its biological effect." [ORCBS:ORCBS] dose equivalent unit "A unit which is a standard measure of the quantity that expresses the ability of radiation to ionize air and thereby create electric charges which can be collected and measured." [ORCBS:ORCBS] exposure unit Bq "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second (dps)." [NIST:NIST] becquerel Ci "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps)." [ORCBS:ORCBS] curie Gy "An absorbed dose unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST] gray "An absorbed dose unit which is equal to 0.01 gray (Gy)." [Wikipedia:Wikipedia] rad R "An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs." [Wikipedia:Wikipedia] roentgen Sv "A dose equivalent unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST] sievert mSv "A dose equivalent unit which is equal to one thousandth of a sievert or 10^[-3] Sv." [NIST:NIST] millisievert uSv "A dose equivalent unit which is equal to one millionth of a sievert or 10^[-6] Sv." [NIST:NIST] microsievert rem "A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem." [Wikipedia:Wikipedia] Roentgen equivalent man uGy "An absorbed dose unit which is equal to one millionth of a gray or 10^[-6] Gy." [NIST:NIST] microgray mGy "An absorbed dose unit which is equal to one thousandth of a gray or 10^[-3] Gy." [NIST:NIST] milligray nGy "An absorbed dose unit which is equal to one thousandth of a millionth of a gray or 10^[-9] Gy." [NIST:NIST] nanogray nSv "A dose equivalent unit which is equal to one thousandth of a millionth of a sievert or 10^[-9] Sv." [NIST:NIST] nanosievert mCi "An activity (of a radionuclide) unit which is equal to one thousandth of a curie or 10^[-3] Ci." [ORCBS:ORCBS] millicurie uCi "An activity (of a radionuclide) unit which is equal to one millionth of a curie or 10^[-6] Ci." [ORCBS:ORCBS] microcurie dpm "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute." [ORCBS:ORCBS] disintegrations per minute cpm "An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute." [ORCBS:ORCBS] counts per minute ns "A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST] nanosecond "A time unit which is equal to 100 years." [Wikipedia:Wikipedia] century "A time unit which represents the period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration." [MGED:MGED] half life ft-c "An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 foot^[2]. One footcandle is equal to 10.76 lux." [Wikipedia:Wikipedia] foot candle "A unit which is a standard measure of the power of electromagnetic radiation at a surface, per unit area." [Wikipedia:Wikipedia] irradiance unit W/m^[2] watt per square metre "An irradiance unit which is equal to 1 watt of radiant power incident per one square meter surface area." [NIST:NIST] watt per square meter einstein per square metre per second einstein/sm^[2] mole per second and square meter mol/sm^2 "An irradiance unit which is equal to one einstein per square meter per second. One einstein is one mole of photons, regardless of their frequency. Therefore, the number of photons in an einstein is Avogadro's number." [Wikipedia:Wikipedia] einstein per square meter per second "A unit which is a standard measure of the intensity of light." [NIST:NIST] light unit W/sr m^[2] watt per steradian per square metre "A radiance unit which is equal to one watt of radiant power incident per steradian solid angle per one square meter projected area of the source, as viewed from the given direction." [NIST:NIST] watt per steradian per square meter "A unit which is a standard measure of the intensity of electromagnetic radiation." [Wikipedia:Wikipedia] radiant intensity unit Jon Ison http://www.ebi.ac.uk/efo/EFO_0004377 microeinstein per second and square meter microeinstein per square metre per second micromole per second and square meter mmol/sm^2 micromole per square meter per second umicroeinstein/sm^[2] "An irradiance unit which is equal to one microeinstein per square meter per second or 10^[-6] microeinstein/sm^[2]." [Wikipedia:Wikipedia] microeinstein per square meter per second "A unit which is a standard measure of the power of electromagnetic radiation through space or through a material medium in the form of electromagnetic waves." [Wikipedia:Wikipedia] radiance unit W/sr "A radiant intensity unit which is equal to one kilogram meter squared per second cubed per steradian." [NIST:NIST] watt per steradian "A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia] parts per notation unit 10^[-2] pph "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 100 regardless of the units of measure as long as they are the same." [UOC:GVG] parts per hundred 10^[-3] ppth "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same." [UOC:GVG] parts per thousand 10^[-6] ppm "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG] parts per million 10^[-9] ppb "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure as long as they are the same or 1 part in 10^[9]." [UOC:GVG] parts per billion 10^[-12] ppt "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[12]." [UOC:GVG] parts per trillion 10^[-15] ppq "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[15]." [UOC:GVG] parts per quadrillion g/ml gram per millilitre "A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter." [UOC:GVG] gram per milliliter kg/L kilogram per litre "A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters." [UOC:GVG] kilogram per liter "A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution." [Webmd:Webmd] unit per volume unit U/ml unit per millilitre "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one milliliter." [Webmd:Webmd] unit per milliliter U/l unit per litre "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter." [UOC:GVG] unit per liter "A concentration unit which is a standard measure of the mass of a substance in a given volume (density)." [Wikipedia:Wikipedia] mass per unit volume U "A catalytic unit activity which is equal to the amount of the enzyme that catalyzes the conversion of 1 micro mole of substrate per minute." [Wikipedia:Wikipedia] enzyme unit "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] density unit "A density unit which is a standard measure of the mass exerting an influence on a one-dimensional object." [Wikipedia:Wikipedia] linear density unit kg/m kilogram per metre "An area density unit which is equal to the mass of an object in kilograms divided by one meter." [NIST:NIST] kilogram per meter "A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia] degree "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] dimensionless unit % "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia] percent "A dimensionless unit which denoted an irrational real number, approximately equal to 3.14159 which is the ratio of a circle's circumference to its diameter in Euclidean geometry." [Wikipedia:Wikipedia] pi count "A dimensionless unit which denotes a simple count of things." [MGED:MGED] count unit "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia] ratio unit "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia] fraction "A dimensionless count unit which denotes the number of molecules." [MGED:MGED] molecule count "A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED] purity percentage "A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED] confluence percentage l/kg litre per kilogram "A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST] liter per kilogram millilitre per kilogram ml/kg "A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST] milliliter per kilogram microlitre per kilogram ul/kg "A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST] microliter per kilogram "A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline] cell concentration unit cells per millilitre cells per ml "A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline] cells per milliliter "A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG] catalytic (activity) concentration unit kat/m^[3] katal per cubic metre "A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST] katal per cubic meter kat/l katal per litre "A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter." [NIST:NIST] katal per liter "A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST] volume per unit volume millilitre per cubic metre ml/m^[3] "A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST] milliliter per cubic meter decilitre dl "A volume unit which is equal to one tenth of a liter or 10^[-1] L." [NIST:NIST] deciliter cfu "A dimensionless count unit which a measure of viable bacterial numbers." [Wikipedia:Wikipedia] colony forming unit pfu "A dimensionless count unit which a measure of plaque forming units in a given volume." [Wikipedia:Wikipedia] plaque forming unit cfu/ml colony forming unit per millilitre "A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia] colony forming unit per milliliter "A concentration unit which a measure of plaque forming units in a given volume." [UOC:GVG] plaque forming unit per volume pfu/ml plaque forming unit per millilitre "A concentration unit which a measure of plaque forming units in one milliliter." [UOC:GVG] plaque forming unit per milliliter dps "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second." [ORCBS:ORCBS] disintegrations per second "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] electric potential difference unit V "An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia] volt "A unit which is a standard measure of the quantity of unbalanced electricity in a body (either positive or negative) and construed as an excess or deficiency of electrons." [WordNet:WordNet] electric charge C "An electrical charge unit which is equal to the amount of charge transferred by a current of 1 ampere in 1 second." [WordNet:WordNet] coulomb Da amu u unified atomic mass unit "An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia] dalton kDa "A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia] kilodalton Wh "An energy unit which is equal to the amount of electrical energy equivalent to a one-watt load drawing power for one hour." [Wikipedia:Wikipedia] watt-hour "An energy unit which is equal to 1,000 watt-hours." [Wikipedia:Wikipedia] kilowatt-hour "A unit which is a standard measure of quantity of magnetism, taking account of the strength and the extent of a magnetic field." [Wikipedia:Wikipedia] magnetic flux unit V s Wb volt-second "A magnetic flux unit which is equal to the amount of flux that when linked with a single turn of wire for an interval of one second will induce an electromotive force of one volt." [ScienceLobby:ScienceLobby] weber B "A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet] magnetic flux density unit T Wb/m2 "A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet] tesla Vh "A magnetic flux unit which is equal to 3600 Wb." [UOC:GVG] volt-hour kVh "A magnetic flux unit which is equal to one thousand volt-hours." [UOC:GVG] kilovolt-hour "A unit which is a standard measure of the amount of information." [Wikipedia:Wikipedia] information unit "An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1)." [Wikipedia:Wikipedia] bit B "An information unit which is equal to 8 bits." [Wikipedia:Wikipedia] byte kB "An information unit which is equal to 1000 bytes." [Wikipedia:Wikipedia] kilobyte MB "An information unit which is equal to 1000 kB." [Wikipedia:Wikipedia] megabyte "An information unit which is a standard measure of the detail an image holds." [Wikipedia:Wikipedia] image resolution unit "An image resolution unit which is a standard measure of the amount of spatial detail in an image." [Wikipedia:Wikipedia] chroma sampling unit "An image resolution unit which is a standard measure of the amount of contrast available in a pixel." [Wikipedia:Wikipedia] dynamic range unit "An image resolution unit which is a standard measure of the way luminance and chrominance may be sampled at different levels." [Wikipedia:Wikipedia] spatial resolution unit dpi "A spatial resolution unit which is a standard measure of the printing resolution, in particular the number of individual dots of ink a printer or toner can produce within a linear one-inch space." [Wikipedia:Wikipedia] dots per inch micrometer pixel "A spatial resolution unit which is equal to a pixel size of one micrometer." [Wikipedia:Wikipedia] micron pixel pixel density ppi "A spatial resolution unit which is a standard measure of the resolution of a computer display, related to the size of the display in inches and the total number of pixels in the horizontal and vertical directions." [Wikipedia:Wikipedia] pixels per inch pixels per millimetre "A spatial resolution unit which is a standard measure of the number of pixels in one millimeter length or width of a digital image divided by the physical length or width of a printed image." [Wikipedia:Wikipedia] pixels per millimeter basepair bp "A count unit which contains one nucleotide." [UO:GVG] base pair KiB "An information unit which is equal to 1024 B." [NIST:NIST] kibibyte MiB "An information unit which is equal to 1024 KiB." [NIST:NIST] mebibyte mV "An electric potential difference unit which is equal to one thousandth of a volt or 10^[-3] V." [UOC:GVG] millivolt kV "An electric potential difference unit which is equal to one thousand volts or 10^[3] V." [UOC:GVG] kilovolt uV "An electric potential difference unit which is equal to one millionth of a volt or 10^[-6] V." [UOC:GVG] microvolt nV "An electric potential difference unit which is equal to one billionth of a volt or 10^[-12] V." [UOC:GVG] nanovolt pV "An electric potential difference unit which is equal to one trillionth of a volt or 10^[-12] V." [UOC:GVG] picovolt MV "An electric potential difference unit which is equal to one million volts or 10^[6] V." [UOC:GVG] megavolt "A unit which is a standard measure of the ability of a liguid to attraction of molecules at its surface as a result of unbalanced molecular cohesive forces." [NIST:NIST] surface tension unit N/m newton per metre "A surface tension unit which is equal to one newton per meter." [NIST:NIST] newton per meter dyn/cm "A surface tension unit which is equal to one dyne per centimeter." [Wikipedia:Wikipedia] dyne per cm "A unit which is a standard measure of the internal resistance of fluids to flow." [UOC:GVG] viscosity unit Pa s "A viscosity unit which is equal to one pascale per second." [NIST:NIST] pascal second P dyne s/cm^2 "A viscosity unit which is equal to one dyne second per square centimeter." [Wikipedia:Wikipedia] poise dB "A ratio unit which is an indicator of sound power per unit area." [techtarget:techtarget] decibel "A unit which is a standard measure of the estimate of the stochastic effect that a non-uniform radiation dose has on a human." [Wikipedia:Wikipedia] effective dose unit "A unit which represents a standard measurement of the transmission of an entity through a medium." [UOC:GVG] conduction unit "A unit which represents a standard measurement of the movement of electrically charged particles through a transmission medium (electrical conductor)." [UOC:GVG] electrical conduction unit "A unit which represents a standard measurement of the spontaneous transfer of thermal energy through matter, from a region of higher temperature to a region of lower temperature." [Wikipedia:Wikipedia] heat conduction unit A V^-1 mho S "An electrical conduction unit which is equal to A/V." [NIST:NIST] siemens W/m K watt per metre kelvin "An heat conduction unit which is equal to one watt divided by meter kelvin." [NIST:NIST] watt per meter kelvin eV electron volt "A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia] electronvolt E-field strength "The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] electric field strength unit V/m volt per metre "The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] volt per meter AU "A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\://en.wikipedia.org/wiki/Absorbance] absorbance unit volumetric flow rate unit "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia] volumetric flow rate unit millimeters of mercury mmHg "A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth." [url:en.wiktionary.org/wiki/mmHg] millimetres of mercury mg/L milligram per litre "A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG] milligram per liter mcg/mL microgram per millilitre ug/ml µg/mL "A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG] microgram per milliliter nanogram per millilitre ng/ml "A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters." [UOC:GVG] nanogram per milliliter mU/ml milliunits per millilitre "A unit per milliliter unit which is equal to one thousandth of a unit of an agreed arbitrary amount per one milliliter." [UOC:GVG] milliunits per milliliter rate unit "A unit which represents a standard measurement occurrence of a process per unit time." [UOC:GVG] rate unit "An area density unit which is equal to the mass of an object in kilograms divided by the surface area in hectares." [UO:GVG] kilogram per hectare 10^[9] G "A prefix in the metric system denoting a factor of ten to the power of 9." [UO:GVG] giga 10^[6] M "A prefix in the metric system denoting a factor of million." [UO:GVG] mega 10^[3] k "A prefix in the metric system denoting a factor of one thousand." [UO:GVG] kilo 10^[-1] d "A prefix in the metric system denoting a factor of one tenth." [UO:GVG] deci 10^[-3] m "A prefix in the metric system denoting a factor of one thousand." [UO:GVG] milli 10^[-2] c "A prefix in the metric system denoting a factor of one hundred." [UO:GVG] centi 10^[-6] "A prefix in the metric system denoting a factor of 10 to the power of -6." [UO:GVG] micro 10^[-9] n "A prefix in the metric system denoting a factor of 10 to the power of -9." [UO:GVG] nano 10^[-12] n "A prefix in the metric system denoting a factor of 10 to the power of -12." [GVG:UO] pico 10^[-15] f "A prefix in the metric system denoting a factor of 10 to the power of -15." [UO:GVG] femto a 10^[-18] "A prefix in the metric system denoting a factor of 10 to the power of -18." [UO:GVG] atto "A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject." [UO:PC] dose unit "A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC] milligram per kilogram "A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject." [UO:PC] milligram per square meter "A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered over time to a recipient subject, expressed in terms of the size of the subject." [UO:PC] dosage unit "A derived unit which is a measure of relative light intensity, as typically measured by a luminometer, spectrophotometer, or fluorimeter in biological research applications." [UO:PC] relative light unit "A relative light unit which is a measure of relative luminescence intensity." [UO:PC] relative luminescence unit "A relative light unit which is a measure of relative fluorescence intensity." [UO:PC] relative fluorescence unit mH megahertz "A frequency unit which is equal to one million hertz or 10^[6] V." [UOC:GVG] megaHertz cM "A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html] centiMorgan cR "A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html] centiRay Mb megabasepair "A unit equal to one million base pairs" [UOC:GVG] mega base pair Gb gigabasepair "A unit equal to one billion base pairs." [UOC:GVG] giga base pair square micrometre "An area unit which is equal to an area enclosed by a square with sides each 1 micrometer long." [NIST:NIST] square micrometer mS "An electrical conduction unit which is equal to one thousandth of a siemen or 10^[-3] siemens." [NIST:NIST] millisiemens "A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST] micromole per litre "A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR] micromole per kilogram mm/day "A speed/velocity unit which is equal to the speed of an object traveling 1 millimeter distance in one day." [UOB:LKSR] millimeters per day kilometre per hour km/h "A speed/velocity unit which is equal to the speed of an object traveling 1 kilometer distance in one hour." [NIST:NIST] kilometer per hour mDa milli unified atomic mass unit millidalton mmu "A mass unit which is equal to 1/12 the mass of 12C" [Wikipedia:Wikipedia] milli HA "An area unit which is equal to an area of 10,000 square meters. Equivalent to 2.471 acres." [Wikipedia:Wikipedia] hectare in "A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia] inch mil th "A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia] thou ft "A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia] foot yd "A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia] yard ch "A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia] chain fur "A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia] furlong mi "A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia] mile lea "A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia] league "A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia] maritime length unit ftm "A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia] fathom "A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia] cable "A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia] nautical mile "An area unit which is equal to an area of 25.292,852,64 square meters, or 1 square rod." [Wikipedia:Wikipedia] perch "An area unit which is equivalent to 1 furlong x 1 rod. This is equal to an area of 1,011.714,1056 square meters, or 40 square rods." [Wikipedia:Wikipedia] rood "An area unit which is equivalent to 1 furlong x 1 chain. This is equal to an area of 4,046.856,4224 square meters, or 43,500 square feet." [Wikipedia:Wikipedia] acre fl oz "An imperial volume unit which is equivalent to 28.413,0625 millilitres." [Wikipedia:Wikipedia] fluid ounce gi "An imperial volume unit which is equivalent to 142.065,3125 millilitres." [Wikipedia:Wikipedia] gill pt "An imperial volume unit which is equivalent to 568.261,25 millilitres." [Wikipedia:Wikipedia] pint qt "An imperial volume unit which is equivalent to 1,136.5225 millilitres, or two pints." [Wikipedia:Wikipedia] quart gal "An imperial volume unit which is equivalent to 4,546.09 millilitres, or 8 pints." [Wikipedia:Wikipedia] gallon gr "An imperial mass unit which is equivalent to 64.798,91 milligrams." [Wikipedia:Wikipedia] grain dr "An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound." [Wikipedia:Wikipedia] drachm oz "An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound." [Wikipedia:Wikipedia] ounce lb "An imperial mass unit which is equivalent to 453.592,37 grams." [Wikipedia:Wikipedia] pound st "An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds." [Wikipedia:Wikipedia] stone qr qtr "An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds." [Wikipedia:Wikipedia] quarter cwt "An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone." [Wikipedia:Wikipedia] hundredweight t "An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds." [Wikipedia:Wikipedia] ton "An imperial gravitational unit which is equivalent to a mass that accelerates by 1ft/s² when a force of one pound (lbf) is exerted on it." [Wikipedia:Wikipedia] slug metric teaspoon tsp "A metric teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 5mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Teaspoon] teaspoon "DEPRECATED: Duplicate of http://purl.obolibrary.org/obo/UO_0000039. A substance unit which is equal to one millionth of a mole." [UOB:LTS] micromole g/m^[2] gram per square metre "An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared." [NIST:NIST] gram per square meter nanogram per microlitre ng/ul "A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters." [UOB:LTS] nanogram per microliter big calorie cal calorie food calorie kcal kilocalorie "A unit of energy widely used in nutrition, equivalent to the amount of heat needed to cause one kilogram of water to rise in temperature by one degree Celsius." [Wikipedia:Wikipedia] large calorie micrograms per bottle "A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS] micrograms per wheaton bottle pA "An electric current unit current which is equal to one trillionth of an ampere or 10^[-12] A." [UOB:LTS] picoampere cGy "An absorbed dose unit which is equal to 0.01 gray (Gy)" [NIST:NIST] centigray GeV "A unit of energy that is equal to one thousand million electronvolts." [] gigaelectronvolt GeV/nucleon "Derived unit which is equal to the total kinetic energy of an atomic nucleus in GeV divided by the number of nucleons in the nucleus" [] gigaelectronvolt per nucleon MeV/nucleon "Derived unit which is equal to the total kinetic energy of an atomic nucleus in MeV divided by the number of nucleons in the nucleus" [] megaelectronvolt per nucleon keV/micron "A derived unit equal to the energy deposited by ionizing radiation per micron of path length in matter" [] kiloelectronvolt per micron Gy/min "A derived absorbed dose unit which is equal to one gray absorbed per minute." [NIST:NIST] gray per minute cGy/min "A derived absorbed dose unit which is equal to one centigray absorbed per minute." [NIST:NIST] centigray per minute mGy/day "A derived absorbed dose unit which is equal to one milligray absorbed per minute." [NIST:NIST] milligray per minute mGy/min "A derived absorbed dose unit which is equal to one milligray absorbed per day." [NIST:NIST] milligray per day mGy/h "A derived absorbed dose unit which is equal to one milligray absorbed per hour." [NIST:NIST] milligray per hour mGy/s "A derived absorbed dose unit which is equal to one milligray absorbed per second." [NIST:NIST] milligray per second kilometre km "A length unit which is equal to one thousand meters." [UOB:LKSR] kilometer mg/dl milligram per decilitre "A mass unit density which is equal to mass of an object in milligrams divided by the volume in deciliters." [UOB:LKSR] milligram per deciliter microgram per decilitre ug/dl "A mass unit density which is equal to mass of an object in micrograms divided by the volume in deciliters." [UOB:LKSR] microgram per deciliter meter based unit second based unit ampere based unit kelvin based unit mole based unit candela based unit angstrom based unit gram based unit degree Celsius based unit minute based unit hour based unit day based unit week based unit month based unit year based unit molar based unit molal based unit normal based unit mole fraction based unit meter per second per second based unit radian per second per second based unit radian per second based unit square meter based unit square centimeter based unit square millimeter based unit gram per cubic centimeter based unit candela per square meter based unit gram per mole based unit cubic meter per mole based unit cubic centimeter per mole based unit turns per second based unit cubic meter per kilogram based unit meter per second based unit cubic meter based unit cubic centimeter based unit liter based unit cubic decimeter based unit hertz based unit newton based unit pascal based unit joule based unit watt based unit lux based unit lumen based unit katal based unit radian based unit steradian based unit becquerel based unit curie based unit gray based unit rad based unit roentgen based unit sievert based unit Roentgen equivalent man based unit disintegrations per minute based unit counts per minute based unit century based unit half life based unit foot candle based unit watt per square meter based unit einstein per square meter per second based unit watt per steradian per square meter based unit watt per steradian based unit mass percentage based unit mass volume percentage based unit volume percentage based unit parts per hundred based unit parts per thousand based unit parts per million based unit parts per billion based unit parts per trillion based unit parts per quadrillion based unit gram per milliliter based unit gram per liter based unit unit per milliliter based unit unit per liter based unit mass per unit volume based unit enzyme unit based unit degree based unit pi based unit molecule count based unit purity percentage based unit confluence percentage based unit degree Fahrenheit based unit pH based unit liter per kilogram based unit cells per milliliter based unit katal per cubic meter based unit katal per liter based unit gram per deciliter based unit colony forming unit based unit plaque forming unit based unit colony forming unit per milliliter based unit plaque forming unit per milliliter based unit disintegrations per second based unit volt based unit coulomb based unit dalton based unit watt-hour based unit weber based unit tesla based unit volt-hour based unit bit based unit byte based unit chroma sampling unit based unit dynamic range unit based unit dots per inch based unit pixels per inch based unit pixels per millimeter based unit base pair based unit kibibyte based unit mebibyte based unit newton per meter based unit dyne per cm based unit pascal second based unit poise based unit effective dose unit based unit siemens based unit watt per meter kelvin based unit electronvolt based unit volt per meter based unit absorbance unit based unit count per nanomolar second based unit count per molar second based unit count per nanomolar based unit count per molar based unit dosage unit based unit relative light unit based unit relative luminescence unit based unit relative fluorescence unit based unit square micrometer based unit hectare based unit inch based unit thou based unit foot based unit yard based unit chain based unit furlong based unit mile based unit league based unit maritime length unit based unit fathom based unit cable based unit nautical mile based unit perch based unit rood based unit acre based unit fluid ounce based unit gill based unit pint based unit quart based unit gallon based unit grain based unit drachm based unit ounce based unit pound based unit stone based unit quarter based unit hundredweight based unit ton based unit slug based unit teaspoon based unit gram per square meter based unit large calorie based unit gray per minute based unit A developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g. blastula stage James Malone Jie Zheng Tomasz Adamusiak true MO:878 NCIt:C43531 development stage developmental_stage life cycle stage This branch will be replaced by, and if necessary merged with an Uberon import in future. developmental stage 129 is a mouse strain as described in Jackson Laboratory http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml James Malone Simpson E. M., Linder C. C., Sargent E. E., Davisson M. T., Mobraaten L. E., and Sharp J. J. (1997) Genetic variation among 129 substrains and its importance for targeted mutagenesis in mice. Nature Genet. 16, 19-27. http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml 129 mouse strain BALB/c is a mouse strain of albion mice. James Malone Sirarat Sarntivijai Tomasz Adamusiak http://en.wikipedia.org/wiki/BALB/c https://www.jax.org/strain/000651 NIFSTD:birnlex_206 BALB/cJ BALBc C Description from https://www.jax.org/strain/000651: BALB/c mice are particularly well known for the production of plasmacytomas following injection with mineral oil forming the basis for the production of monoclonal antibodies. Although not all BALB/c substrains have been examined for plasmacytoma induction, substrains derived from the Andervont (An) lineage (which includes BALB/cByJ) typically are susceptible, while those descended from BALB/cJ are resistant (see: Potter M, 1985). Mammary tumor incidence is normally low but infection with mammary tumor virus by fostering to MMTV+ C3H mice dramatically increases tumor number and age of onset. BALB/c mice develop other cancers later in life including reticular neoplasms, primary lung tumors, and renal tumors. Rare spontaneous myoepitheliomas arising from myoepithelial cells of various exocrine glands have been observed in both BALB/cJ and BALB/cByJ substrains. White et al. reported a variation in thioglycolate medium-induced peritoneal leukocyte recruitment in 4 analyzed strains. The response of total leukocyte recruitment, from greatest to least, was C57BL/6J>BALB/c>CD1>129X1/SvJ. Variations were also found in the timeline of response and cell types most impacted. BALB/c mice immunized with PLP180-199 develop an atypical form of experimental autoimmune encephalomyelitis (EAE) in which susceptibility is determined by location. In the spinal cord 60-70% mice develop pathological lesions and in the brain and cerebellum 100% of mice develop sever lesions. Dorso-ventral vaginal septa is observed in some BALB/cJ females, and may contribute to non-productive females in this strain. (Cunliffe-Beamer T, Lab Anim Sci, 1976) BALB/c BALB is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/001026.html James Malone http://jaxmice.jax.org/strain/001026.html BALB/cByJ A/J is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000646.html James Malone Tomasz Adamusiak http://jaxmice.jax.org/strain/000646.html NIFSTD:birnlex_577 A AJ A/J C3H/HeJ is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000659.html James Malone JAX:000659 C3 C3H C3H Heston C3H/HeJ CB6F1 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/100007.html James Malone JAX:100007 CB6F1 B6C3F1 is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/100010.html James Malone JAX:100010 B6C3F1 Helen Parkinson Mus musculus subspecies A designator of mouse strain information indicating the genetic homo or heterogenetity e.g. inbred strain Helen Parkinson Mus musculus strain type An inbred strain carrying one or more phenotypic mutations. For example, the mutant strain C3H/H3eSn-bc3J/J carries the bouncy 3 Jackson phenotypic mutation. http://www.findmice.org/glossary.jsp inbred Mus musculus strain Property of an organism which indicates that the organism's parents were genetically related (potentially for several generations). Inbreeding results in closer homozygosity. James Malone inbred Anatomical structure which has as its parts one or more ordered aggregates of nucleotide, amino acid fatty acid or sugar molecules bonded to one another. biological macromolecule The original group of Swiss mice that served as progenitors of this stock consisted of two male and seven female albino mice derived from a non-inbred stock in the laboratory of Dr. de Coulon, Centre Anticancereux Romand, Lausanne, Switzerland. http://www.criver.com/en-US/ProdServ/ByType/ResModOver/ResMod/Pages/CD-1Mouse.aspx CD-1 mus Crl:CD1(ICR) CD1 mus strain Inbred Strain TJL Mating System: Sibling x Sibling (Female x Male) Species: laboratory mouse H2 Haplotype: d Generation: F219p (14-DEC-06) Appearance: dilute brown Related Genotype: a/a Tyrp1b/Tyrp1b Myo5ad/Myo5ad Important Note This strain is homozygous for Cdh23ahl, the age related hearing loss 1 mutation, which on this background results in progressive hearing loss that is already severe by 3 months of age. Strain Description DBA/2J is a widely used inbred strain that is valuable in a wide number of research areas including cardiovascular biology, neurobiology, and sensorineural research. James Malone Beck, J.A., et al., Genealogies of mouse inbred strains (2000), Nature, Jan2000, v24, p23 D2 D2J DBA/2 DBA2 DBA/2J Originally inbred at the Rockefeller Institute, AKR mice are widely used in cancer research for their high leukemia incidence (60-90%) and in immunology as a source of the Thy1.1 (theta AKR) antigen. AKR/J mice are viremic from birth, and express the ecotropic retrovirus AKV in all tissues. The hair interior defect (hid) mutation, a strain characteristic of AKR mice, causes alterations in hair development that is only evident microscopically. Adrenocortical lipid depletion (ald) in AKR mice is caused by a mutation in sterol O-acyltransferase 1 (Soat1), and leads to a truncated SOAT1 protein. AKR/J mice are relatively resistant to aortic lesion formation on a semi-synthetic high fat diet and are hyporesponsive to diets containing high levels of fat and cholesterol. Sirarat Sarntivijai https://www.jax.org/strain/000648 AK AKR AKR/J Both CAST/EiJ and CASA/RkJ (Stock No. 000735) were derived from wild mice trapped in Thailand. CAST is often combined with the common laboratory strains to generate F1 hybrids with high levels of heterozygosity for use in genetic mapping. Unlike the wild-derived strain SPRET, male F1 mice from a CAST cross are fertile. Like CASA, CAST is resistant to flavivirus infection. The flavivirus family includes pathogens responsible for dengue, yellow fever and several forms of encephalitis. Most common laboratory mice are sensitive to flavivirus infection. Resistance/sensitivity is conferred through the oligoA synthase Oas1b locus. In a comparison of multiple strains, CASA and CAST exhibit reduced numbers of retinal ganglion cells as compared to common laboratory strains and other wild-derived strains. In a 2015 study comparing CAST/Ei and the other Collaborative Cross inbred strains (A/J, C3H/HeJ, C57BL/6J, DBA/2J, 129S1/SvImJ, NOD/LtJ, NZO/HlLtJ, and WSB/EiJ), dorsal root ganglion neurons from CAST/Ei mice demonstrate a significantly improved ability to regenerate axons in an inhibitory environment as determined by an increase in number of neurons with neurites and longer axonal process per neuron under both naive and pre-injured conditions. In addition, as compared to neurons from C57BL/6 mice, CAST/Ei neurons exhibit more extensive axonal regeneration in the spinal cord and optic nerve following injury and show greater sprouting following ischemic stroke. Wild-derived mice are genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and are valuable tools for genetic mapping, evolution and systematics research. Sirarat Sarntivijai https://www.jax.org/strain/000928 CAST CAST/EiJ FVB/NJ was inbred for the Fv1b allele which confers sensitivity to the Friend leukemia virus B strain. Due to the prominent pronuclei in their fertilized eggs and the large litter size, FVB/NJ mice are commonly used for transgenic injection. Compared to many other inbred strains, FVB/NJ is highly susceptible to asthma-like airway responsiveness with significant generation of antigen-specific IgE. Despite having the H2q MHC haplotype, FVB/NJ are resistant to collagen-induced arthritis. This resistance stems from coding polymorphisms in Tcra-V11.1 and a genomic deletion of some Tcrb-V genes that includes Tcrb-V8.2. FVB/NJ have higher than average activity, anxiety, and basal body temperature, low stress-induced hyperthermia, and are homozygous for the Pde6brd1 allele, which results in early onset retinal degeneration. Although FVB/N typically do not develop spontaneous tumors, they are highly susceptible to chemically induced squamous cell carcinomas with a high rate of malignant conversion from papilloma to carcinoma. Sirarat Sarntivijai https://www.jax.org/strain/001800 FVB Friend Virus B NIH Jackson FVB/NJ NZO mice of both sexes exhibit high birth weights and are significantly heavier at weaning age. Severe obesity (including both visceral and subcuatneous fat depots) develops even when mice are maintained on a standard diet containing 4.5% fat. Both males and females of the NZO/Hl substrain exhibit impaired glucose tolerance (IGT), but subsequent type 2 maturity onset (NIDDM) diabetes development is limited to males, with a phenotype penetrance of 50% or less. NZO/Hl mice also show anti-insulin receptor antibodies, a defect in leptin transport, and hypertension. The genetic lesion appears to be within the islets of Langerhans as transfer of pancreatic islets from normal mice returns body weights and blood glucose levels to within normal range. Ovarian granulosa cell tumors, lymphomas, duodenal, and lung tumors have also been noted to occur in NZO mice at an elevated frequency. F1 hybrids of NON/ShiLt and NZO/Hl provide a new model of obesity-induced diabetes. Male (NON/ShiLt x NZO/Hl)F1 hybrids are obese (BW = 53.5 g by 16 weeks) and almost all develop maturity onset NIDDM. F1 males on a 4% diet will develop hyperglycemia around 20 to 24 weeks of age; increasing the fat content of the diet accelerates diabetes onset to 16 to 20 weeks of age. (NZO/Hl x NON/ShiLt)F1 hybrids will develop diabetes slightly faster than their reciprocal cross due to the NZO maternal environment; however this cross is difficult to produce due to the inherently poor breeding performance of NZO/HlJ female mice. F1 females exhibit a weight gain similar to the NZO parent, and have impaired glucose tolerance but are resistant to diabetes development. Diabetes development can be accelerated to eight to 12 weeks by fostering onto an F1 dam. Reciprocal backcrosses to the parental strains and analysis of (NON/ShiLt x NZO/Hl)F2 mice has led to the identification of a number of complex diabetes-predisposing ("diabesity") QTLs. Dr. Leiter's research group at The Jackson Laboratory is currently developing a series of nine recombinant congenic strains (RCS) made by backcrossing the (NZO/Hl x NON/ShiLt)F1 for two generations onto the NON/ShiLt background before inbreeding (~12% NZO/Hl, 88% NON/ShiLt genomes). Preliminary analysis indicates that body weight gains of all RCS are higher than NON/ShiLt, but none are as obese as NZO/Hl; some of these RCS develop NIDDM while others are resistant. These new strains will be useful to further analyze diabesity QTLs and as new models for type 2 (NIDDM) diabetes. An additional benefit of the RCS is better breeding performance than NZO/Hl. Sirarat Sarntivijai https://www.jax.org/strain/002105 New Zealand Obese NZO/HlLtJ PWK was derived from wild mice trapped near Prague, Czech Republic. PWK has a biochemical profile that is similar to the inbred strain PWD (also originating from the Czech Republic - Stock No. 004660) with the exception of the isoenzyme variant esterase 13 (Es13b). Wild-derived mice are genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and are valuable tools for genetic mapping, evolution and systematics research. Sirarat Sarntivijai https://www.jax.org/strain/003715 PWK/PhJ Watkins Star Line B (WSB) was derived from wild mice trapped in Eastern Shore, Maryland. WSB is characterized by a distinct and consistent white head blaze, variable ventral spotting and a slight coat dilution on the agouti background. The variation in pigment is the result of the spontaneous mutation blaze (Kitlblz).Wild-derived mice are genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and are valuable tools for genetic mapping, evolution and systematics research. Sirarat Sarntivijai https://www.jax.org/strain/001145 WSB WSB/EiJ LP/J mice display a high susceptibility to audiogenic seizures. This strain is also reported to have a fairly high incidence of tumors that develop later in life, including mammary tumors, lymphoma, lung and soft-tissue sarcomas. LP/J mice are also homozygous for the spontaneous mutation piebald in the endothelin receptor type B gene (Ednrbs). The piebald spontaneous mutation is the result of a mutation in the endothelin receptor type B gene, Ednrb. Mice show irregular white spotting, the amount of which is greatly influenced by minor modifying genes. They also have dark eyes. The white areas of the coat are completely lacking in neural crest-derived melanocytes, and there is a reduction in the number of melanocytes in the choroid layer of the eye. Sirarat Sarntivijai https://www.jax.org/strain/000676 LP LP/J The wild-derived inbred strain SPRET/Ei is often used in crosses with common inbred strains to create highly polymorphic panels for genetic mapping. SPRET/Ei mice are resistant to high doses of tumor necrosis factor alpha (TNFa) (Staelens et al 2002). Mice from a C57BL/6 x SPRET/Ei F1 cross were protected from TNFa-induced arthritis and partially protected against induced allergic asthma (Staelens et al 2004). SPRET/Ei may be useful in understanding certain inflammatory diseases. Sirarat Sarntivijai https://www.jax.org/strain/001146 SPRET/Ei SPRET/EiJ The wild-derived inbred strain SPRET/Ei is often used in crosses with common inbred strains to create highly polymorphic panels for genetic mapping. SPRET/Ei mice are resistant to high doses of tumor necrosis factor alpha (TNFa) (Staelens et al 2002). Mice from a C57BL/6 x SPRET/Ei F1 cross were protected from TNFa-induced arthritis and partially protected against induced allergic asthma (Staelens et al 2004). SPRET/Ei may be useful in understanding certain inflammatory diseases. https://orcid.org/0000-0002-3110-8220 CBA/J inbred mice are widely used as a general purpose strain. CBA/J strain is the only CBA substrain that carries the Pde6brd1 mutation, which causes blindness by wean age. CBA/J mice are not histocompatible with the CBA/CaJ (Stock No. 000654) substrain (Green and Kaufer, 1965). The CBA/J inbred mouse strain is used to study granulomatous experimental autoimmune thyroiditis (G-EAT), are relatively resistant to diet-induced atherosclerosis (Paigen et al. 1990), and develop a mild hearing loss late in life, with most of the hearing loss occurring in the higher frequencies (Sweet et al. 1988). Renal tubulointerstitial lesions have been observed in this strain at a high frequency (Rudofsky 1978). Some CBA/J mice spontaneously develop exocrine pancreatic insufficiency syndrome (Eppig and Leiter 1977, Leiter et al. 1977). Sirarat Sarntivijai https://www.jax.org/strain/000656 CBA Jackson CBA/J CAROLI was derived from wild mice trapped in Thailand and is from the species Mus caroli, which is distantly related to laboratory mice and does not breed with laboratory mice. These mice are characterized by black feet. This wild derived mouse strain is genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and is a valuable tool for sequence comparison, evolution and systematics research. Sirarat Sarntivijai https://www.jax.org/strain/000926 JAX:000926 CAROLI/EiJ CAROLI was derived from wild mice trapped in Thailand and is from the species Mus caroli, which is distantly related to laboratory mice and does not breed with laboratory mice. These mice are characterized by black feet. This wild derived mouse strain is genetically distinct from common laboratory mice for a number of complex phenotypic characteristics and is a valuable tool for sequence comparison, evolution and systematics research. https://orcid.org/0000-0002-3110-8220 ICR/HaJ is a mouse strain as described in Jackson Laboratory strain index. This inbred strain is derived from the outbred strain ICR. It may be useful in therapeutic drug testing and genetic analysis of carcinogen-induced colon cancer. Dani Welter https://www.jax.org/strain/009122 ICR ICR/HaJ A Mus musculus individual that is a substrain of C57BL/6J (mother) and CAST/EiJ (father). paola PMID:27668657 https://orcid.org/0000-0002-3163-0115 C57BL/6JxCAST/EiJ Inbred Strain. Zoe May Pendlington 2023-11-02T09:06:58Z MGI:2159849 TGEMO:00019 DBA Strain family. Zoe May Pendlington 2023-11-02T09:09:47Z MGI:2159850 TGEMO:00108 C CB XXXIX CBA 2019-03-05T17:25:21Z Western Australia Ecoregion WWF:AA1310 https://www.worldwildlife.org/ecoregions/aa1310 Western Australian Mulga Shrublands Ecoregion 2019-03-05T17:51:32Z https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands Australasia Ecoregion 2019-03-05T17:52:41Z Southern central Australia Ecoregion WWF:AA1309 https://www.worldwildlife.org/ecoregions/aa1309 Tirari-Sturt Stony Desert Ecoregion 2019-03-05T17:54:35Z Eastern central Australia Ecoregion WWF:AA1308 https://www.worldwildlife.org/ecoregions/aa1308 Simpson Desert Region 2019-03-05T17:56:13Z Western Australia Ecoregion WWF:AA1307 https://www.worldwildlife.org/ecoregions/aa1307 Pilbara Shrublands Ecoregion 2019-03-05T18:10:52Z Western coast of Australia Ecoregion WWF:AA1301 https://www.worldwildlife.org/ecoregions/aa1301 Carnarvon Xeric Shrublands Ecoregion 2019-03-05T18:12:28Z Central Australia Ecoregion WWF:AA1302 https://www.worldwildlife.org/ecoregions/aa1302 Central Ranges Xeric Shrub Ecoregion 2019-03-05T18:15:11Z Western central Australia WWF:AA1303 https://www.worldwildlife.org/ecoregions/aa1303 Gibson Desert Ecoregion 2019-03-05T18:17:15Z Northwestern Australia WWF:AA1304 https://www.worldwildlife.org/ecoregions/aa1304 The Great Sandy-Tanami Desert Ecoregion 2019-03-05T18:24:06Z Southern Australia Ecoregion WWF:AA1305 https://www.worldwildlife.org/ecoregions/aa1305 Great Victoria Desert Ecoregion 2019-03-05T18:26:16Z Southern Australia Ecoregion WWF:AA1306 https://www.worldwildlife.org/ecoregions/aa1306 Nullarbor Plains Xeric Shrubland Ecoregion 2019-03-06T22:01:41Z https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands Afrotropical Ecoregion 2019-03-06T22:02:37Z Southern Africa: Southern Namibia into South Africa WWF:AT1322 https://www.worldwildlife.org/ecoregions/at1322 Succulent Karoo Ecoregion 2019-03-06T22:07:38Z WWF:AT1321 https://www.worldwildlife.org/ecoregions/at1321 Arabian Peninsula: Yemen and Saudi Arabia Yemen and Saudi Arabia Ecoregion 2019-03-06T22:11:38Z WWF:AT1320 https://www.worldwildlife.org/ecoregions/at1320 Arabian Peninsula: Yemen, Saudi Arabia, and Oman Yemen, Saudi Arabia, and Oman Ecoregion 2019-03-06T22:13:00Z WWF:AT1319 https://www.worldwildlife.org/ecoregions/at1319 Somali montane xeric woodlands ecoregion Somali Montane Xeric Woodland Ecoregion 2019-03-06T22:15:07Z Islands east of the Horn of Africa and south of Yemen Ecoregion WWF:AT1318 https://www.worldwildlife.org/ecoregions/at1318 Socotran Archipelago Ecoregion 2019-03-06T22:18:55Z WWF:AT1317 https://www.worldwildlife.org/ecoregions/at1317 Red Sea Coastal Desert Ecoregion 2019-03-06T22:20:56Z WWF:AT1316 https://www.worldwildlife.org/ecoregions/at1316 Namibian Savanna Woodland Ecoregion 2019-03-06T22:24:28Z Africa: Namibia Ecoregion WWF:AT1315 https://www.worldwildlife.org/ecoregions/at1315 Namib Desert Ecoregion 2019-03-06T22:26:15Z WWF:AT1314 https://www.worldwildlife.org/ecoregions/at1314 Nama Karoo Ecoregion 2019-03-06T22:28:43Z WWF:AT1313 https://www.worldwildlife.org/ecoregions/at1313 Masai Xeric Grasslands and Shrublands Ecoregion 2019-03-06T22:30:23Z WWF:AT1312 https://www.worldwildlife.org/ecoregions/at1312 Madagascar Succulent Woodlands Ecoregion 2019-03-06T22:31:29Z WWF:AT1311 https://www.worldwildlife.org/ecoregions/at1311 Madagascar spiny desert ecoregion Madagascar Spiny Thickets Ecoregion 2019-03-06T22:39:32Z WWF:AT1310 https://www.worldwildlife.org/ecoregions/at1310 Africa: Coastal Namibia and Angola Ecoregion Kaokoveld Desert Ecoregion 2019-03-06T22:42:47Z WWF:AT1309 https://www.worldwildlife.org/ecoregions/at1309 Kalahari Xeric Savanna Ecoregion 2019-03-06T22:44:54Z WWF:AT1308 https://www.worldwildlife.org/ecoregions/at1308 Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion Ile Europa and Bassas da India Ecoregion 2019-03-06T22:46:58Z Eastern Africa: Somalia WWF:AT1307 https://www.worldwildlife.org/ecoregions/at1307 Hobyo Grassland and Shrubland Ecoregion 2019-03-06T22:54:57Z WWF:AT1306 https://www.worldwildlife.org/ecoregions/at1306 Arabian Peninsula: Oman and United Arab Emirates Ecoregion Oman and United Arab Emirates Ecoregion 2019-03-07T00:08:06Z WWF:AT1305 https://www.worldwildlife.org/ecoregions/at1305 Ethiopian Xeric Grasslands and Shrublands Ecoregion 2019-03-07T00:11:29Z WWF:AT1304 https://www.worldwildlife.org/ecoregions/at1304 Eritrean Coastal Desert Ecoregion 2019-03-07T00:13:33Z WWF:AT1303 https://www.worldwildlife.org/ecoregions/at1303 North central Africa: Eastern Chad and small area of western Sudan East Saharan Montane Xeric Woodland Ecoregion 2019-03-07T00:16:12Z WWF:AT1302 https://www.worldwildlife.org/ecoregions/at1302 Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion Oman, Yemen, and Saudi Arabia Ecoregion 2019-03-07T00:18:09Z WWF:AT1301 https://www.worldwildlife.org/ecoregions/at1301 Aldabra Island Xeric Scrub Ecoregion 2019-04-26T23:38:50Z Indo-Malay Ecoregion 2019-04-26T23:40:13Z WWF:IM1304 Southern Asia: Western India into Pakistan Thar Desert 2019-04-27T00:12:51Z WWF:IM1303 Southern Asia: Eastern India and western Pakistan Northwestern Thorn Scrub Forests A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. 2019-08-20T13:47:18Z envoAtmo envoPolar Arctic front A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. 2019-08-20T13:48:44Z envoAtmo envoPolar Antarctic front A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. Stellar radiation emitted from Sol. 2020-05-19T22:27:44Z Solar radiation example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Transformation-ML Transformation-ML file describing parameter transformations used in a GvHD experiment. Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf Transformation-ML ACS d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) person:Jennifer Fostel web-page:http://www.isac-net.org/content/view/607/150/ ACS XML RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel web-page:http://www.w3.org/XML/ XML RDF A FOAF file, a SKOS file, an OWL file. RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) person:Jennifer Fostel web-page:http://www.w3.org/RDF/ RDF zip MagicDraw MDZIP archive, Java JAR file. zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) person:Jennifer Fostel web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ zip tar Example.tar file. tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) person:Jennifer Fostel web-page:http://www.gnu.org/software/tar/manual/ tar FCS d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) person:Jennifer Fostel web-page:http://www.fcspress.com/ FCS Compensation-ML compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML Gating-ML foogate.xml, Gating-ML file describing gates used in a GvHD experiment. Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) person:Jennifer Fostel web-page:http://www.flowcyt.org/gating/ Gating-ML OWL OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) person:Jennifer Fostel web-page:http://www.w3.org/2004/OWL/ OWL Affymetrix Affymetrix supplied microarray An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Thermo Philippe Rocca-Serra Thermo Waters Philippe Rocca-Serra Waters BIO-RAD Philippe Rocca-Serra BIO-RAD GenePattern hierarchical clustering James Malone GenePattern hierarchical clustering Ambion Philippe Rocca-Serra Ambion Helicos Philippe Rocca-Serra Helicos Roche Philippe Rocca-Serra Roche Illumina Philippe Rocca-Serra Illumina GenePattern PCA GenePattern PCA GenePattern module SVM GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM GenePattern k-nearest neighbors James Malone GenePattern k-nearest neighbors GenePattern LOOCV GenePattern LOOCV GenePattern k-means clustering James Malone GenePattern k-means clustering Agilent Philippe Rocca-Serra Agilent GenePattern module KMeansClustering GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern module KMeansClustering GenePattern CART James Malone GenePattern CART GenePattern module CARTXValidation GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation Li-Cor Philippe Rocca-Serra Li-Cor Bruker Corporation Philippe Rocca-Serra Bruker Corporation GenePattern module KNNXValidation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module KNNXValidation GenePattern module PeakMatch GenePattern module PeakMatch GenePattern module KNN GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN GenePattern module HierarchicalClustering GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering GenePattern SVM James Malone GenePattern SVM Applied Biosystems Philippe Rocca-Serra Applied Biosystems GenePattern module PCA GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern module PCA GenePattern peak matching James Malone Ryan Brinkman GenePattern peak matching Bruker Daltonics Philippe Rocca-Serra Bruker Daltonics GenePattern HeatMapViewer data visualization The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization GenePattern HierarchicalClusteringViewer data visualization The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization GenePattern module HeatMapViewer A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer GenePattern module HierarchicalClusteringViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 Sysmex Corporation, Kobe, Japan U.S. Food and Drug Administration FDA U.S. Food and Drug Administration right handed right handed ambidexterous ambidexterous left handed left handed Edingburgh handedness inventory The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. PERSON:Alan Ruttenberg PERSON:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edingburgh handedness inventory eBioscience Karin Breuer WEB:http://www.ebioscience.com/@2011/04/11 eBioscience Cytopeia Karin Breuer WEB:http://www.cytopeia.com/@2011/04/11 Cytopeia Exalpha Biological Karin Breuer WEB:http://www.exalpha.com/@2011/04/11 Exalpha Biological Apogee Flow Systems Karin Breuer WEB:http://www.apogeeflow.com/@2011/04/11 Apogee Flow Systems Exbio Antibodies Karin Breuer WEB:http://www.exbio.cz/@2011/04/11 Exbio Antibodies Becton Dickinson (BD Biosciences) Karin Breuer WEB:http://www.bdbiosciences.com/@2011/04/11 Becton Dickinson (BD Biosciences) Dako Cytomation Karin Breuer WEB:http://www.dakousa.com/@2011/04/11 Dako Cytomation Millipore Karin Breuer WEB:http://www.guavatechnologies.com/@2011/04/11 Millipore Antigenix Karin Breuer WEB:http://www.antigenix.com/@2011/04/11 Antigenix Partec Karin Breuer WEB:http://www.partec.de/@2011/04/11 Partec Beckman Coulter Karin Breuer WEB:http://www.beckmancoulter.com/@2011/04/11 Beckman Coulter Advanced Instruments Inc. (AI Companies) Karin Breuer WEB:http://www.aicompanies.com/@2011/04/11 Advanced Instruments Inc. (AI Companies) Miltenyi Biotec Karin Breuer WEB:http://www.miltenyibiotec.com/@2011/04/11 Miltenyi Biotec AES Chemunex Karin Breuer WEB:http://www.aeschemunex.com/@2011/04/11 AES Chemunex Bentley Instruments Karin Breuer WEB:http://bentleyinstruments.com/@2011/04/11 Bentley Instruments Invitrogen Karin Breuer WEB:http://www.invitrogen.com/@2011/04/11 Invitrogen Luminex Karin Breuer WEB:http://www.luminexcorp.com/@2011/04/11 Luminex CytoBuoy Karin Breuer WEB:http://www.cytobuoy.com/@2011/04/11 CytoBuoy Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen Pacific Biosciences An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences NanoString Technologies An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies Thermo Fisher Scientific An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific Thermo Fisher Scientific G1: Well differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. Chris Stoeckert, Helena Ellis G1 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G1: Well differentiated G2: Moderately differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. Chris Stoeckert, Helena Ellis G2 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G2: Moderately differentiated G3: Poorly differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G3 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G3: Poorly differentiated G4: Undifferentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G4 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G4: Undifferentiated G1 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. Chris Stoeckert, Helena Ellis Grade 1 NCI BBRB, OBI NCI BBRB G1 (Fuhrman) G2 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Chris Stoeckert, Helena Ellis Grade 2 NCI BBRB, OBI NCI BBRB G2 (Fuhrman) G3 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Chris Stoeckert, Helena Ellis Grade 3 NCI BBRB, OBI NCI BBRB G3 (Fuhrman) G4 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. Chris Stoeckert, Helena Ellis Grade 4 NCI BBRB, OBI NCI BBRB G4 (Fuhrman) Low grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Chris Stoeckert, Helena Ellis Low grade NCI BBRB, OBI NCI BBRB Low grade ovarian tumor High grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. Chris Stoeckert, Helena Ellis High grade NCI BBRB, OBI NCI BBRB High grade ovarian tumor G1 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. Chris Stoeckert, Helena Ellis G1 NCI BBRB, OBI NCI BBRB G1 (WHO) G2 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. Chris Stoeckert, Helena Ellis G2 NCI BBRB, OBI NCI BBRB G2 (WHO) G3 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. Chris Stoeckert, Helena Ellis G3 NCI BBRB, OBI NCI BBRB G3 (WHO) G4 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. Chris Stoeckert, Helena Ellis G4 NCI BBRB, OBI NCI BBRB G4 (WHO) pT0 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT0 (colon) pTis (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pTis (colon) pT1 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT1 (colon) pT2 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT2 (colon) pT3 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT3 (colon) pT4a (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4a (colon) pT4b (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4b (colon) pT0 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT0 (lung) pTis (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pTis (lung) pT1 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1 (lung) pT1a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1a (lung) pT1b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1b (lung) pT2 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2 (lung) pT2a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2a (lung) pT2b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2b (lung) pT3 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT3 (lung) pT4 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT4 (lung) pT0 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT0 (kidney) pT1 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1 (kidney) pT1a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1a (kidney) pT1b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1b (kidney) pT2 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2 (kidney) pT2a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2a (kidney) pT2b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2b (kidney) pT3 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3 (kidney) pT3a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3a (kidney) pT3b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3b (kidney) pT3c (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3c (kidney) pT4 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT4 (kidney) pT0 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT0 (ovary) pT1 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1 (ovary) pT1a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1a (ovary) pT1b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1b (ovary) pT1c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1c (ovary) pT2 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2 (ovary) pT2a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2a (ovary) pT2b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2b (ovary) pT2c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2c (ovary) pT3 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3 (ovary) pT3a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3a (ovary) pT3b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3b (ovary) pT3c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3c (ovary) pN0 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN0 (colon) pN1 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1 (colon) pN1a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1a (colon) pN1b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1b (colon) pN1c (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1c (colon) pN2 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2 (colon) pN2a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2a (colon) pN2b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2b (colon) pN0 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN0 (lung) pN1 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN1 (lung) pN2 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN2 (lung) pN3 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN3 (lung) pN0 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN0 (kidney) pN1 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN1 (kidney) pN0 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN0 (ovary) pN1 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN1 (ovary) cM0 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM0 (colon) cM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM1 (colon) cM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1a (colon) cM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1b (colon) pM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1 (colon) pM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1a (colon) pM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1b (colon) cM0 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM0 (lung) cM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1 (lung) cM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1a (lung) cM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1b (lung) pM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1 (lung) pM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1a (lung) pM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1b (lung) cM0 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM0 (kidney) cM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM1 (kidney) pM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB pM1 (kidney) cM0 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM0 (ovary) cM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM1 (ovary) pM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB pM1 (ovary) Occult Carcinoma (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. Chris Stoeckert, Helena Ellis Occult Carcinoma http://www.medilexicon.com/dictionary/14371 NCI BBRB Occult Carcinoma (AJCC 7th) Stage 0 (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. Chris Stoeckert, Helena Ellis Stage 0 https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage 0 (AJCC 7th) Stage I (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Chris Stoeckert, Helena Ellis Stage I https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage I (AJCC 7th) Stage IIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIA (AJCC 7th) Stage IIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIB (AJCC 7th) Stage IIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. Chris Stoeckert, Helena Ellis Stage IIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIC (AJCC 7th) Stage IIIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIA (AJCC 7th) Stage IIIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIB (AJCC 7th) Stage IIIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. Chris Stoeckert, Helena Ellis Stage IIIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIC (AJCC 7th) Stage IVA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVA (AJCC 7th) Stage IVB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVB (AJCC 7th) Stage IA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. Chris Stoeckert, Helena Ellis Stage IA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA (FIGO) Stage IA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. Chris Stoeckert, Helena Ellis Stage IA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA1 (FIGO) Stage IA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. Chris Stoeckert, Helena Ellis Stage IA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA2 (FIGO) Stage IB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA Chris Stoeckert, Helena Ellis Stage IB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB (FIGO) Stage IB1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB1 (FIGO) Stage IB2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB2 (FIGO) Stage IIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA (FIGO) Stage IIA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA1 (FIGO) Stage IIA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA2 (FIGO) Stage IIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIB (FIGO) Stage IIIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIA (FIGO) Stage IIIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIB (FIGO) Stage IVA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVA (FIGO) Stage IVB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVB (FIGO) Stage 1 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1 (FIGO) Stage 1A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1A (FIGO) Stage 1B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1B (FIGO) Stage 1C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1C (FIGO) Stage 2 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2 (FIGO) Stage 2A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2A (FIGO) Stage 2B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2B (FIGO) Stage 2C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2C (FIGO) Stage 3 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). Chris Stoeckert, Helena Ellis Stage 3 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3 (FIGO) Stage 3A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3A (FIGO) Stage 3B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3B (FIGO) Stage 3C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). Chris Stoeckert, Helena Ellis Stage 3C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3C (FIGO) Stage 4 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Chris Stoeckert, Helena Ellis Stage 4 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 4 (FIGO) Stage Unknown (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). Chris Stoeckert, Helena Ellis Stage Unknown https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage Unknown (FIGO) 3: symptomatic in bed more than 50% of the day but not bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 3: symptomatic in bed more than 50% of the day but not bed ridden 2: symptomatic but in bed less than 50% of the day An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 2: symptomatic but in bed less than 50% of the day 4: bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 4: bed ridden 0: asymptomatic An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 0: asymptomatic 1: symptomatic but fully ambulatory An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 1: symptomatic but fully ambulatory 100: asymptomatic A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 100: asymptomatic 80-90: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 80-90: symptomatic but fully ambulatory 60-70: symptomatic but in bed less than 50% of the day A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 60-70: symptomatic but in bed less than 50% of the day 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden Oxford Nanopore Technologies An organization that is developing and selling nanopore sequencing products and is based in the UK. James A. Overton https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies Oxford Nanopore Technologies BioGents An organization that manufactures mosquito traps and other mosquito control products. John Judkins WEB:https://eu.biogents.com/about-biogents/ BioGents Abbott A manufacturer of rapid point-of-care assay devices. John Judkins ORCID:0000-0001-6595-0902 WEB:https://www.globalpointofcare.abbott/en/about.html https://github.com/obi-ontology/obi/issues/1456 Abbott J. Mitra A manufacturer of in vitro diagnostic assay kits in India. John Judkins ORCID:0000-0001-6595-0902 WEB:https://jmitra.co.in/about-us/ https://github.com/obi-ontology/obi/issues/1456 J. Mitra InBios A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. John Judkins ORCID:0000-0001-6595-0902 WEB:https://inbios.com/about/ https://github.com/obi-ontology/obi/issues/1456 InBios The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope NSRL GCRSim The samples were irradiated using the NSRL Galactic Cosmic Ray Simulation. The NSRL Galactic Cosmic Ray Simulation is comprised of seven different species of ion, and fourteen different energies of H and He for 33 separate beams in a single GCRSim exposure. (https://www.bnl.gov/nsrl/userguide/GCRSim.php) NSRL GCRSim NSRL Galactic Cosmic Ray Simulation NSRL The experiment was conducted at the NSRL A particle accelerator beamline located at Brookhaven National Laboratory Jack Miller NSRL NASA Space Radiation Laboratory HIMAC The experiment was carried out at HIMAC A particle accelerator at the National Institute of Radiological Sciences in Chiba, Japan HIMAC; NIRS-HIMAC Heavy Ion Medical Accelerator at Chiba ISS The experiment was conducted aboard the International Space Station An instance of an Earth-orbiting space station that went operational in the year 2000. Jack Miller term editor ISS International Space Station The experiment was conducted on the Mir space station An instance of an Earth-orbiting space station, operational from1986 to 2001, operated by the Soviet Union and later by Russia. Wikipedia Mir The biological payload was carried into orbit by the Space Shuttle An instance of a reusable spacecraft designed to carry passengers and equipment into low Earth orbit and return to Earth. Operated by the United States and operational from 1981 to 2011. Wikipedia Space Shuttle The experiment was conducted aboard the Bion-MI satellite. An instance of a Russian-operated Earth satellite carrying biological samples. Launched April 19, 2013 and returned to Earth May 19, 2013 Jack Miller Wikipedia Bion-M1 The samples were flown on the Foton-M4 satellite An instance of a Russian-operated Earth satellite carrying biological samples. Launched July 19, 2014 and returned to Earth September 1, 2014 Wikipedia Foton-M4 The experiment was conducted on the Shenzhou-8 space station An instance of a Chinese-operated Earth satellite carrying biological samples. Launched October 31, 2011 and returned to Earth November 17, 2011. Wikipedia Shenzhou-8 US Lab The experiment was conducted in the US Laboratory on the ISS An instance of a module on the International Space Station, operated by the United States Wikipedia Destiny|US Lab ISS-US Laboratory JEM The experiment was conducted on the Japanese Experiment Module A Japanese science module for the International Space Station developed by JAXA. It is the largest single ISS module, and is attached to the Harmony module. The first two pieces of the module were launched on Space Shuttle missions STS-123 and STS-124. Wikipedia JEM|Kibo ISS-Japanese Experiment Module Columbus The experiment was conducted on the Columbus module on the ISS An instance of a module on the International Space Station, operated by the European Space Agency. Wikipedia Columbus laboratory ISS-Columbus Zvezda The experiment was conducted in the Zvezda module of the ISS. An instance of a module on the International Space Station, operated by the Russian Space Agency. Wikipedia Russian Service Module ISS-Zvezda The experiment was carried out at the SIS-18 accelerator. An particle accelerator located at the GSI Helmholtz Centre for Heavy Ion Research, Darmstadt, Germay. SIS18 NSRL SPESim The samples were irradiated using the NSRL Solar Particle Event Simulation. The NSRL SPE simulatoris based on the fluence of the August 1972 event, with an energy spectrum similar to the March 1989 event. The majority of the protons are at very low energies, below 1 MeV, and pose little to no risk to astronauts in a space craft or space suit. The SPESim begins with 50 MeV protons, which amounts to 91.66% of the total dose. Then the beam energy increments in steps of 10 MeV up to 150 MeV where 0.14% of the total dose is delivered. NSRL SPESim NSRL Solar Particle Event Simulation NSRL SimGCRSim The samples were irradiated using the NSRL Simplified Galactic Cosmic Ray Simulation. The NSRL Simplified Galactic Cosmic Ray Simulation uses 6 beams and 5 different ions including protons at two different energies. https://www.bnl.gov/nsrl/userguide/SimGCRSim.php NSRL SimGCRSim NSRL Simplified Galactic Cosmic Ray Simulation KUR-HWNIF The samples were irradiated with thermal neutrons at the KUR-HWNIF A heavy water tank of approximately 2 m3 adjacent to the core of the Kyoto University Research Reactor (KUR), a light-water moderated tank-type reactor. KUR-HWNIF Kyoto University Research Reactor-Heavy Water Neutron Irradiation Facility HIRRAC The samples were irradiated with fast neutrons at the HIRRAC. A neutron generator at the Research Institute for Radiation Biology and Medicine, Hiroshima University (RIRBM). Monoenergetic neutrons of which energy is less than 1.3 MeV are generated by the 7Li(p,n)7 Be reaction at proton energies up to 3 MeV. HIRRAC Hiroshima University Radiobiological Research Accelerator BNL GRSF The Gamma Radiation Facility known as GRSF houses a cesium-137 gamma ray source which can provide gamma rays at a variety of dose rates. The gamma source is an industry standar dJ.L. Shepherd Mark I Model 68A 137Cs ? Irradiator. The photon energy from the source is 662 keV, with a Lineal Energy Transfer (LET) in water of approximately 0.8 keV/um. (https://www.bnl.gov/nsrl/grsf/) Jack Miller BNL GRSF Brookhaven National Laboratory Gamma Radiation Source Facility http://www.theratronics.ca/PDFs/GC40_BTMB_8008GC40E_2_v112013_webSECURE.pdf Gammacell 40 https://www.crr.columbia.edu/services/ion-beam-and-neutron-core-facility RARAF 5.5 MV microbeam https://www.nasa.gov/feature/ames/nasa-small-business-partnership-prepares-drone-for-30-day-science-flights Swift HALE https://www.nasa.gov/centers/armstrong/aircraft/ER-2/index.html ER-2 https://airbornescience.nasa.gov/aircraft/WB-57_-_JSC WB-57 doi: 10.2349/biij.2.1.e1 Faxitron CP160 https://precisionxray.com/x-rad/xrad-320/ X-Rad320 third planet from the Sun in the Solar System Earth third planet from the Sun in the Solar System https://www.wikidata.org/wiki/Q2 Sun Sol Earth's interconnected water system World Ocean Earth's interconnected water system https://www.wikidata.org/wiki/Q715269 meter metre m m A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. meter "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST] kilogram kg kg kilogram "A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." [BIPM:BIPM, NIST:NIST] A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. s s second sec A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST] second cm centimeter cm centimeter centimetre "A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST] A length unit which is equal to one hundredth of a meter or 10^[-2] m. A length unit which is equal to one thousandth of a meter or 10^[-3] m. mm mm millimeter millimetre millimeter "A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST] micrometer micron "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST] micrometre micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. um um nm nm nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nanometre nanometer "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST] angstrom angstrom "A length unit which is equal to 10 [-10] m." [NIST:NIST] A length unit which is equal to 10 [-10] m. Å gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. gram g g "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST] milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. mg "A mass unit which is equal to one thousandth of a gram or 10^[-3] g." [UOC:GVG] milligram mg microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. ug ug "A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG] microgram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. nanogram ng "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG] nanogram ng picogram A mass unit which is equal to 10^[-12] g. "A mass unit which is equal to 10^[-12] g." [UOC:GVG] picogram pg pg degree Celsius "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST] degree C A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. C C degree Celsius minute min min minute A time unit which is equal to 60 seconds. "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia] hour hour h h hr A time unit which is equal to 3600 seconds or 60 minutes. "A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia] day "A time unit which is equal to 24 hours." [Wikipedia:Wikipedia] A time unit which is equal to 24 hours. day week "A time unit which is equal to 7 days." [Wikipedia:Wikipedia] week A time unit which is equal to 7 days. month "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." [Wikipedia:Wikipedia] month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia] year "A substance unit equal to a millionth of a mol or 10^[-6] mol." [NIST:NIST] micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. umol micromole umol nmol nmol "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol." [NIST:NIST] nanomole nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. pmol pmol "A substance unit equal to 10^[-12] mol." [NIST:NIST] A substance unit equal to 10^[-12] mol. picomole picomole M M "A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." [UOC:GVG] A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). molar molar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. mM millimolar mM millimolar "A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." [UOC:GVG] micromolar uM A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. uM micromolar "A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." [UOC:GVG] nM nM nanomolar "A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." [UOC:GVG] A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nanomolar pM picomolar pM "A unit of molarity which is equal to 10^[-12] M." [UOC:GVG] picomolar A unit of molarity which is equal to 10^[-12] M. cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cubic centimetre cubic centimeter cm^3 cc "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." [NIST:NIST] cc "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST] milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. millilitre ml milliliter ml litre A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. liter "A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." [NIST:NIST] L l L liter "A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." [NIST:NIST] cubic decimeter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter cubic decimetre dm^[3] microliter microliter ul A volume unit which is equal to one millionth of a liter or 10^[-6] L. microlitre ul "A volume unit which is equal to one millionth of a liter or 10^[-6] L." [NIST:NIST] A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nanoliter "A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." [NIST:NIST] nanoliter nanolitre nl nl picoliter picolitre picoliter A volume unit which is equal to 10^[-12] L. pl "A volume unit which is equal to 10^[-12] L." [NIST:NIST] pl s^1 hertz Hz "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST] A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz mass percentage weight-weight percentage mass percentage w/w % w/w "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia] percent weight pr weight A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. (w/v) mass volume percentage % w/v A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. mass volume percentage percent vol per vol weight-volume percentage "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG] volume percentage % v/v "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG] A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. % (v/v) percent vol per vol volume percentage g per L A mass unit density which is equal to mass of an object in grams divided by the volume in liters. gram per liter gram per litre "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG] gram per liter g/L g/L "A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters." [UOC:GVG] milligram per milliliter milligram per millilitre mg per ml A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. milligram per milliliter mg/ml mg/ml A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. degree Fahrenheit F "A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [Wikipedia:Wikipedia] degree Fahrenheit pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia] pH ml/l ml/l milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. ml per L millilitre per litre "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [NIST:NIST] milliliter per liter g/dl gram per deciliter "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG] gram per decilitre A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. gram per deciliter g/dl colony forming unit per volume colony forming unit per volume "A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia] A concentration unit which a measure of viable bacterial numbers in a given volume. A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG] microliters per minute uL/min microlitres per minute nM^-1 s^-1 count per nanomolar second "A rate unit which is equal to one over one nanomolar second." [UOC:GVG] A rate unit which is equal to one over one nanomolar second. count per nanomolar second "A rate unit which is equal to one over one molar second." [UOC:GVG] count per molar second count per molar second A rate unit which is equal to one over one molar second. M^-1 s^-1 nM^-1 A rate unit which is equal to one over one nanomolar. 1/nM "A rate unit which is equal to one over one nanomolar." [UO:GVG] count per nanomolar count per nanomolar count per molar M^-1 1/M A rate unit which is equal to one over one molar. count per molar "A rate unit which is equal to one over one molar." [UO:GVG] "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG] A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. ug/L ug/L microgram per litre ng/ml microgram per liter microgram per liter milligram per kilogram per day "A dosage unit which is equal to 1 milligram per day of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC] 2 1 2 2 PMID:16417468 FMA FMA FMA-abduced-lr definitional https://github.com/obophenotype/uberon/wiki/The-neural-crest only in species that have a stomach Wikipedia:Vitelline_vein FMA Wikipedia:Vitelline_vein may be present in other parts in other species FMA right arch 4 in human embryology.ch FMA Wikipedia:Vitelline_vein Wikipedia PMID:22179203 FMA FMA FMA FMA FMA FMA FMA FMA FMA FMA FMA https://github.com/obophenotype/uberon/wiki/The-neural-crest FMA FMA FMA FMA cjm ZFA PMID:16417468 PMID:16417468 AAO https://github.com/geneontology/go-ontology/issues/16143 teleosts Mammals conservatively place at deuterostome, excluding acoelomates FMA true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP This can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).