Aaron Zhang Leigh Carmody Peter Robinson An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. Medical Action Ontology https://creativecommons.org/licenses/by/4.0/ Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label The user interface label is the label that should be placed on a datum when presented on a form or report Damion Dooley user interface label A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report Damion Dooley user interface feature 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 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 has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status 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. 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.obfoundry.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> definition_editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes true curator_notes curator note curator notes term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand expression to OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by term replaced by An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. https://orcid.org/0000-0002-6601-2165 RO:0002174 uberon dubious_for_taxon true true dubious_for_taxon This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost dubious for taxon dubious_for_taxon S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S https://orcid.org/0000-0002-6601-2165 RO:0002175 applicable for taxon uberon present_in_taxon true true present_in_taxon present in taxon present_in_taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S defined by inverse logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of 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 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). RO:0002604 quality is_opposite_of true true is_opposite_of is opposite of is_opposite_of cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. cjm 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. A textual description of an axiom loss in this ontology compared to an external ontology. UBPROP:0000002 uberon axiom_lost_from_external_ontology true axiom_lost_from_external_ontology This annotation property may be replaced with an annotation property from an external ontology such as IAO axiom_lost_from_external_ontology A textual description of an axiom loss in this ontology compared to an external ontology. Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes Notes on the homology status of this class. An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. UBPROP:0000005 uberon external_comment true external_comment This annotation property may be replaced with an annotation property from an external ontology such as IAO external_comment An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. UBPROP:0000006 uberon implements_design_pattern true implements_design_pattern implements_design_pattern Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the how instances of this class vary across species. Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 uberon function_notes true function_notes function_notes Notes on the evolved function of instances of this class. Notes on the structure, composition or histology of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000010 uberon structure_notes true structure_notes structure_notes Notes on the structure, composition or histology of instances of this class. Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 uberon development_notes true development_notes development_notes Notes on the ontogenic development of instances of this class. Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes Notes on how similar or equivalent classes are represented in other ontologies. Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000013 uberon terminology_notes true terminology_notes terminology_notes Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. UBPROP:0000100 uberon is_count_of true is_count_of is count of A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates) UBPROP:0000101 uberon preceding_element_is true preceding_element_is preceding element is A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates) x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch. gill arch N = PA N-2. the term branchial_arch is ambiguous. UBPROP:0000103 uberon pharyngeal_arch_number true pharyngeal_arch_number pharyngeal arch number x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch. FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 uberon fma_set_term true fma_set_term fma_set_term FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term FMA INN IUPAC NAME Preliminary entries Annotated by 3rd party Manually annotated by ChEBI Team Term not to be used for direct annotation Term not to be used for direct manual annotation AGR slim Aspergillus GO slim Candida GO slim ChEMBL protein targets summary Drosophila GO slim FlyBase Drosophila GO ribbon slim Generic GO slim Metagenomics GO slim Mouse GO slim PIR GO slim Plant GO slim Fission yeast GO slim Yeast GO slim Abnormal/normal slim Attribute slim cell_quality Pathology slim Value slim eco subset abbreviation A historic synonym, no longer encouraged dubious or contested synonym a synonym made on the basis of a possibly homologous structure in another species preferred term when talking about an instance of this class in Homo sapiens indicates that a synonym is used in an inconsistent or confusing way, typically between species latin term a mis-spelling that is in common use and thus recorded synonym that is inappropriate for mammals expert consultation and attribution required plural term taxonomic disambiguation CUMBO developmental_classification A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes. EFO slim derived from the union of EHDAA2 and EMAPA - still to be checked functional_classification Subset consisting of classes creating for grouping purposes A grouping class that depends on an assumption of homology between subclasses classes that have some inconsistency with FMA somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads abstract class brought in to group ontology classes but not informative organs, excluding individual muscles and skeletal elements Phenotype slim A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA Uberon slim - subset that excludes obscure terms and deep compositional terms Indicates that the class encompasses classes from other AOs that have not been verified abstract upper-level terms not directly useful for analysis core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO uberon dc-contributor true dc-contributor contributor uberon dc-creator true dc-creator creator uberon dc-description true dc-description description uberon dc-source true dc-source derived from resource uberon dc-title true dc-title title An image of the item. ,In Protege, this can be a URL. subset_property consider has_alternative_id has broad synonym has_broad_synonym database cross reference database_cross_reference has_exact_synonym has narrow synonym has_narrow_synonym has_obo_namespace has_related_synonym has_scope has synonym has_synonym_type in_subset shorthand label label label uberon seeAlso true seeAlso see also uberon depicted_by true depicted_by depicted by uberon foaf-page true foaf-page page 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) 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 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 BFO:0000050 external quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL: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) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. 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 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 BFO:0000051 chebi_ontology external quality uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) 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 BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes 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 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 external occurs_in 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 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 bisects an organism from head end to opposite end of body or tail: bearer cjm 2009-07-31T02:15:46Z BSPO:0000096 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 bisects an organism from head end to opposite end of body or tail: bearer x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). 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 bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 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 bisects an organism from back (e.g. spinal column) to front (e.g. belly). 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 bisects an organism from head end to opposite end of body or tail. BSPO:0000099 caudal_to 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 bisects an organism from head end to opposite end of body or tail. x proximal_to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 uberon proximal_to proximal_to proximal_to x proximal_to y iff x is closer to the point of attachment with the body than y. 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 bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 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 bisects an organism from back (e.g. spinal column) to front (e.g. belly). Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 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. Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:0000120 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 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 left and right portions, X is part_of the right portion. BSPO:0000121 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 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 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 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 proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in_proximal_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:PATO_mtg_2009 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in_distal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X 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 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 X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost_part_of X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y This relation holds when both the deep_to and ajdacent_to relationship similarly hold. BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost_part_of X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y X intersects_median_plane of iff X crosses the midine plane of Y. BSPO:0005001 uberon intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects_midsagittal_plane_of BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in_dorsal_side_of has taxonomic identifier This document is about information artifacts and their representations is_about is 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 A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by 2020-01-28T19:01:13Z avoided behavior 2019-06-12T14:23:27Z avoided medical action 2019-07-12T14:23:27Z avoided food inheres in this fragility inheres in this vase this red color inheres in this apple 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 inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility 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 uberon bearer_of bearer_of bearer of bearer of 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 a relation between a continuant and a process, in which the continuant is somehow involved in the process 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) 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 has participant 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 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 role of 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 RO:0000086 uberon 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 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 https://code.google.com/p/obo-relations/wiki/ROAndTime 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 RO:0001019 uberon contains contains 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 https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 uberon located_in located_in located in 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 RO:0002000 uberon boundary_of boundary_of 2D boundary of 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. David Osumi-Sutherland has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply FMA:85999 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. 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 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 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 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 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 has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand dos 2017-09-17T13:52:24Z 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. 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 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. 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 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. 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 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. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of 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 A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps overlaps true 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. David Osumi-Sutherland <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 http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland 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 two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' RO:0002158 uberon homologous_to homologous_to VBO calls this homologous_to homologous_to shares ancestor with 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). Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. 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 Connection does not imply overlaps. connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. 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). Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. 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. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) 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 Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. 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 attaches_to_part_of attached to part of attaches_to_part_of true true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. relation between an artery and the structure is supplies with blood. 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 arterial supply of uberon supplies supplies source: FMA supplies supplies arterial supply of FMA:86003 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 drains blood from drains from uberon drains drains source: Wikipedia 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 uberon has_component has_component 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. 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 participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, 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 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 directly develops into 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 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. 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. 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_0000053 some (RO_0000054 only ?Y) RO:0002215 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_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent has active participant obsolete has active participant 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 x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y Chris Mungall RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded_by x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y 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. x adjacent_to y iff: x and y share a boundary This relation acts as a join point with BSPO Chris Mungall RO:0002220 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 inverse of surrounded_by Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds inverse of surrounded_by 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 https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Relation between occurrents, shares a start boundary with. inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Relation between occurrents, shares a start boundary with. Allen: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 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 This relation take from EHDAA2 - precise semantics yet to be defined develops in develops_in Relation between occurrents, shares an end boundary with. inverse of ends with Chris Mungall RO:0002229 finishes uberon ends ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes 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 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 Chris Mungall starts with process that occurs in 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 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 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 at the beginning of p. Chris Mungall produces has output 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 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to developmentally_contributes_to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. 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 anatomical structure type T to T', where T' develops_from T Chris Mungall David Osumi-Sutherland Melissa Haendel 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 sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by developmentally_induced_by t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. GO:0001759 Inverse of developmentally induced by Chris Mungall 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 uberon developmentally_preceded_by 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 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. 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. affects 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 Chris Mungall replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of cjm 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 cjm 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 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 inheres in part of Chris Mungall inheres in part of true A relationship that holds via some environmental process Chris Mungall 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 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 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. 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 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of 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 involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by 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 uberon member_of member_of 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 uberon output_of output_of output of output 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 Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_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. m has_muscle_origin s iff m is attaches_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. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has muscle origin has_muscle_origin We need to import uberon muscle to create a stricter domain constraint m has_muscle_origin s iff m is attaches_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. 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. 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. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002373 uberon has_muscle_insertion has_muscle_insertion The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles has muscle insertion has_muscle_insertion We need to import uberon muscle into RO to use as 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. 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. Chris Mungall 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) 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. Chris Mungall 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 drains into tributary_of tributary_of tributary of tributary_of http://en.wikipedia.org/wiki/Tributary drains into dbpowl:drainsTo 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 spatially coextensive with 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 we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve Chris Mungall 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 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 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 Chris Mungall 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 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 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 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes 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 p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall 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. Chris Mungall 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. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall 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 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 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 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 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 enables activity in 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. 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. Chris Mungall 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. in pairwise interaction with interacts with 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 molecularly interacts with 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. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall molecularly controls activity directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall activates molecularly increases activity of activity 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. x composed_primarily_of y iff: more than half of the mass of x is made from parts of y Chris Mungall RO:0002473 uberon RO:0002473 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 has part that occurs in true Chris Mungall is kinase activity Chris Mungall 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. relation between structure and stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. 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). Chris Mungall RO:0002488 begins_to_exist_during uberon RO:0002488 existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. Relation between continuant and occurrent, such that c comes into existence at the start of p. 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). Chris Mungall RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant and occurrent, such that c comes into existence at the start of p. 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)) Chris Mungall 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 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). Chris Mungall RO:0002492 ceases_to_exist_during uberon RO:0002492 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. Relation between continuant and occurrent, such that c ceases to exist at the end of p. 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). Chris Mungall 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 Relation between continuant and occurrent, such that c ceases to exist at the end of p. 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 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 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 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_transformation_of immediately transforms from SIO:000658 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). Chris Mungall 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. Chris Mungall 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 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. 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. 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. causal relation between material entities 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. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall 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 sekeletal support has supporting framework 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. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. 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. Chris Mungall Wikipedia:Antagonist_(muscle) RO:0002568 uberon has_muscle_antagonist has_muscle_antagonist has muscle antagonist has_muscle_antagonist m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. inverse of branching part of Chris Mungall RO:0002569 uberon has_branching_part has_branching_part has branching part 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. Chris Mungall GOC:cjm 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 Chris Mungall RO:0002572 uberon luminal_space_of luminal_space_of luminal space of A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. has modifier inverse of has skeleton Chris Mungall 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. Chris Mungall directly regulates (processual) 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 has part structure that is capable 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 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. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. 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. capable of positively regulating Inverse of 'causal agent in process' process has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. obsolete related via dependence to related via dependence to true Process(P1) directly postively regulates process(P2) 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 P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) 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 P1 directly negatively regulates P2. directly negatively regulates (process to process) 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 A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. cjm 2017-11-05T04:06:02Z disease has location 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 enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z 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 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 acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. cjm 2018-09-26T00:00:32Z disease relationship chebi_ontology has_functional_parent false false has functional parent 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_enantiomer_of true false is enantiomer 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. carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for 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. uberon existence_starts_and_ends_during existence starts and ends during uberon extends_fibers_into extends_fibers_into 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 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. 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. uberon sexually_homologous_to sexually_homologous_to 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 . uberon transitively_anteriorly_connected_to transitively anteriorly connected to . uberon transitively_connected_to transitively_connected to . uberon transitively_distally_connected_to transitively distally connected to . . uberon transitively_proximally_connected_to transitively proximally connected to . 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 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] 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. 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 heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso 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]) 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] 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. 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) (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] 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 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 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. 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] 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. 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] 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 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 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] 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 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. 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. (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] specifically dependent continuant 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 (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 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. 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. 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] 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-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 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] 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] material MaterialEntity 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 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. 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] 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] 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 anatomical entity anatomical structure connected anatomical structure material anatomical entity immaterial anatomical entity cell part (CARO) cell part multi-cell-part structure neuron projection bundle multicellular anatomical structure biological entity 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 The conjugate base of gamma-amino-beta-hydroxybutyric acid arising from deprotonation of the carboxy group. -1 C4H8NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8)/p-1 YQGDEPYYFWUPGO-UHFFFAOYSA-M 118.11126 118.05097 NCC(O)CC([O-])=O CAS:352-21-6 KEGG:C03678 4-Amino-3-hydroxybutanoate chebi_ontology CHEBI:11955 4-amino-3-hydroxybutanoate CAS:352-21-6 KEGG COMPOUND KEGG:C03678 ChEBI 4-Amino-3-hydroxybutanoate KEGG_COMPOUND Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. chebi_ontology Mycoplasma genitalium metabolites CHEBI:131604 Mycoplasma genitalium metabolite Mycoplasma genitalium metabolites ChEBI A steroid compound with a structure based on a 27-carbon (cholestane) skeleton. chebi_ontology C27-steroids CHEBI:131619 C27-steroid C27-steroids ChEBI A steroid compound with a structure based on a 24-carbon (cholane) skeleton. chebi_ontology C24-steroids CHEBI:131620 C24-steroid C24-steroids ChEBI Any steroid (or derivative) based on a cholane skeleton. chebi_ontology cholane derivatives CHEBI:131657 cholane derivative cholane derivatives ChEBI Any steroid acid anion based on a cholanic acid skeleton. PMID:1527482 chebi_ontology cholanic acid anions cholanoic acid anion cholanoic acid anions CHEBI:131878 cholanic acid anion PMID:1527482 SUBMITTER cholanic acid anions ChEBI cholanoic acid anion SUBMITTER cholanoic acid anions ChEBI 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 Any member of the class of benzoquinones that is 1,4-benzoquinone or its C-substituted derivatives. 0 C6O2R4 104.063 103.98983 O=C1C(*)=C(*)C(=O)C(*)=C1* chebi_ontology a quinone p-benzoquinones para-benzoquinones CHEBI:132124 1,4-benzoquinones a quinone UniProt p-benzoquinones ChEBI para-benzoquinones ChEBI Any quinone in which one or more of the carbons making up the quinone moiety is substituted by a hydroxy group. chebi_ontology hydroxyquinones CHEBI:132130 hydroxyquinone hydroxyquinones ChEBI Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa. Wikipedia:Volatile_organic_compound chebi_ontology VOC VOCs volatile organic compounds CHEBI:134179 volatile organic compound VOC ChEBI VOCs ChEBI volatile organic compounds ChEBI A compound that, on administration, undergoes conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the active agent for which it is a pro-agent. PMID:26449612 chebi_ontology pro-agents proagent proagents CHEBI:136859 pro-agent PMID:26449612 Europe PMC pro-agents ChEBI proagent ChEBI proagents 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 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 Any saturated fatty acid containing 4 carbons. 0 CHO2R 45.017 44.99765 *C(O)=O chebi_ontology CHEBI:140601 fatty acid 4:0 0 C62H88CoN13O14PR 1329.350 1328.56433 [Co-3]1234(N5C6=C(C7=[N+]4C(=CC8=[N+]3C(=C(C9=[N+]2[C@@]([C@]5([C@@H]([C@@]6(C)CCC(=O)NC[C@H](OP(O[C@@H]%10[C@H](O[C@H](N%11C=[N+]1C%12=CC(=C(C=C%12%11)C)C)[C@@H]%10O)CO)(=O)[O-])C)CC(=O)N)[H])([C@]([C@@H]9CCC(N)=O)(CC(=O)N)C)C)C)[C@](C)([C@@H]8CCC(=O)N)CC(N)=O)C([C@@H]7CCC(=O)N)(C)C)C)* MetaCyc:CPD-20938 chebi_ontology an alkylcob(III)alamin CHEBI:140785 alkylcob(III)alamin MetaCyc:CPD-20938 SUBMITTER an alkylcob(III)alamin UniProt An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1 WHUUTDBJXJRKMK-UHFFFAOYSA-M 146.12136 146.04588 [NH3+]C(CCC([O-])=O)C([O-])=O Gmelin:327908 glutamate(1-) hydrogen glutamate chebi_ontology 2-ammoniopentanedioate glutamate glutamic acid monoanion CHEBI:14321 glutamate(1-) Gmelin:327908 Gmelin glutamate(1-) JCBN hydrogen glutamate IUPAC 2-ammoniopentanedioate IUPAC glutamate UniProt glutamic acid monoanion JCBN 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 A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 NC(CS)C(O)=O CHEBI:14061 CHEBI:23508 CHEBI:4050 Beilstein:1721406 CAS:3374-22-9 Gmelin:2933 KEGG:C00736 KNApSAcK:C00001351 KNApSAcK:C00007323 PMID:17439666 PMID:25181601 Reaxys:1721406 Wikipedia:Cysteine Cysteine cysteine chebi_ontology 2-Amino-3-mercaptopropionic acid 2-amino-3-mercaptopropanoic acid 2-amino-3-sulfanylpropanoic acid C Cys Cystein Hcys Zystein cisteina CHEBI:15356 cysteine Beilstein:1721406 Beilstein CAS:3374-22-9 ChemIDplus CAS:3374-22-9 KEGG COMPOUND CAS:3374-22-9 NIST Chemistry WebBook Gmelin:2933 Gmelin PMID:17439666 Europe PMC PMID:25181601 Europe PMC Reaxys:1721406 Reaxys Cysteine KEGG_COMPOUND cysteine ChEBI cysteine IUPAC 2-Amino-3-mercaptopropionic acid KEGG_COMPOUND 2-amino-3-mercaptopropanoic acid JCBN 2-amino-3-sulfanylpropanoic acid IUPAC C ChEBI Cys ChEBI Cystein ChEBI Hcys IUPAC Zystein ChEBI cisteina ChEBI A simple monocarboxylic acid containing two carbons. acetic acid http://langual.org 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 Codex::260 Drug_Central:4211 Europe::260 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 http://www.langual.org/langual_thesaurus.asp?termid=B2977 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 acetic acid, glacial CHEBI:15366 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): acidity regulator, preservative. 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 The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain. glycine http://langual.org 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06664 75.03203 NCC(O)=O CHEBI:10792 CHEBI:14344 CHEBI:24368 CHEBI:42964 CHEBI:5460 Beilstein:635782 CAS:56-40-6 Codex::640 DrugBank:DB00145 Drug_Central:1319 ECMDB:ECMDB00123 Europe::640 Gmelin:1808 HMDB:HMDB0000123 KEGG:C00037 KEGG:D00011 KNApSAcK:C00001361 MetaCyc:GLY PDBeChem:GLY PMID:10930630 PMID:11019925 PMID:11174716 PMID:11542461 PMID:11806864 PMID:12631515 PMID:12754315 PMID:12770151 PMID:12921899 PMID:15331688 PMID:15388434 PMID:15710237 PMID:16105183 PMID:16151895 PMID:16214212 PMID:16417482 PMID:16444815 PMID:16664855 PMID:16901953 PMID:16918424 PMID:16986325 PMID:16998855 PMID:17154252 PMID:17383967 PMID:17582620 PMID:17970719 PMID:18079355 PMID:18396796 PMID:18440992 PMID:18593588 PMID:18816054 PMID:18840508 PMID:19028609 PMID:19120667 PMID:19449910 PMID:19526731 PMID:19544666 PMID:19738917 PMID:19916621 PMID:19924257 PMID:21751272 PMID:22044190 PMID:22079563 PMID:22234938 PMID:22264337 PMID:22293292 PMID:22401276 PMID:22434786 Reaxys:635782 Wikipedia:Glycine YMDB:YMDB00016 http://www.langual.org/langual_thesaurus.asp?termid=B3110 GLYCINE Glycine aminoacetic acid glycine chebi_ontology Aminoacetic acid Aminoessigsaeure G Gly Glycin Glycocoll Glykokoll Glyzin H2N-CH2-COOH Hgly Leimzucker aminoethanoic acid CHEBI:15428 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): flavour enhancer. glycine Beilstein:635782 Beilstein CAS:56-40-6 ChemIDplus CAS:56-40-6 KEGG COMPOUND CAS:56-40-6 NIST Chemistry WebBook Drug_Central:1319 DrugCentral Gmelin:1808 Gmelin PMID:10930630 Europe PMC PMID:11019925 Europe PMC PMID:11174716 Europe PMC PMID:11542461 Europe PMC PMID:11806864 Europe PMC PMID:12631515 Europe PMC PMID:12754315 Europe PMC PMID:12770151 Europe PMC PMID:12921899 Europe PMC PMID:15331688 Europe PMC PMID:15388434 Europe PMC PMID:15710237 Europe PMC PMID:16105183 Europe PMC PMID:16151895 Europe PMC PMID:16214212 Europe PMC PMID:16417482 Europe PMC PMID:16444815 Europe PMC PMID:16664855 Europe PMC PMID:16901953 Europe PMC PMID:16918424 Europe PMC PMID:16986325 Europe PMC PMID:16998855 Europe PMC PMID:17154252 Europe PMC PMID:17383967 Europe PMC PMID:17582620 Europe PMC PMID:17970719 Europe PMC PMID:18079355 Europe PMC PMID:18396796 Europe PMC PMID:18440992 Europe PMC PMID:18593588 Europe PMC PMID:18816054 Europe PMC PMID:18840508 Europe PMC PMID:19028609 Europe PMC PMID:19120667 Europe PMC PMID:19449910 Europe PMC PMID:19526731 Europe PMC PMID:19544666 Europe PMC PMID:19738917 Europe PMC PMID:19916621 Europe PMC PMID:19924257 Europe PMC PMID:21751272 Europe PMC PMID:22044190 Europe PMC PMID:22079563 Europe PMC PMID:22234938 Europe PMC PMID:22264337 Europe PMC PMID:22293292 Europe PMC PMID:22401276 Europe PMC PMID:22434786 Europe PMC Reaxys:635782 Reaxys GLYCINE PDBeChem Glycine KEGG_COMPOUND aminoacetic acid IUPAC glycine IUPAC Aminoacetic acid KEGG_COMPOUND Aminoessigsaeure ChEBI G ChEBI Gly KEGG_COMPOUND Glycin ChemIDplus Glycocoll ChemIDplus Glykokoll ChEBI Glyzin ChEBI H2N-CH2-COOH IUPAC Hgly IUPAC Leimzucker ChemIDplus aminoethanoic acid ChEBI aminoethanoic acid JCBN Any alpha-amino acid having L-configuration at the alpha-carbon. 0 C2H4NO2R 74.05870 74.02420 N[C@@H]([*])C(O)=O CHEBI:13072 CHEBI:13243 CHEBI:13797 CHEBI:21224 CHEBI:6175 KEGG:C00151 L-alpha-amino acid L-alpha-amino acids chebi_ontology L-2-Amino acid L-Amino acid L-alpha-amino acids CHEBI:15705 L-alpha-amino acid L-alpha-amino acid IUPAC L-alpha-amino acids IUPAC L-2-Amino acid KEGG_COMPOUND L-Amino acid KEGG_COMPOUND L-alpha-amino acids ChEBI A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it. 0 CH3OR 31.034 31.01839 *C(O)([H])[H] CHEBI:13676 CHEBI:14887 CHEBI:26262 CHEBI:57489 CHEBI:8406 KEGG:C00226 Primary alcohol chebi_ontology 1-Alcohol a primary alcohol primary alcohols CHEBI:15734 primary alcohol Primary alcohol KEGG_COMPOUND 1-Alcohol KEGG_COMPOUND a primary alcohol UniProt primary alcohols ChEBI Any N-acyl-amino acid in which the amino acid moiety has D configuration. 0 C3H3NO3R2 101.06080 101.01129 OC(=O)[C@@H]([*])NC([*])=O CHEBI:12474 CHEBI:21631 CHEBI:7224 chebi_ontology CHEBI:15778 N-acyl-D-amino acid +1 C62H90CoN13O15P InChI=1S/C62H90N13O14P.Co.H2O/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;1H2/q;+3;/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 YOZNUFWCRFCGIH-WZHZPDAFSA-L 1347.36310 1346.57434 [H][O+]([H])[Co-3]1234N5C6=C(C)C7=[N+]1C(=CC1=[N+]2C(=C(C)C2=[N+]3[C@@](C)([C@@]5([H])[C@H](CC(N)=O)[C@@]6(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@@H]3[C@@H](CO)O[C@@H]([C@@H]3O)n3c[n+]4c4cc(C)c(C)cc34)[C@@](C)(CC(N)=O)[C@@H]2CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]1CCC(N)=O)C(C)(C)[C@@H]7CCC(N)=O CHEBI:13851 CHEBI:22589 CHEBI:2794 CAS:13422-52-1 KEGG:C00992 Aquacob(III)alamin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-aquacobamide aquacob(III)alamin chebi_ontology Aquacobalamin aquacobalamin vitamin B-12a CHEBI:15852 aquacob(III)alamin CAS:13422-52-1 ChemIDplus CAS:13422-52-1 KEGG COMPOUND Aquacob(III)alamin KEGG_COMPOUND Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-aquacobamide IUPAC aquacob(III)alamin UniProt Aquacobalamin KEGG_COMPOUND aquacobalamin CBN vitamin B-12a CBN Any 3-hydroxy steroid whose skeleton is closely related to cholestan-3-ol (additional carbon atoms may be present in the side chain). 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCC(C4)O)C CHEBI:13688 CHEBI:15114 CHEBI:26771 CHEBI:9266 KEGG:C00370 LIPID_MAPS_class:LMST01 MetaCyc:Sterols Wikipedia:Sterol Sterol sterols chebi_ontology 3-hydroxysteroids a sterol CHEBI:15889 sterol LIPID_MAPS_class:LMST01 LIPID MAPS Sterol KEGG_COMPOUND sterols IUPAC 3-hydroxysteroids ChEBI a sterol UniProt An optically active form of glutamic acid having D-configuration. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-N 147.12930 147.05316 N[C@H](CCC(O)=O)C(O)=O CHEBI:21023 CHEBI:4183 Beilstein:1723800 CAS:6893-26-1 DrugBank:DB02517 Gmelin:201189 HMDB:HMDB0003339 KEGG:C00217 KNApSAcK:C00019577 MetaCyc:D-GLT PDBeChem:DGL Reaxys:1723800 (2R)-2-aminopentanedioic acid D-Glutamic acid D-glutamic acid chebi_ontology (R)-2-aminopentanedioic acid D-2-Aminoglutaric acid D-Glutaminic acid D-Glutaminsaeure DGL glutamic acid D-form CHEBI:15966 D-glutamic acid Beilstein:1723800 Beilstein CAS:6893-26-1 ChemIDplus CAS:6893-26-1 KEGG COMPOUND CAS:6893-26-1 NIST Chemistry WebBook Gmelin:201189 Gmelin Reaxys:1723800 Reaxys (2R)-2-aminopentanedioic acid IUPAC D-Glutamic acid KEGG_COMPOUND D-glutamic acid IUPAC (R)-2-aminopentanedioic acid ChEBI D-2-Aminoglutaric acid KEGG_COMPOUND D-Glutaminic acid KEGG_COMPOUND D-Glutaminsaeure ChEBI DGL PDBeChem glutamic acid D-form ChemIDplus An optically active form of glutamic acid having L-configuration. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-N 147.12930 147.05316 N[C@@H](CCC(O)=O)C(O)=O CHEBI:21304 CHEBI:42825 CHEBI:6224 BPDB:2297 Beilstein:1723801 CAS:56-86-0 DrugBank:DB00142 Drug_Central:1310 Gmelin:3502 HMDB:HMDB0000148 KEGG:C00025 KEGG:D00007 KNApSAcK:C00001358 LINCS:LSM-36375 MetaCyc:GLT PDBeChem:GLU_LFOH PMID:15739367 PMID:15930465 PMID:16719819 PMID:16892196 PMID:19581495 PMID:22219301 PMID:22735334 Reaxys:1723801 Wikipedia:L-Glutamic_Acid (2S)-2-aminopentanedioic acid L-Glutamic acid L-glutamic acid chebi_ontology (S)-2-aminopentanedioic acid (S)-glutamic acid E GLUTAMIC ACID Glu Glutamate L-Glu L-Glutaminic acid L-Glutaminsaeure acide glutamique acido glutamico acidum glutamicum glutamic acid CHEBI:16015 L-glutamic acid Beilstein:1723801 Beilstein CAS:56-86-0 ChemIDplus CAS:56-86-0 KEGG COMPOUND CAS:56-86-0 NIST Chemistry WebBook Drug_Central:1310 DrugCentral Gmelin:3502 Gmelin PMID:15739367 Europe PMC PMID:15930465 Europe PMC PMID:16719819 Europe PMC PMID:16892196 Europe PMC PMID:19581495 Europe PMC PMID:22219301 Europe PMC PMID:22735334 Europe PMC Reaxys:1723801 Reaxys (2S)-2-aminopentanedioic acid IUPAC L-Glutamic acid KEGG_COMPOUND L-glutamic acid IUPAC (S)-2-aminopentanedioic acid ChEBI (S)-glutamic acid NIST_Chemistry_WebBook E ChEBI GLUTAMIC ACID PDBeChem Glu ChEBI Glutamate KEGG_COMPOUND L-Glu ChEBI L-Glutaminic acid KEGG_COMPOUND L-Glutaminsaeure ChEBI acide glutamique ChEBI acido glutamico ChEBI acidum glutamicum ChEBI glutamic acid ChEBI A gamma-amino acid comprising 4-aminobutyric acid having a 2-hydroxy substituent. 0 C4H9NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8) YQGDEPYYFWUPGO-UHFFFAOYSA-N 119.11920 119.05824 NCC(O)CC(O)=O CHEBI:1780 CHEBI:20311 Beilstein:1721708 Beilstein:1752568 CAS:352-21-6 Drug_Central:1263 KEGG:C03678 KEGG:D00174 4-amino-3-hydroxybutanoic acid gamma-Amino-beta-hydroxybutyric acid chebi_ontology 3-hydroxy-GABA 4-Amino-3-hydroxybutanoic acid 4-amino-3-hydroxybutyric acid GABOB CHEBI:16080 gamma-amino-beta-hydroxybutyric acid Beilstein:1721708 Beilstein Beilstein:1752568 Beilstein CAS:352-21-6 ChemIDplus CAS:352-21-6 KEGG COMPOUND Drug_Central:1263 DrugCentral 4-amino-3-hydroxybutanoic acid IUPAC gamma-Amino-beta-hydroxybutyric acid KEGG_COMPOUND 3-hydroxy-GABA ChemIDplus 4-Amino-3-hydroxybutanoic acid KEGG_COMPOUND 4-amino-3-hydroxybutyric acid ChemIDplus GABOB KEGG_COMPOUND A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. 0 C27H46O InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1 HVYWMOMLDIMFJA-DPAQBDIFSA-N 386.655 386.35487 C1[C@@]2([C@]3(CC[C@]4([C@]([C@@]3(CC=C2C[C@H](C1)O)[H])(CC[C@@]4([C@H](C)CCCC(C)C)[H])[H])C)[H])C CHEBI:13982 CHEBI:23204 CHEBI:3659 CHEBI:41564 Beilstein:2060565 CAS:57-88-5 DrugBank:DB04540 Gmelin:550297 HMDB:HMDB0000067 KEGG:C00187 KEGG:D00040 KNApSAcK:C00003648 LIPID_MAPS_instance:LMST01010001 MetaCyc:CHOLESTEROL PDBeChem:CLR PMID:10901445 PMID:11412894 PMID:16341241 PMID:24287311 PMID:25308664 PMID:25451949 PMID:25522988 PMID:25658343 PMID:25977713 PMID:4696527 PMID:8838010 Reaxys:2060565 Wikipedia:Cholesterol CHOLESTEROL Cholesterol cholest-5-en-3beta-ol cholesterol chebi_ontology (3beta,14beta,17alpha)-cholest-5-en-3-ol Cholest-5-en-3beta-ol Cholesterin CHEBI:16113 cholesterol Beilstein:2060565 Beilstein CAS:57-88-5 ChemIDplus CAS:57-88-5 KEGG COMPOUND CAS:57-88-5 NIST Chemistry WebBook Gmelin:550297 Gmelin LIPID_MAPS_instance:LMST01010001 LIPID MAPS PMID:10901445 Europe PMC PMID:11412894 Europe PMC PMID:16341241 Europe PMC PMID:24287311 Europe PMC PMID:25308664 Europe PMC PMID:25451949 Europe PMC PMID:25522988 Europe PMC PMID:25658343 Europe PMC PMID:25977713 Europe PMC PMID:4696527 Europe PMC PMID:8838010 Europe PMC Reaxys:2060565 Reaxys CHOLESTEROL PDBeChem Cholesterol KEGG_COMPOUND cholest-5-en-3beta-ol IUPAC cholesterol UniProt (3beta,14beta,17alpha)-cholest-5-en-3-ol IUPAC Cholest-5-en-3beta-ol KEGG_COMPOUND Cholesterin NIST_Chemistry_WebBook 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 carbonyl group with two C-bound amine groups. carbamide http://langual.org 0 CH4N2O InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) XSQUKJJJFZCRTK-UHFFFAOYSA-N 60.05534 60.03236 NC(N)=O CHEBI:15292 CHEBI:27218 CHEBI:46379 CHEBI:9888 Beilstein:635724 CAS:57-13-6 Codex::927b DrugBank:DB03904 Drug_Central:4264 ECMDB:ECMDB04172 Europe::927b Gmelin:1378 HMDB:HMDB0000294 KEGG:C00086 KEGG:D00023 KNApSAcK:C00007314 MetaCyc:UREA PDBeChem:URE PMID:18037357 PMID:22770225 PPDB:1728 Reaxys:635724 UM-BBD_compID:c0165 Wikipedia:Urea YMDB:YMDB00003 http://www.langual.org/langual_thesaurus.asp?termid=B3058 UREA Urea urea chebi_ontology 1728 Carbamide E927b H2NC(O)NH2 Harnstoff Karbamid carbamide carbonyldiamide ur uree urea (carbamide) CHEBI:16199 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): flour treatment agent. urea Beilstein:635724 Beilstein CAS:57-13-6 ChemIDplus CAS:57-13-6 KEGG COMPOUND CAS:57-13-6 NIST Chemistry WebBook Drug_Central:4264 DrugCentral Gmelin:1378 Gmelin PMID:18037357 Europe PMC PMID:22770225 Europe PMC Reaxys:635724 Reaxys UM-BBD_compID:c0165 UM-BBD UREA PDBeChem Urea KEGG_COMPOUND urea IUPAC urea UniProt 1728 PPDB Carbamide KEGG_COMPOUND E927b ChEBI H2NC(O)NH2 ChEBI Harnstoff NIST_Chemistry_WebBook Karbamid ChEBI carbamide ChEBI carbonyldiamide NIST_Chemistry_WebBook ur IUPAC uree ChEBI An optically active form of cysteine having D-configuration. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-N 121.15922 121.01975 N[C@H](CS)C(O)=O CHEBI:12919 CHEBI:20921 CHEBI:4111 CHEBI:41887 Beilstein:1721407 CAS:921-01-7 DrugBank:DB03201 ECMDB:ECMDB03417 Gmelin:363236 HMDB:HMDB0003417 KEGG:C00793 KNApSAcK:C00007323 PDBeChem:DCY PMID:13761469 PMID:23340406 PMID:24800864 Reaxys:1721407 YMDB:YMDB00913 D-CYSTEINE D-Cysteine D-cysteine chebi_ontology (2S)-2-amino-3-mercaptopropanoic acid (2S)-2-amino-3-sulfanylpropanoic acid (S)-2-amino-3-mercaptopropanoic acid D-Amino-3-mercaptopropionic acid D-Cystein D-Zystein DCY CHEBI:16375 D-cysteine Beilstein:1721407 Beilstein CAS:921-01-7 ChemIDplus CAS:921-01-7 KEGG COMPOUND Gmelin:363236 Gmelin PMID:13761469 Europe PMC PMID:23340406 Europe PMC PMID:24800864 Europe PMC Reaxys:1721407 Reaxys D-CYSTEINE PDBeChem D-Cysteine KEGG_COMPOUND D-cysteine IUPAC (2S)-2-amino-3-mercaptopropanoic acid JCBN (2S)-2-amino-3-sulfanylpropanoic acid IUPAC (S)-2-amino-3-mercaptopropanoic acid ChEBI D-Amino-3-mercaptopropionic acid KEGG_COMPOUND D-Cystein ChEBI D-Zystein ChEBI DCY PDBeChem Any benzoquinone derived from 2,3-dimethoxy-5-methylbenzoquinone; one of a group of naturally occurring homologues. The redox-active quinoid moiety usually carries a polyprenoid side chain at position 6, the number of isoprenoid units in which is species-specific. Ubiquinones are involved in the control of mitochondrial electron transport, and are also potent anti-oxidants. 0 C9H10O4(C5H8)n CHEBI:15279 CHEBI:27186 CHEBI:9852 CAS:1339-63-5 KEGG:C00399 PMID:15788391 PMID:7599208 Ubiquinones chebi_ontology CoQ Coenzym Q Coenzyme Q Koenzym Q Q Ubichinon Ubiquinone a ubiquinone coenzyme Q coenzymes Q mitochondrial ubiquinone mitochondrial ubiquinones mitoquinones CHEBI:16389 ubiquinones CAS:1339-63-5 ChemIDplus CAS:1339-63-5 KEGG COMPOUND PMID:15788391 Europe PMC PMID:7599208 Europe PMC Ubiquinones ChemIDplus CoQ KEGG_COMPOUND Coenzym Q ChEBI Coenzyme Q KEGG_COMPOUND Koenzym Q ChEBI Q KEGG_COMPOUND Ubichinon ChEBI Ubiquinone KEGG_COMPOUND a ubiquinone UniProt coenzyme Q ChEBI coenzymes Q ChEBI mitochondrial ubiquinone ChEBI mitochondrial ubiquinones ChEBI mitoquinones ChEBI The R-enantiomer of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-N 105.09262 105.04259 N[C@H](CO)C(O)=O CHEBI:13019 CHEBI:143888 CHEBI:21090 CHEBI:42262 CHEBI:4245 Beilstein:1721403 CAS:312-84-5 DrugBank:DB03929 ECMDB:ECMDB03406 Gmelin:1041392 HMDB:HMDB0003406 KEGG:C00740 MetaCyc:D-SERINE PDBeChem:DSN PMID:11864625 PMID:12850593 PMID:19212759 PMID:19217074 PMID:21295046 PMID:21914633 PMID:21956571 PMID:22117694 PMID:22128843 PMID:22266400 PMID:22280157 PMID:22362148 PMID:22369458 PMID:22445805 PMID:22465696 PMID:22486999 Reaxys:1721403 YMDB:YMDB00284 D-SERINE D-Serine D-serine chebi_ontology (2R)-2-amino-3-hydroxypropanoic acid (R)-2-Amino-3-hydroxy-propionic acid (R)-2-amino-3-hydroxypropanoic acid D-Serin DSN CHEBI:16523 D-serine Beilstein:1721403 Beilstein CAS:312-84-5 ChemIDplus CAS:312-84-5 KEGG COMPOUND CAS:312-84-5 NIST Chemistry WebBook Gmelin:1041392 Gmelin PMID:11864625 Europe PMC PMID:12850593 Europe PMC PMID:19212759 Europe PMC PMID:19217074 Europe PMC PMID:21295046 Europe PMC PMID:21914633 Europe PMC PMID:21956571 Europe PMC PMID:22117694 Europe PMC PMID:22128843 Europe PMC PMID:22266400 Europe PMC PMID:22280157 Europe PMC PMID:22362148 Europe PMC PMID:22369458 Europe PMC PMID:22445805 Europe PMC PMID:22465696 Europe PMC PMID:22486999 Europe PMC Reaxys:1721403 Reaxys D-SERINE PDBeChem D-Serine KEGG_COMPOUND D-serine IUPAC (2R)-2-amino-3-hydroxypropanoic acid IUPAC (R)-2-Amino-3-hydroxy-propionic acid ChEMBL (R)-2-amino-3-hydroxypropanoic acid ChEBI D-Serin ChEBI DSN PDBeChem 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 carbohidrato carbohidratos glucide glucides glucido glucidos hydrates de carbone saccharide saccharides saccharidum CHEBI:16646 carbohydrate carbohydrate IUPAC carbohydrates IUPAC Kohlenhydrat ChEBI Kohlenhydrate ChEBI carbohidrato IUPAC carbohidratos IUPAC glucide ChEBI glucides ChEBI glucido ChEBI glucidos ChEBI hydrates de carbone ChEBI saccharide IUPAC saccharides IUPAC saccharidum ChEBI A ribonucleoside composed of a molecule of uracil attached to a ribofuranose moiety via a beta-N(1)-glycosidic bond. 0 C9H12N2O6 InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1 DRTQHJPVMGBUCF-XVFCMESISA-N 244.20146 244.06954 OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1ccc(=O)[nH]c1=O CHEBI:15296 CHEBI:27227 CHEBI:46386 CHEBI:46391 CHEBI:46460 CHEBI:9893 Beilstein:754904 CAS:58-96-8 DrugBank:DB02745 ECMDB:ECMDB00296 Gmelin:397474 HMDB:HMDB0000296 KEGG:C00299 KNApSAcK:C00019674 MetaCyc:URIDINE PDBeChem:URI PMID:12084455 PMID:15621516 PMID:16839635 PMID:17190852 PMID:22392515 PMID:22770225 Reaxys:754904 Wikipedia:Uridine YMDB:YMDB00127 URIDINE Uridine uridine chebi_ontology 1-beta-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione 1-beta-D-ribofuranosyluracil Urd Uridin beta-Uridine u CHEBI:16704 uridine Beilstein:754904 Beilstein CAS:58-96-8 ChemIDplus CAS:58-96-8 KEGG COMPOUND Gmelin:397474 Gmelin PMID:12084455 Europe PMC PMID:15621516 Europe PMC PMID:16839635 Europe PMC PMID:17190852 Europe PMC PMID:22392515 Europe PMC PMID:22770225 Europe PMC Reaxys:754904 Reaxys URIDINE PDBeChem Uridine KEGG_COMPOUND uridine IUPAC uridine UniProt 1-beta-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione ChEBI 1-beta-D-ribofuranosyluracil HMDB Urd CBN Uridin ChemIDplus beta-Uridine HMDB u ChEBI 0 C2H4NO2R 74.05870 74.02420 N[C@H]([*])C(O)=O CHEBI:12909 CHEBI:13625 CHEBI:20906 CHEBI:4097 KEGG:C00405 D-alpha-amino acid D-alpha-amino acids chebi_ontology D-Amino acid D-alpha-amino acids CHEBI:16733 D-alpha-amino acid D-alpha-amino acid ChEBI D-alpha-amino acids IUPAC D-Amino acid KEGG_COMPOUND D-alpha-amino acids ChEBI A dihydroxy-5beta-cholanic acid that is (5beta)-cholan-24-oic acid substituted by hydroxy groups at positions 3 and 7 respectively. 0 C24H40O4 InChI=1S/C24H40O4/c1-14(4-7-21(27)28)17-5-6-18-22-19(9-11-24(17,18)3)23(2)10-8-16(25)12-15(23)13-20(22)26/h14-20,22,25-26H,4-13H2,1-3H3,(H,27,28)/t14-,15+,16-,17-,18+,19+,20-,22+,23+,24-/m1/s1 RUDATBOHQWOJDD-BSWAIDMHSA-N 392.57200 392.29266 [H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC(O)=O CHEBI:23094 CHEBI:3588 CHEBI:3593 Beilstein:3219887 CAS:474-25-9 DrugBank:DB06777 Drug_Central:4361 HMDB:HMDB0000518 KEGG:C02528 KEGG:D00163 LINCS:LSM-5353 LIPID_MAPS_instance:LMST04010032 PDBeChem:JN3 PMID:11530998 PMID:16037564 PMID:24448653 PMID:24464484 Reaxys:3219887 Wikipedia:Chenodiol 3alpha,7alpha-dihydroxy-5beta-cholan-24-oic acid Chenodeoxycholic acid chebi_ontology 3alpha,7alpha-Dihydroxy-5beta-cholanic acid 7alpha-hydroxylithocholic acid CDCA Chenix Chenodiol anthropodeoxycholic acid anthropodesoxycholic acid chenic acid gallodesoxycholic acid CHEBI:16755 chenodeoxycholic acid Beilstein:3219887 Beilstein CAS:474-25-9 ChemIDplus CAS:474-25-9 KEGG COMPOUND Drug_Central:4361 DrugCentral LIPID_MAPS_instance:LMST04010032 LIPID MAPS PMID:11530998 Europe PMC PMID:16037564 Europe PMC PMID:24448653 Europe PMC PMID:24464484 Europe PMC Reaxys:3219887 Reaxys 3alpha,7alpha-dihydroxy-5beta-cholan-24-oic acid IUPAC Chenodeoxycholic acid KEGG_COMPOUND 3alpha,7alpha-Dihydroxy-5beta-cholanic acid KEGG_COMPOUND 7alpha-hydroxylithocholic acid ChemIDplus CDCA IUPHAR Chenix ChemIDplus Chenodiol KEGG_COMPOUND anthropodeoxycholic acid ChemIDplus anthropodesoxycholic acid ChemIDplus chenic acid ChemIDplus gallodesoxycholic acid ChemIDplus A sulfur-containing amino acid that is butyric acid bearing an amino substituent at position 2 and a methylthio substituent at position 4. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8) FFEARJCKVFRZRR-UHFFFAOYSA-N 149.21238 149.05105 CSCCC(N)C(O)=O CHEBI:14590 CHEBI:25229 CHEBI:6829 Beilstein:636185 CAS:59-51-8 Gmelin:3117 KEGG:C01733 KEGG:D04983 PMID:16702333 PMID:22264337 PMID:2543976 Reaxys:636185 UM-BBD_compID:c0094 Wikipedia:Methionine Methionine methionine chebi_ontology 2-Amino-4-(methylthio)butyric acid 2-amino-4-(methylsulfanyl)butanoic acid 2-amino-4-(methylthio)butanoic acid DL-Methionine Hmet M Met Methionin Racemethionine alpha-amino-gamma-methylmercaptobutyric acid metionina CHEBI:16811 methionine Beilstein:636185 Beilstein CAS:59-51-8 ChemIDplus CAS:59-51-8 KEGG COMPOUND CAS:59-51-8 NIST Chemistry WebBook Gmelin:3117 Gmelin PMID:16702333 Europe PMC PMID:22264337 Europe PMC PMID:2543976 Europe PMC Reaxys:636185 Reaxys UM-BBD_compID:c0094 UM-BBD Methionine KEGG_COMPOUND methionine ChEBI methionine IUPAC 2-Amino-4-(methylthio)butyric acid KEGG_COMPOUND 2-amino-4-(methylsulfanyl)butanoic acid IUPAC 2-amino-4-(methylthio)butanoic acid JCBN DL-Methionine KEGG_DRUG Hmet IUPAC M ChEBI Met ChEBI Methionin ChEBI Racemethionine KEGG_DRUG alpha-amino-gamma-methylmercaptobutyric acid NIST_Chemistry_WebBook metionina ChEBI A glycine derivative having methyl and amidino groups attached to the nitrogen. 0 C4H9N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9) CVSVTCORWBXHQV-UHFFFAOYSA-N 131.13328 131.06948 CN(CC(O)=O)C(N)=N CHEBI:14028 CHEBI:23404 CHEBI:3909 CHEBI:41678 Beilstein:907175 CAS:57-00-1 DrugBank:DB00148 Drug_Central:4661 Gmelin:240513 HMDB:HMDB0000064 KEGG:C00300 MetaCyc:CREATINE PDBeChem:CRN PMID:11356982 PMID:11483809 PMID:11867929 PMID:12085493 PMID:12184144 PMID:12878267 PMID:16445883 PMID:17190852 PMID:17253521 PMID:18555535 PMID:19082141 PMID:19651674 PMID:19741514 PMID:19968328 PMID:21556832 PMID:21660517 PMID:21698493 PMID:22038587 PMID:22101931 PMID:22196490 PMID:22252611 PMID:22347384 PMID:22386973 PMID:22422801 PMID:22429992 PMID:22465051 PMID:22521466 PMID:7752905 Reaxys:907175 Wikipedia:Creatine Creatine N-[amino(imino)methyl]-N-methylglycine chebi_ontology ((amino(imino)methyl)(methyl)amino)acetic acid (N-methylcarbamimidamido)acetic acid (alpha-methylguanido)acetic acid Creatin Kreatin Methylglycocyamine N-(aminoiminomethyl)-N-methylglycine N-Methyl-N-guanylglycine N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE N-amidinosarcosine N-carbamimidoyl-N-methylglycine N-methyl-N-guanylglycine alpha-Methylguanidino acetic acid CHEBI:16919 creatine PMID:18555535 Europe PMC PMID:19082141 Europe PMC PMID:19651674 Europe PMC PMID:19741514 Europe PMC PMID:19968328 Europe PMC PMID:21556832 Europe PMC PMID:21660517 Europe PMC PMID:21698493 Europe PMC PMID:22038587 Europe PMC PMID:22101931 Europe PMC PMID:22196490 Europe PMC PMID:22252611 Europe PMC PMID:22347384 Europe PMC PMID:22386973 Europe PMC PMID:22422801 Europe PMC PMID:22429992 Europe PMC PMID:22465051 Europe PMC PMID:22521466 Europe PMC PMID:7752905 Europe PMC Reaxys:907175 Reaxys Creatine KEGG_COMPOUND N-[amino(imino)methyl]-N-methylglycine IUPAC ((amino(imino)methyl)(methyl)amino)acetic acid HMDB (N-methylcarbamimidamido)acetic acid ChEBI (alpha-methylguanido)acetic acid HMDB (alpha-methylguanido)acetic acid NIST_Chemistry_WebBook Creatin ChemIDplus Kreatin ChemIDplus Methylglycocyamine KEGG_COMPOUND N-(aminoiminomethyl)-N-methylglycine NIST_Chemistry_WebBook N-Methyl-N-guanylglycine HMDB N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE PDBeChem N-amidinosarcosine ChemIDplus N-carbamimidoyl-N-methylglycine PDBeChem N-methyl-N-guanylglycine ChemIDplus alpha-Methylguanidino acetic acid KEGG_COMPOUND Beilstein:907175 Beilstein CAS:57-00-1 ChemIDplus CAS:57-00-1 KEGG COMPOUND CAS:57-00-1 NIST Chemistry WebBook Drug_Central:4661 DrugCentral Gmelin:240513 Gmelin PMID:11356982 Europe PMC PMID:11483809 Europe PMC PMID:11867929 Europe PMC PMID:12085493 Europe PMC PMID:12184144 Europe PMC PMID:12878267 Europe PMC PMID:16445883 Europe PMC PMID:17190852 Europe PMC PMID:17253521 Europe PMC D-Ribitol in which the hydroxy group at position 5 is substituted by a 7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl moiety. It is a nutritional factor found in milk, eggs, malted barley, liver, kidney, heart, and leafy vegetables, but the richest natural source is yeast. The free form occurs only in the retina of the eye, in whey, and in urine; its principal forms in tissues and cells are as flavin mononucleotide and flavin-adenine dinucleotide. riboflavin vitamin b2 http://langual.org 0 C17H20N4O6 InChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t11-,12+,14-/m0/s1 AUNGANRZJHBGPY-SCRDCRAPSA-N 376.36390 376.13828 Cc1cc2nc3c(nc(=O)[nH]c3=O)n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C CHEBI:15044 CHEBI:27299 CHEBI:45214 CHEBI:529204 CHEBI:8843 Beilstein:97831 CAS:83-88-5 Codex::101(i) DrugBank:DB00140 Drug_Central:2834 Europe::101 HMDB:HMDB0000244 KEGG:C00255 KEGG:D00050 KNApSAcK:C00001552 LINCS:LSM-4084 MetaCyc:RIBOFLAVIN PDBeChem:RBF PMID:16658098 PMID:22770225 PMID:24643482 PMID:25108762 Patent:US2807611 Patent:US2876169 Reaxys:97831 Wikipedia:Riboflavin http://www.langual.org/langual_thesaurus.asp?termid=B3233 http://www.langual.org/langual_thesaurus.asp?termid=B3756 5-deoxy-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol Riboflavin riboflavin chebi_ontology 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol 6,7-dimethyl-9-D-ribitylisoalloxazine 7,8-Dimethyl-10-ribitylisoalloxazine 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)benzo[g]pteridine-2,4(3H,10H)-dione 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)isoalloxazine E101 Lactoflavin RIBOFLAVINE Vitamin B2 riboflavin riboflavina riboflavine riboflavinum vitamin B2 vitamin G riboflavin, synthetic CHEBI:17015 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): colour. riboflavin Beilstein:97831 Beilstein CAS:83-88-5 ChemIDplus CAS:83-88-5 KEGG COMPOUND CAS:83-88-5 NIST Chemistry WebBook Drug_Central:2834 DrugCentral PMID:16658098 Europe PMC PMID:22770225 Europe PMC PMID:24643482 Europe PMC PMID:25108762 Europe PMC Reaxys:97831 Reaxys 5-deoxy-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol IUPAC Riboflavin KEGG_COMPOUND riboflavin ChEMBL 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol NIST_Chemistry_WebBook 6,7-dimethyl-9-D-ribitylisoalloxazine ChemIDplus 7,8-Dimethyl-10-ribitylisoalloxazine KEGG_COMPOUND 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)benzo[g]pteridine-2,4(3H,10H)-dione ChEBI 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)isoalloxazine ChemIDplus E101 ChEBI Lactoflavin KEGG_COMPOUND RIBOFLAVINE PDBeChem Vitamin B2 KEGG_COMPOUND riboflavin ChemIDplus riboflavina ChemIDplus riboflavine ChemIDplus riboflavinum ChemIDplus vitamin B2 ChEBI vitamin G DrugBank 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 The L-enantiomer of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-N 105.09262 105.04259 N[C@@H](CO)C(O)=O CHEBI:13167 CHEBI:21387 CHEBI:45440 CHEBI:45451 CHEBI:45590 CHEBI:45597 CHEBI:45677 CHEBI:6301 Beilstein:1721404 CAS:56-45-1 DrugBank:DB00133 Drug_Central:4127 ECMDB:ECMDB00187 Gmelin:2570 HMDB:HMDB0000187 KEGG:C00065 KEGG:D00016 KNApSAcK:C00001393 MetaCyc:SER PDBeChem:SER PMID:1650428 PMID:17439666 PMID:19062365 PMID:21956576 PMID:22265470 PMID:22393170 PMID:22547037 PMID:22566084 PMID:22566694 Reaxys:1721404 Wikipedia:L-serine YMDB:YMDB00112 L-Serine L-serine chebi_ontology (2S)-2-amino-3-hydroxypropanoic acid (S)-(-)-serine (S)-2-amino-3-hydroxypropanoic acid (S)-alpha-Amino-beta-hydroxypropionic acid (S)-serine L-(-)-serine L-2-Amino-3-hydroxypropionic acid L-3-Hydroxy-2-aminopropionic acid L-3-Hydroxy-alanine L-Ser L-Serin S SERINE Ser Serine beta-Hydroxy-L-alanine beta-Hydroxyalanine CHEBI:17115 L-serine Beilstein:1721404 Beilstein CAS:56-45-1 ChemIDplus CAS:56-45-1 KEGG COMPOUND CAS:56-45-1 NIST Chemistry WebBook Drug_Central:4127 DrugCentral Gmelin:2570 Gmelin PMID:1650428 Europe PMC PMID:17439666 Europe PMC PMID:19062365 Europe PMC PMID:21956576 Europe PMC PMID:22265470 Europe PMC PMID:22393170 Europe PMC PMID:22547037 Europe PMC PMID:22566084 Europe PMC PMID:22566694 Europe PMC Reaxys:1721404 Reaxys L-Serine KEGG_COMPOUND L-serine IUPAC (2S)-2-amino-3-hydroxypropanoic acid IUPAC (S)-(-)-serine NIST_Chemistry_WebBook (S)-2-amino-3-hydroxypropanoic acid NIST_Chemistry_WebBook (S)-alpha-Amino-beta-hydroxypropionic acid HMDB (S)-serine ChemIDplus L-(-)-serine NIST_Chemistry_WebBook L-2-Amino-3-hydroxypropionic acid KEGG_COMPOUND L-3-Hydroxy-2-aminopropionic acid HMDB L-3-Hydroxy-alanine KEGG_COMPOUND L-Ser DrugBank L-Serin ChEBI S ChEBI SERINE PDBeChem Ser ChEBI Serine KEGG_COMPOUND beta-Hydroxy-L-alanine HMDB beta-Hydroxyalanine HMDB An amino-acid betaine that is butanoate substituted with a hydroxy group at position C-3 and a trimethylammonium group at C-4. 0 C7H15NO3 InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3 PHIQHXFUZVPYII-UHFFFAOYSA-N 161.19894 161.10519 C[N+](C)(C)CC(O)CC([O-])=O CHEBI:11817 CHEBI:13947 CHEBI:20047 CHEBI:23038 Beilstein:1866665 CAS:461-06-3 DrugBank:DB02648 KEGG:C00487 MetaCyc:DL-CARNITINE PMID:22770225 PMID:23868375 Patent:US4255449 Patent:US4315944 Reaxys:1866665 Wikipedia:Carnitine 3-hydroxy-4-(trimethylammonio)butanoate carnitine chebi_ontology D,L-carnitine CHEBI:17126 carnitine Beilstein:1866665 Beilstein CAS:461-06-3 ChemIDplus PMID:22770225 Europe PMC PMID:23868375 Europe PMC Reaxys:1866665 Reaxys 3-hydroxy-4-(trimethylammonio)butanoate IUPAC carnitine UniProt D,L-carnitine MetaCyc Any 3beta-hydroxy-steroid that contains a double bond between positions 5 and 6. 0 C19H29OR 273.434 273.22184 C12C(C3C(C(CC3)*)(C)CC1)CC=C4C2(CC[C@@H](C4)O)C CHEBI:13608 CHEBI:136845 CHEBI:20245 KEGG:C03836 MetaCyc:3b-hydroxy-D5-steroids chebi_ontology 3beta-hydroxy Delta(5)-steroids 3beta-hydroxy-Delta(5)-steroids a 3beta-hydroxy-Delta(5)-steroid CHEBI:1722 3beta-hydroxy-Delta(5)-steroid 3beta-hydroxy Delta(5)-steroids ChEBI 3beta-hydroxy-Delta(5)-steroids ChEBI a 3beta-hydroxy-Delta(5)-steroid UniProt A straight-chain saturated fatty acid containing five carbon atoms. 0 C5H10O2 InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7) NQPDZGIKBAWPEJ-UHFFFAOYSA-N 102.13170 102.06808 CCCCC(O)=O CHEBI:113448 CHEBI:27263 CHEBI:27264 CHEBI:43606 CHEBI:44803 CHEBI:7980 Beilstein:969454 CAS:109-52-4 DrugBank:DB02406 Gmelin:26714 HMDB:HMDB0000892 KEGG:C00803 KNApSAcK:C00001208 LIPID_MAPS_instance:LMFA01010005 PDBeChem:LEA PMID:20507156 PPDB:3130 Reaxys:969454 Wikipedia:Valeric_acid Valeric acid pentanoic acid chebi_ontology 1-butanecarboxylic acid CH3-[CH2]3-COOH PENTANOIC ACID Pentanoate Pentanoic acid Valerate Valerianic acid Valeriansaeure n-BuCOOH n-Pentanoate n-Valeric acid n-pentanoic acid n-valeric acid pentoic acid propylacetic acid valeric acid, normal CHEBI:17418 valeric acid Beilstein:969454 Beilstein CAS:109-52-4 ChemIDplus CAS:109-52-4 KEGG COMPOUND CAS:109-52-4 NIST Chemistry WebBook Gmelin:26714 Gmelin LIPID_MAPS_instance:LMFA01010005 LIPID MAPS PMID:20507156 Europe PMC Reaxys:969454 Reaxys Valeric acid KEGG_COMPOUND pentanoic acid IUPAC 1-butanecarboxylic acid ChemIDplus 1-butanecarboxylic acid NIST_Chemistry_WebBook CH3-[CH2]3-COOH IUPAC PENTANOIC ACID PDBeChem Pentanoate KEGG_COMPOUND Pentanoic acid KEGG_COMPOUND Valerate KEGG_COMPOUND Valerianic acid KEGG_COMPOUND Valeriansaeure ChEBI n-BuCOOH ChEBI n-Pentanoate KEGG_COMPOUND n-Valeric acid KEGG_COMPOUND n-pentanoic acid ChemIDplus n-valeric acid ChemIDplus pentoic acid ChEBI propylacetic acid ChemIDplus valeric acid, normal ChemIDplus A complex cob(III)alamin in which cobalt is positioned in the centre of a planar corrin tetrapyrrole ring and bound axially to a 5,6-dimethylbenzimidazole moiety and a cyano group. It is one of several forms of the vitamin known as vitamin B12. cyanocobalamin http://langual.org 0 C63H88CoN14O14P InChI=1S/C62H90N13O14P.CN.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;1-2;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;/q;;+2/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 RMRCNWBMXRMIRW-WZHZPDAFSA-L 1355.36520 1354.56740 [H][C@@]1(C)CNC(=O)CC[C@]2(C)[C@@H](CC(N)=O)[C@@]3([H])N4C2=C(C)C2=[N+]5C(=CC6=[N+]7C(=C(C)C8=[N+]([C@]3(C)[C@@](C)(CC(N)=O)[C@@H]8CCC(N)=O)[Co-3]457(C#N)[n+]3cn([C@H]4O[C@H](CO)[C@@H](OP([O-])(=O)O1)[C@H]4O)c1cc(C)c(C)cc31)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O)C(C)(C)[C@@H]2CCC(N)=O CHEBI:14041 CHEBI:23435 CHEBI:3979 CHEBI:48820 CHEBI:60496 CAS:68-19-9 DrugBank:DB00115 Gmelin:249901 Gmelin:457955 KEGG:C02823 KEGG:D00166 KNApSAcK:C00001534 PDBeChem:CNC PMID:29286160 http://www.langual.org/langual_thesaurus.asp?termid=B3779 Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-cyanocobamide Cyanocob(III)alamin cyanocob(III)alamin chebi_ontology CN-Cbl CO-CYANOCOBALAMIN Dicopac Vitamin B12 complex cyanocobalamin vitamin B-12 CHEBI:17439 cyanocob(III)alamin CAS:68-19-9 ChemIDplus CAS:68-19-9 KEGG COMPOUND Gmelin:249901 Gmelin Gmelin:457955 Gmelin PMID:29286160 Europe PMC Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-cyanocobamide IUPAC Cyanocob(III)alamin KEGG_COMPOUND cyanocob(III)alamin IUPAC cyanocob(III)alamin UniProt CN-Cbl CBN CO-CYANOCOBALAMIN PDBeChem Dicopac KEGG_COMPOUND Vitamin B12 complex KEGG_COMPOUND cyanocobalamin KEGG_DRUG vitamin B-12 CBN 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 An optically active form of cysteine having L-configuration. l-cysteine http://langual.org 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-N 121.15800 121.01975 N[C@@H](CS)C(O)=O CHEBI:13095 CHEBI:21261 CHEBI:41227 CHEBI:41700 CHEBI:41768 CHEBI:41781 CHEBI:41811 CHEBI:6207 Beilstein:1721408 CAS:52-90-4 Codex::920 DrugBank:DB00151 Drug_Central:769 ECMDB:ECMDB00574 Europe::920 Gmelin:49991 HMDB:HMDB0000574 KEGG:C00097 KEGG:D00026 KNApSAcK:C00001351 MetaCyc:CYS PDBeChem:CYS PMID:11732994 PMID:13761469 PMID:22735334 Reaxys:1721408 Wikipedia:Cysteine YMDB:YMDB00046 http://www.langual.org/langual_thesaurus.asp?termid=B4426 L-Cysteine L-cysteine chebi_ontology (2R)-2-amino-3-mercaptopropanoic acid (2R)-2-amino-3-sulfanylpropanoic acid (R)-2-amino-3-mercaptopropanoic acid C CYSTEINE Cys E 920 E-920 E920 FREE CYSTEINE L-2-Amino-3-mercaptopropionic acid L-Cystein L-Zystein cysteine, l- and its hydrochlorides - sodium and potassium salts CHEBI:17561 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): flour treatment agent. L-cysteine Beilstein:1721408 Beilstein CAS:52-90-4 ChemIDplus CAS:52-90-4 KEGG COMPOUND CAS:52-90-4 NIST Chemistry WebBook Drug_Central:769 DrugCentral Gmelin:49991 Gmelin PMID:11732994 Europe PMC PMID:13761469 Europe PMC PMID:22735334 Europe PMC Reaxys:1721408 Reaxys L-Cysteine KEGG_COMPOUND L-cysteine IUPAC (2R)-2-amino-3-mercaptopropanoic acid JCBN (2R)-2-amino-3-sulfanylpropanoic acid IUPAC (R)-2-amino-3-mercaptopropanoic acid NIST_Chemistry_WebBook C ChEBI CYSTEINE PDBeChem Cys ChEBI E 920 ChEBI E-920 ChEBI E920 ChEBI FREE CYSTEINE PDBeChem L-2-Amino-3-mercaptopropionic acid KEGG_COMPOUND L-Cystein ChEBI L-Zystein ChEBI A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription. 0 C4H4N2O2 InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) ISAKRJDGNUQOIC-UHFFFAOYSA-N 112.08684 112.02728 O=c1cc[nH]c(=O)[nH]1 CHEBI:15288 CHEBI:27210 CHEBI:46375 CHEBI:9882 Beilstein:606623 CAS:66-22-8 DrugBank:DB03419 Gmelin:2896 HMDB:HMDB0000300 KEGG:C00106 KEGG:D00027 KNApSAcK:C00001513 MetaCyc:URACIL PDBeChem:URA PMID:11279060 PMID:12855717 PMID:15274295 PMID:16834123 PMID:17439666 PMID:18533995 PMID:18815805 PMID:19175333 PMID:22020693 PMID:22074393 PMID:22120518 PMID:22171528 PMID:22237209 PMID:22299724 PMID:22356544 PMID:22447672 PMID:22483865 PMID:22567906 PMID:22685418 PMID:3654008 Reaxys:606623 Wikipedia:Uracil URACIL Uracil pyrimidine-2,4(1H,3H)-dione uracil chebi_ontology 2,4(1H,3H)-pyrimidinedione 2,4-Dioxopyrimidine 2,4-Pyrimidinedione U Ura Urazil CHEBI:17568 uracil Beilstein:606623 Beilstein CAS:66-22-8 ChemIDplus CAS:66-22-8 KEGG COMPOUND CAS:66-22-8 NIST Chemistry WebBook Gmelin:2896 Gmelin PMID:11279060 Europe PMC PMID:12855717 Europe PMC PMID:15274295 Europe PMC PMID:16834123 Europe PMC PMID:17439666 Europe PMC PMID:18533995 Europe PMC PMID:18815805 Europe PMC PMID:19175333 Europe PMC PMID:22020693 Europe PMC PMID:22074393 Europe PMC PMID:22120518 Europe PMC PMID:22171528 Europe PMC PMID:22237209 Europe PMC PMID:22299724 Europe PMC PMID:22356544 Europe PMC PMID:22447672 Europe PMC PMID:22483865 Europe PMC PMID:22567906 Europe PMC PMID:22685418 Europe PMC PMID:3654008 Europe PMC Reaxys:606623 Reaxys URACIL PDBeChem Uracil KEGG_COMPOUND pyrimidine-2,4(1H,3H)-dione IUPAC uracil UniProt 2,4(1H,3H)-pyrimidinedione NIST_Chemistry_WebBook 2,4-Dioxopyrimidine HMDB 2,4-Pyrimidinedione HMDB U ChEBI Ura CBN Urazil ChEBI A compound showing blue fluorescence, formed by a photolysis of riboflavin in acid or neutral solution. 0 C12H10N4O2 InChI=1S/C12H10N4O2/c1-5-3-7-8(4-6(5)2)14-10-9(13-7)11(17)16-12(18)15-10/h3-4H,1-2H3,(H2,14,15,16,17,18) ZJTJUVIJVLLGSP-UHFFFAOYSA-N 242.23356 242.08038 Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C CHEBI:14534 CHEBI:25080 CHEBI:43772 CHEBI:6561 Beilstein:226631 CAS:1086-80-2 DrugBank:DB04345 KEGG:C01727 KNApSAcK:C00030694 MetaCyc:CPD-605 PDBeChem:LUM PMID:15819908 PMID:21126007 PMID:22953948 PMID:24001807 PMID:24451190 PMID:24643482 Reaxys:226631 7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione LUMICHROME Lumichrome lumichrome chebi_ontology 7,8-Dimethylalloxazine CHEBI:17781 lumichrome Beilstein:226631 Beilstein CAS:1086-80-2 ChemIDplus CAS:1086-80-2 KEGG COMPOUND CAS:1086-80-2 NIST Chemistry WebBook PMID:15819908 Europe PMC PMID:21126007 Europe PMC PMID:22953948 Europe PMC PMID:24001807 Europe PMC PMID:24451190 Europe PMC PMID:24643482 Europe PMC Reaxys:226631 Reaxys 7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione IUPAC LUMICHROME PDBeChem Lumichrome KEGG_COMPOUND lumichrome UniProt 7,8-Dimethylalloxazine KEGG_COMPOUND The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group. 0 CH4O InChI=1S/CH4O/c1-2/h2H,1H3 OKKJLVBELUTLKV-UHFFFAOYSA-N 32.04186 32.02621 CO CHEBI:14588 CHEBI:25227 CHEBI:44080 CHEBI:44553 CHEBI:6816 Beilstein:1098229 CAS:67-56-1 Gmelin:449 HMDB:HMDB0001875 KEGG:C00132 KEGG:D02309 MetaCyc:METOH PDBeChem:MOH PMID:11141607 PMID:11430978 PMID:11489599 PMID:11680737 PMID:11684179 PMID:14012711 PMID:14678513 PMID:14760634 PMID:15172721 PMID:15906011 PMID:16705261 PMID:17451998 PMID:17733096 PMID:19064074 PMID:19850112 PMID:20314698 Reaxys:1098229 UM-BBD_compID:c0132 Wikipedia:Methanol METHANOL Methanol methanol chebi_ontology CH3OH MeOH Methyl alcohol Methylalkohol carbinol spirit of wood wood alcohol wood naphtha wood spirit CHEBI:17790 methanol Beilstein:1098229 Beilstein CAS:67-56-1 ChemIDplus CAS:67-56-1 KEGG COMPOUND CAS:67-56-1 NIST Chemistry WebBook Gmelin:449 Gmelin PMID:11141607 Europe PMC PMID:11430978 Europe PMC PMID:11489599 Europe PMC PMID:11680737 Europe PMC PMID:11684179 Europe PMC PMID:14012711 Europe PMC PMID:14678513 Europe PMC PMID:14760634 Europe PMC PMID:15172721 Europe PMC PMID:15906011 Europe PMC PMID:16705261 Europe PMC PMID:17451998 Europe PMC PMID:17733096 Europe PMC PMID:19064074 Europe PMC PMID:19850112 Europe PMC PMID:20314698 Europe PMC Reaxys:1098229 Reaxys UM-BBD_compID:c0132 UM-BBD METHANOL PDBeChem Methanol KEGG_COMPOUND methanol IUPAC methanol UniProt CH3OH ChEBI MeOH ChEBI Methyl alcohol KEGG_COMPOUND Methylalkohol NIST_Chemistry_WebBook carbinol ChemIDplus spirit of wood HMDB wood alcohol ChemIDplus wood naphtha ChemIDplus wood spirit NIST_Chemistry_WebBook An alpha-amino acid that is alanine substituted at position 3 by a hydroxy group. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7) MTCFGRXMJLQNBG-UHFFFAOYSA-N 105.09262 105.04259 NC(CO)C(O)=O CHEBI:15081 CHEBI:26648 CHEBI:9116 Beilstein:1721402 CAS:302-84-1 Gmelin:26429 KEGG:C00716 KNApSAcK:C00001393 Reaxys:1721402 Wikipedia:Serine Serine serine chebi_ontology 2-Amino-3-hydroxypropionic acid 2-amino-3-hydroxypropanoic acid 3-Hydroxyalanine Serin CHEBI:17822 serine Beilstein:1721402 Beilstein CAS:302-84-1 ChemIDplus CAS:302-84-1 KEGG COMPOUND CAS:302-84-1 NIST Chemistry WebBook Gmelin:26429 Gmelin Reaxys:1721402 Reaxys Serine KEGG_COMPOUND serine IUPAC 2-Amino-3-hydroxypropionic acid KEGG_COMPOUND 2-amino-3-hydroxypropanoic acid IUPAC 3-Hydroxyalanine KEGG_COMPOUND Serin 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 A short-chain fatty acid anion that is the conjugate base of butyric acid, obtained by deprotonation of the carboxy group. -1 C4H7O2 InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6)/p-1 FERIUCNNQQJTOY-UHFFFAOYSA-M 87.09718 87.04515 CCCC([O-])=O CHEBI:13924 CHEBI:22946 Beilstein:3601060 CAS:461-55-2 Gmelin:324289 KEGG:C00246 MetaCyc:BUTYRIC_ACID PMID:17190852 PMID:7496326 Reaxys:3601060 UM-BBD_compID:c0035 butanoate butyrate chebi_ontology 1-butanoate 1-butyrate 1-propanecarboxylate CH3-[CH2]2-COO(-) butanate butanoate butanoic acid, ion(1-) n-butanoate n-butyrate propanecarboxylate propylformate CHEBI:17968 butyrate Beilstein:3601060 Beilstein CAS:461-55-2 ChemIDplus Gmelin:324289 Gmelin PMID:17190852 Europe PMC PMID:7496326 Europe PMC Reaxys:3601060 Reaxys UM-BBD_compID:c0035 UM-BBD butanoate IUPAC butyrate IUPAC 1-butanoate ChEBI 1-butyrate ChEBI 1-propanecarboxylate ChEBI CH3-[CH2]2-COO(-) IUPAC butanate ChEBI butanoate ChEBI butanoate UniProt butanoic acid, ion(1-) ChemIDplus n-butanoate ChEBI n-butyrate ChemIDplus propanecarboxylate ChEBI propylformate ChEBI '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 The parent compound of the citrulline class consisting of ornithine having a carbamoyl group at the N(5)-position. 0 C6H13N3O3 InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12) RHGKLRLOHDJJDR-UHFFFAOYSA-N 175.18584 175.09569 NC(CCCNC(N)=O)C(O)=O CHEBI:14002 CHEBI:3730 Beilstein:1725417 Beilstein:2328251 CAS:627-77-0 PMID:11094453 PMID:11113071 PMID:11696417 PMID:1378088 PMID:16082501 PMID:16708633 PMID:17005970 PMID:17513438 PMID:17558653 PMID:17693747 PMID:18437289 PMID:18440672 PMID:18989563 PMID:19144577 PMID:21129371 PMID:21482070 Reaxys:1725417 Wikipedia:Citrulline 2-amino-5-(carbamoylamino)pentanoic acid Citrulline N(5)-carbamoylornithine citrulline chebi_ontology 2-Amino-5-uredovaleric acid Cit Citrullin DL-2-amino-5-ureidovaleric acid N(5)-(aminocarbonyl)-DL-ornithine N(5)-(aminocarbonyl)ornithine N(5)-carbamoyl-DL-ornithine citrulina dl-citrulline CHEBI:18211 citrulline Beilstein:1725417 Beilstein Beilstein:2328251 Beilstein CAS:627-77-0 ChemIDplus CAS:627-77-0 NIST Chemistry WebBook PMID:11094453 Europe PMC PMID:11113071 Europe PMC PMID:11696417 Europe PMC PMID:1378088 Europe PMC PMID:16082501 Europe PMC PMID:16708633 Europe PMC PMID:17005970 Europe PMC PMID:17513438 Europe PMC PMID:17558653 Europe PMC PMID:17693747 Europe PMC PMID:18437289 Europe PMC PMID:18440672 Europe PMC PMID:18989563 Europe PMC PMID:19144577 Europe PMC PMID:21129371 Europe PMC PMID:21482070 Europe PMC Reaxys:1725417 Reaxys 2-amino-5-(carbamoylamino)pentanoic acid IUPAC Citrulline KEGG_COMPOUND N(5)-carbamoylornithine IUPAC citrulline IUPAC 2-Amino-5-uredovaleric acid KEGG_COMPOUND Cit IUPAC Citrullin ChEBI DL-2-amino-5-ureidovaleric acid ChemIDplus N(5)-(aminocarbonyl)-DL-ornithine NIST_Chemistry_WebBook N(5)-(aminocarbonyl)ornithine ChEBI N(5)-carbamoyl-DL-ornithine NIST_Chemistry_WebBook citrulina ChEBI dl-citrulline NIST_Chemistry_WebBook An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2. glutamic acid http://langual.org 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10) WHUUTDBJXJRKMK-UHFFFAOYSA-N 147.12930 147.05316 NC(CCC(O)=O)C(O)=O CHEBI:24314 CHEBI:5431 Beilstein:1723799 CAS:617-65-2 Codex::620 Europe::620 Gmelin:101971 KEGG:C00302 KEGG:D04341 KNApSAcK:C00001358 KNApSAcK:C00019577 PMID:15739367 PMID:17190852 PMID:24616376 PMID:24984001 Reaxys:1723799 Wikipedia:Glutamic_acid http://www.langual.org/langual_thesaurus.asp?termid=B3106 2-aminopentanedioic acid Glutamic acid glutamic acid chebi_ontology 2-Aminoglutaric acid DL-Glutamic acid DL-Glutaminic acid E Glu Glutamate Glutaminic acid Glutaminsaeure glutamic acid, l(+)- CHEBI:18237 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): flavour enhancer. glutamic acid Beilstein:1723799 Beilstein CAS:617-65-2 ChemIDplus CAS:617-65-2 KEGG COMPOUND CAS:617-65-2 NIST Chemistry WebBook Gmelin:101971 Gmelin PMID:15739367 Europe PMC PMID:17190852 Europe PMC PMID:24616376 Europe PMC PMID:24984001 Europe PMC Reaxys:1723799 Reaxys 2-aminopentanedioic acid IUPAC Glutamic acid KEGG_COMPOUND glutamic acid IUPAC 2-Aminoglutaric acid KEGG_COMPOUND DL-Glutamic acid KEGG_DRUG DL-Glutaminic acid KEGG_COMPOUND E ChEBI Glu ChEBI Glutamate KEGG_COMPOUND Glutaminic acid KEGG_COMPOUND Glutaminsaeure ChEBI Any nucleoside where the sugar component is D-ribose. 0 C5H9O4R 133.123 133.05008 OC[C@H]1O[C@@H]([*])[C@H](O)[C@@H]1O CHEBI:13014 CHEBI:13015 CHEBI:13685 CHEBI:21085 CHEBI:26560 CHEBI:4240 CHEBI:8844 KEGG:C00911 Ribonucleoside chebi_ontology a ribonucleoside ribonucleosides CHEBI:18254 ribonucleoside Ribonucleoside KEGG_COMPOUND a ribonucleoside UniProt ribonucleosides ChEBI An alpha-amino acid that is pentanoic acid bearing two amino substituents at positions 2 and 5. 0 C5H12N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9) AHLPHDHHMVZTML-UHFFFAOYSA-N 132.16106 132.08988 NCCCC(N)C(O)=O CHEBI:7784 Beilstein:1722296 CAS:616-07-9 Gmelin:847696 KEGG:C01602 KNApSAcK:C00001384 PMID:15449570 PMID:17190852 PMID:22264337 Reaxys:1722296 2,5-diaminopentanoic acid Ornithine ornithine chebi_ontology 2,5-Diaminopentanoic acid 2,5-Diaminovaleric acid DL-Ornithine Orn CHEBI:18257 ornithine Beilstein:1722296 Beilstein CAS:616-07-9 ChemIDplus Gmelin:847696 Gmelin PMID:15449570 Europe PMC PMID:17190852 Europe PMC PMID:22264337 Europe PMC Reaxys:1722296 Reaxys 2,5-diaminopentanoic acid IUPAC Ornithine KEGG_COMPOUND ornithine IUPAC 2,5-Diaminopentanoic acid KEGG_COMPOUND 2,5-Diaminovaleric acid KEGG_COMPOUND DL-Ornithine ChemIDplus Orn IUPAC 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 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 N-acetyl-amino acid having D-configuration. CHEBI:7109 KEGG:C03135 chebi_ontology N-Acetyl-D-amino-acid N-acetyl-D-amino acids CHEBI:21501 N-acetyl-D-amino acid N-Acetyl-D-amino-acid KEGG_COMPOUND N-acetyl-D-amino acids ChEBI An L-amino acid having an N-acetyl substituent. chebi_ontology CHEBI:21545 N-acetyl-L-amino acid An N-acyl-amino acid that has acetyl as the acyl group. CHEBI:7105 KEGG:C02847 chebi_ontology N-Acetyl amino acid N-acetyl-amino acids CHEBI:21575 N-acetyl-amino acid N-Acetyl amino acid KEGG_COMPOUND N-acetyl-amino acids ChEBI Any N-acylamino acid having L-configuration. chebi_ontology CHEBI:21644 N-acyl-L-amino acid A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. glycosylamine chebi_ontology N-glycoside N-glycosides N-glycosyl compounds glycosylamines CHEBI:21731 N-glycosyl compound glycosylamine IUPAC N-glycoside ChEBI N-glycosides ChEBI N-glycosyl compounds ChEBI glycosylamines IUPAC Compounds with the general formula RNHC(=O)CH3. chebi_ontology CHEBI:22160 acetamides Any amino acid derivative that is the N-acetyl or O-acetyl derivative of an amino acid. chebi_ontology acetyl-amino acids CHEBI:22195 acetyl-amino acid acetyl-amino acids ChEBI chebi_ontology CHEBI:22198 acetylcysteine 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 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 substance that destroys or inhibits replication of viruses. chebi_ontology anti-viral agent anti-viral agents antiviral antiviral agents antivirals CHEBI:22587 antiviral agent anti-viral agent ChEBI anti-viral agents ChEBI antiviral ChEBI antiviral agents ChEBI antivirals 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 Any quinone resulting from the formal oxidation of catechol, hydroquinone, or their C-substituted derivatives. chebi_ontology CHEBI:22729 benzoquinones Any amino acid-derived zwitterion - such as glycine betaine (N,N,N-trimethylammonioacetate) - in which the ammonium nitrogen carries three methyl substituents. chebi_ontology amino acid betaines amino-acid betaines betaines CHEBI:22860 amino-acid betaine amino acid betaines ChEBI amino-acid betaines ChEBI betaines ChEBI The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. 0 CH2NO 44.03272 44.01364 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 0 CO 28.01010 27.99491 carbonyl carbonyl group chebi_ontology >C=O CHEBI:23019 carbonyl group carbonyl IUPAC carbonyl group ChEBI carbonyl group UniProt >C=O IUPAC chebi_ontology CHEBI:23324 citrullines chebi_ontology CHEBI:23333 cob(III)alamins chebi_ontology CHEBI:23334 cobalamins chebi_ontology CHEBI:23341 cobamides 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 CHEBI:23390 cobalt-corrinoid hexaamide An amino acid derivative resulting from reaction of cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of cysteine by a heteroatom. The definition normally excludes peptides containing cysteine residues. cysteine derivative chebi_ontology CHEBI:23509 cysteine derivative cysteine derivative ChEBI A hydroxy-5beta-cholanic acid carrying two hydroxy groups at unspecified positions. 0 C24H40O4 392.573 392.29266 chebi_ontology dihydroxy-5beta-cholanic acids CHEBI:23775 dihydroxy-5beta-cholanic acid dihydroxy-5beta-cholanic acids ChEBI 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 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 An amino acid derivative resulting from reaction of glutamic acid at the amino group or either of the carboxy groups, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing glutamic acid residues. chebi_ontology CHEBI:24315 glutamic acid derivative An L-alpha-amino acid which is L-glutamic acid or any of the essential amino acids biosynthesised from it (glutamine, proline and arginine). A closed class. PMID:20716061 chebi_ontology glutamine family amino acids CHEBI:24318 glutamine family amino acid PMID:20716061 Europe PMC glutamine family amino acids ChEBI An EC 6.3.* (C-N bond-forming ligase) inhibitor that interferes with the action of glutamate--ammonia ligase (EC 6.3.1.2). Wikipedia:Glutamine_synthetase chebi_ontology EC 6.3.1.2 (glutamate--ammonia ligase) inhibitors EC 6.3.1.2 inhibitor EC 6.3.1.2 inhibitors L-glutamate:ammonia ligase (ADP-forming) inhibitor L-glutamate:ammonia ligase (ADP-forming) inhibitors L-glutamine synthetase inhibitor L-glutamine synthetase inhibitors glutamate--ammonia ligase (EC 6.3.1.2) inhibitor glutamate--ammonia ligase (EC 6.3.1.2) inhibitors glutamate--ammonia ligase inhibitor glutamate--ammonia ligase inhibitors glutamine synthetase inhibitor glutamine synthetase inhibitors glutamylhydroxamic synthetase inhibitor glutamylhydroxamic synthetase inhibitors CHEBI:24319 EC 6.3.1.2 (glutamate--ammonia ligase) inhibitor EC 6.3.1.2 (glutamate--ammonia ligase) inhibitors ChEBI EC 6.3.1.2 inhibitor ChEBI EC 6.3.1.2 inhibitors ChEBI L-glutamate:ammonia ligase (ADP-forming) inhibitor ChEBI L-glutamate:ammonia ligase (ADP-forming) inhibitors ChEBI L-glutamine synthetase inhibitor ChEBI L-glutamine synthetase inhibitors ChEBI glutamate--ammonia ligase (EC 6.3.1.2) inhibitor ChEBI glutamate--ammonia ligase (EC 6.3.1.2) inhibitors ChEBI glutamate--ammonia ligase inhibitor ChEBI glutamate--ammonia ligase inhibitors ChEBI glutamine synthetase inhibitor ChEBI glutamine synthetase inhibitors ChEBI glutamylhydroxamic synthetase inhibitor ChEBI glutamylhydroxamic synthetase inhibitors ChEBI A proteinogenic amino acid derivative resulting from reaction of glycine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. chebi_ontology CHEBI:24373 glycine derivative 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 Any organonitrogen compound containing a carbamimidamido (guanidino) group. Guanidines have the general structure (R(1)R(2)N)(R(3)R(4)N)C=N-R(5) and are related structurally to amidines and ureas. chebi_ontology CHEBI:24436 guanidines 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 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 carboxylic acid with at least one hydroxy group. chebi_ontology hydroxy carboxylic acids hydroxycarboxylic acid hydroxycarboxylic acids CHEBI:24669 hydroxy carboxylic acid hydroxy carboxylic acids ChEBI hydroxycarboxylic acid ChEBI hydroxycarboxylic acids ChEBI 0 CH3O 31.03392 31.01839 hydroxymethyl chebi_ontology -CH3-OH serine side-chain CHEBI:24712 hydroxymethyl group hydroxymethyl IUPAC -CH3-OH IUPAC serine side-chain ChEBI 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 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 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 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 An oxoacid containing a single carboxy group. chebi_ontology monocarboxylic acids CHEBI:25384 monocarboxylic acid monocarboxylic acids 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 chebi_ontology organic heteromonocyclic compounds CHEBI:25693 organic heteromonocyclic compound organic heteromonocyclic compounds 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 An alcohol derived from an aliphatic compound. 0 HOR 17.007 17.00274 O* KEGG:C02525 Aliphatic alcohol chebi_ontology aliphatic alcohols an aliphatic alcohol CHEBI:2571 aliphatic alcohol Aliphatic alcohol KEGG_COMPOUND aliphatic alcohols ChEBI an aliphatic alcohol UniProt An oxide is a chemical compound of oxygen with other chemical elements. oxide chebi_ontology oxides CHEBI:25741 oxide oxide ChEBI oxides ChEBI Any fatty acid anion containing at least one C-C unsaturated bond; formed by deprotonation of the carboxylic acid moiety. chebi_ontology CHEBI:2580 unsaturated fatty acid anion 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 A quinone in which the two oxo groups of the quinone are located para to each other on the 6-membered quinonoid ring. chebi_ontology p-quinone para-quinones CHEBI:25830 p-quinones p-quinone ChEBI para-quinones ChEBI Any amino acid whose side chain is capable of forming one or more hydrogen bonds. 0 C2H4NO2R 74.059 74.02420 OC(C(*)N)=O CHEBI:8283 MetaCyc:Polar-amino-acids PMID:12016058 polar amino acid chebi_ontology polar amino acids polar amino-acid polar amino-acids CHEBI:26167 polar amino acid PMID:12016058 Europe PMC polar amino acid ChEBI polar amino acids ChEBI polar amino-acid ChEBI polar amino-acids ChEBI Any fatty acid containing more than one double bond. Acids in this group are reported to have cardioprotective effects; and levels are lowered in chronic fatigue syndrome. PMID:14977874 PMID:16380690 PMID:17891522 chebi_ontology PUFA PUFAs polyunsaturated fatty acids CHEBI:26208 polyunsaturated fatty acid PMID:14977874 Europe PMC PMID:16380690 Europe PMC PMID:17891522 Europe PMC PUFA ChEBI PUFAs ChEBI polyunsaturated fatty acids ChEBI A quinone substituted by a polyprenyl-derived side-chain. Prenylquinones occur in all living cells. Due to their amphiphilic character, they are mainly located in biological membranes where they function as electron and proton carriers in the photosynthetic and respiratory electron transport chains. Some prenylquinones also perform more specialised roles sucy as antioxidants and enzyme cofactors. Prenylquinones are classified according to ring structure: the main classes are menaquinones, phylloquinones, ubiquinones and plastoquinones. CHEBI:72751 PMID:19928587 PMID:21777468 PMID:21844348 PMID:22371323 PMID:3985624 chebi_ontology polyprenylquinone polyprenylquinones prenylquinones CHEBI:26255 prenylquinone PMID:19928587 Europe PMC PMID:21777468 Europe PMC PMID:21844348 Europe PMC PMID:22371323 Europe PMC PMID:3985624 Europe PMC polyprenylquinone ChEBI polyprenylquinones ChEBI prenylquinones ChEBI chebi_ontology CHEBI:26373 pteridines chebi_ontology CHEBI:26375 pterins Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives. chebi_ontology CHEBI:26421 pyridines A nucleobase whose skeleton is derived from pyrimidine. 0 C4HN2R4 77.064 77.01397 N1C(=C(C(=NC1=*)*)*)* pyrimidine nucleobase chebi_ontology a pyrimidine nucleobase pyrimidine bases pyrimidine nucleobases CHEBI:26432 pyrimidine nucleobase pyrimidine nucleobase ChEBI a pyrimidine nucleobase UniProt pyrimidine bases ChEBI pyrimidine nucleobases ChEBI KEGG:C03169 chebi_ontology N-D-Ribosylpyrimidine pyrimidine nucleosides CHEBI:26440 pyrimidine nucleoside N-D-Ribosylpyrimidine KEGG_COMPOUND pyrimidine nucleosides ChEBI A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen. chebi_ontology CHEBI:26469 quaternary nitrogen compound Any fatty acid containing no carbon to carbon multiple bonds. Known to produce adverse biological effects when ingested to excess. PMID:16492686 PMID:19763019 PMID:20237329 saturated fatty acid chebi_ontology SFA SFAs saturated fatty acids CHEBI:26607 saturated fatty acid PMID:16492686 Europe PMC PMID:19763019 Europe PMC PMID:20237329 Europe PMC saturated fatty acid ChEBI SFA ChEBI SFAs ChEBI saturated fatty acids ChEBI An L-alpha-amino acid which is biosynthesised from 3-phosphoglycerate (i.e. serine, glycine, cysteine and homocysteine). A closed class. PMID:20709681 chebi_ontology 3-phosphoglycerate family amino acid 3-phosphoglycerate family amino acids serine family amino acids CHEBI:26650 serine family amino acid PMID:20709681 Europe PMC 3-phosphoglycerate family amino acid ChEBI 3-phosphoglycerate family amino acids ChEBI serine family amino acids ChEBI An aliphatic monocarboxylic acid with a chain length of less than C6. If any non-hydrocarbon substituent is present, the compound is not normally regarded as a short-chain fatty acid. 0 CH2OR 45.017 44.99765 OC([*])=O PMID:16633129 PMID:16870803 PMID:18203540 PMID:20148677 chebi_ontology SCFA SCFAs short-chain fatty acids CHEBI:26666 short-chain fatty acid PMID:16633129 Europe PMC PMID:16870803 Europe PMC PMID:18203540 Europe PMC PMID:20148677 Europe PMC SCFA ChEBI SCFAs ChEBI short-chain fatty acids 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 chebi_ontology sulfur-containing amino acids CHEBI:26834 sulfur-containing amino acid sulfur-containing amino acids ChEBI sulfur molecular entity chebi_ontology sulfur molecular entities CHEBI:26835 sulfur molecular entity sulfur molecular entity ChEBI sulfur molecular entities ChEBI Any oxacycle having an oxolane (tetrahydrofuran) skeleton. chebi_ontology CHEBI:26912 oxolanes 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 CHEBI:26932 tetrapyrrole tetrapyrrole IUPAC tetrapyrroles IUPAC http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3755 vitamin b1 chebi_ontology thiamines CHEBI:26948 thiamine thiamines ChEBI An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms. chebi_ontology heterotricyclic compounds organic heterotricyclic compounds CHEBI:26979 organic heterotricyclic compound heterotricyclic compounds ChEBI organic heterotricyclic compounds ChEBI micronutrient role 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 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 Any fatty acid containing at least one C=C or C#C bond. LIPID_MAPS_class:LMFA0103 PMID:5322381 chebi_ontology alkene acid olefinic acid unsaturated fatty acids CHEBI:27208 unsaturated fatty acid LIPID_MAPS_class:LMFA0103 LIPID MAPS PMID:5322381 Europe PMC alkene acid ChEBI olefinic acid ChEBI unsaturated fatty acids ChEBI unsaturated fatty acids LIPID_MAPS chebi_ontology CHEBI:27242 uridines vitamin b6 http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3759 Vitamin B6 chebi_ontology vitamin B-6 vitamina B6 vitamine B6 CHEBI:27306 vitamin B6 Vitamin B6 ChEBI vitamin B-6 JCBN vitamina B6 ChEBI vitamine B6 ChEBI water-soluble vitamin role chebi_ontology wasserloesliche Vitamine water-soluble vitamins CHEBI:27314 water-soluble vitamin wasserloesliche Vitamine ChEBI water-soluble vitamins 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 chebi_ontology zinc compounds zinc molecular entities CHEBI:27364 zinc molecular entity zinc compounds ChEBI zinc molecular entities 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 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 Cobalt KEGG_COMPOUND Kobalt NIST_Chemistry_WebBook cobalt ChEBI cobalto ChEBI cobaltum ChEBI hydroxocobalamin http://langual.org 0 C62H89CoN13O15P InChI=1S/C62H90N13O14P.Co.H2O/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;1H2/q;+3;/p-3/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 YOZNUFWCRFCGIH-WZHZPDAFSA-K 1346.35510 1345.56706 [H]O[Co-3]1234N5C6=C(C)C7=[N+]1C(=CC1=[N+]2C(=C(C)C2=[N+]3[C@@](C)([C@@]5([H])[C@H](CC(N)=O)[C@@]6(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]3[C@@H](O)[C@H](O[C@@H]3CO)n3c[n+]4c4cc(C)c(C)cc34)[C@@](C)(CC(N)=O)[C@@H]2CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]1CCC(N)=O)C(C)(C)[C@@H]7CCC(N)=O CHEBI:24652 CHEBI:5795 CHEBI:5803 CAS:13422-51-0 DrugBank:DB00200 Gmelin:5723 KEGG:C08230 KEGG:D01027 http://www.langual.org/langual_thesaurus.asp?termid=B3780 Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-hydroxocobamide Hydroxocobalamin hydroxocobalamin chebi_ontology Hydroxycobalamin OH-Cbl vitamin B-12b CHEBI:27786 hydroxocobalamin CAS:13422-51-0 ChemIDplus CAS:13422-51-0 KEGG COMPOUND Gmelin:5723 Gmelin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-hydroxocobamide IUPAC Hydroxocobalamin KEGG_COMPOUND hydroxocobalamin CBN Hydroxycobalamin KEGG_COMPOUND OH-Cbl CBN vitamin B-12b CBN 0 C63H91CoN13O14P InChI=1S/C62H90N13O14P.CH3.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);1H3;/q;;+2/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 JEWJRMKHSMTXPP-WZHZPDAFSA-L 1344.38230 1343.58780 [H][C@]12[C@H](CC(N)=O)[C@@]3(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]4[C@@H](O)[C@H](O[C@@H]4CO)n4c[n+](c5cc(C)c(C)cc45)[Co-3]456(C)N1C3=C(C)C1=[N+]4C(=CC3=[N+]5C(=C(C)C4=[N+]6[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O CHEBI:25291 CHEBI:48831 CHEBI:6869 CAS:13422-55-4 COMe:MOL000085 DrugBank:DB03614 Gmelin:124528 KEGG:C06453 KEGG:D03246 PDBeChem:COB Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-methylcobamide Methylcobalamin methylcobalamin chebi_ontology CO-METHYLCOBALAMIN MeCbl mecobalamin methylcob(III)alamin CHEBI:28115 methylcobalamin CAS:13422-55-4 ChemIDplus CAS:13422-55-4 KEGG COMPOUND Gmelin:124528 Gmelin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-methylcobamide IUPAC Methylcobalamin KEGG_COMPOUND methylcobalamin CBN CO-METHYLCOBALAMIN PDBeChem MeCbl CBN mecobalamin ChEBI methylcob(III)alamin UniProt 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 The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13634 CHEBI:24022 CHEBI:4985 KEGG:C02403 PMID:18628202 Fatty acid anion chebi_ontology Alkanate Fettsaeureanion Fettsaeureanionen a fatty acid acido graso anionico acidos grasos anionicos anion de l'acide gras fatty acid anions CHEBI:28868 fatty acid anion PMID:18628202 Europe PMC Fatty acid anion KEGG_COMPOUND Alkanate KEGG_COMPOUND Fettsaeureanion ChEBI Fettsaeureanionen ChEBI a fatty acid UniProt acido graso anionico ChEBI acidos grasos anionicos ChEBI anion de l'acide gras ChEBI fatty acid anions ChEBI 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 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 ion PDBeChem An N-acetyl-L-amino acid that is the N-acetylated derivative of the natural amino acid L-cysteine. 0 C5H9NO3S InChI=1S/C5H9NO3S/c1-3(7)6-4(2-10)5(8)9/h4,10H,2H2,1H3,(H,6,7)(H,8,9)/t4-/m0/s1 PWKSKIMOESPYIA-BYPYZUCNSA-N 163.19590 163.03031 CC(=O)N[C@@H](CS)C(O)=O CHEBI:21548 CHEBI:2418 CHEBI:45481 Beilstein:1724426 CAS:616-91-1 DrugBank:DB06151 Drug_Central:66 Gmelin:142554 HMDB:HMDB0001890 KEGG:C06809 KEGG:D00221 LINCS:LSM-4672 MetaCyc:CPD-9175 PDBeChem:SC2 PMID:10651166 PMID:17174578 PMID:2026726 PMID:24119926 PMID:25553484 Reaxys:1724426 Wikipedia:Acetylcysteine N-ACETYL-L-CYSTEINE N-acetyl-L-cysteine chebi_ontology (2R)-2-acetylamino-3-sulfanylpropanoic acid (R)-2-acetylamino-3-mercaptopropanoic acid (R)-mercapturic acid Acetylcysteine L-acetylcysteine L-alpha-acetamido-beta-mercaptopropionic acid N-acetyl-L-(+)-cysteine N-acetylcysteine NAC acetilcisteina acetylcysteinum mercapturic acid CHEBI:28939 N-acetyl-L-cysteine Beilstein:1724426 Beilstein CAS:616-91-1 ChemIDplus CAS:616-91-1 KEGG COMPOUND CAS:616-91-1 NIST Chemistry WebBook Drug_Central:66 DrugCentral Gmelin:142554 Gmelin PMID:10651166 Europe PMC PMID:17174578 Europe PMC PMID:2026726 Europe PMC PMID:24119926 Europe PMC PMID:25553484 Europe PMC Reaxys:1724426 Reaxys N-ACETYL-L-CYSTEINE PDBeChem N-acetyl-L-cysteine IUPAC (2R)-2-acetylamino-3-sulfanylpropanoic acid IUPAC (R)-2-acetylamino-3-mercaptopropanoic acid ChEBI (R)-mercapturic acid ChemIDplus Acetylcysteine KEGG_COMPOUND L-acetylcysteine ChemIDplus L-alpha-acetamido-beta-mercaptopropionic acid NIST_Chemistry_WebBook N-acetyl-L-(+)-cysteine NIST_Chemistry_WebBook N-acetylcysteine ChemIDplus NAC ChEBI acetilcisteina ChemIDplus acetylcysteinum ChemIDplus mercapturic acid ChemIDplus 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 An alpha-amino acid that is glycine in which the alpha-is substituted by a 3-guanidinopropyl group. 0 C6H14N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10) ODKSFYDXXFIFQN-UHFFFAOYSA-N 174.20112 174.11168 NC(CCCNC(N)=N)C(O)=O CHEBI:22616 CHEBI:2643 Beilstein:1725411 CAS:7200-25-1 KEGG:C02385 PMID:10848923 Reaxys:1725411 Wikipedia:L-Arginine Arginine arginine chebi_ontology 2-Amino-5-guanidinovaleric acid 2-amino-5-(carbamimidamido)pentanoic acid 2-amino-5-guanidinopentanoic acid Arginin Harg CHEBI:29016 arginine Beilstein:1725411 Beilstein CAS:7200-25-1 ChemIDplus PMID:10848923 Europe PMC Reaxys:1725411 Reaxys Arginine KEGG_COMPOUND arginine IUPAC 2-Amino-5-guanidinovaleric acid KEGG_COMPOUND 2-amino-5-(carbamimidamido)pentanoic acid IUPAC 2-amino-5-guanidinopentanoic acid JCBN Arginin ChEBI Harg IUPAC 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 -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 A carboxamide derived from a monocarboxylic acid. 0 CNOR3 42.01680 41.99799 [*]N([*])C([*])=O CHEBI:13211 CHEBI:22207 CHEBI:25383 CHEBI:6977 chebi_ontology monocarboxylic acid amides CHEBI:29347 monocarboxylic acid amide monocarboxylic acid amides ChEBI An alpha-amino-acid anion that is the conjugate base of L-glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-M 146.12136 146.04588 [NH3+][C@@H](CCC([O-])=O)C([O-])=O CHEBI:13107 CHEBI:21301 CAS:11070-68-1 Gmelin:936654 MetaCyc:GLT L-glutamate(1-) hydrogen L-glutamate chebi_ontology (2S)-2-ammoniopentanedioate L-glutamate L-glutamic acid monoanion L-glutamic acid, ion(1-) CHEBI:29985 L-glutamate(1-) CAS:11070-68-1 ChemIDplus Gmelin:936654 Gmelin L-glutamate(1-) JCBN hydrogen L-glutamate IUPAC (2S)-2-ammoniopentanedioate IUPAC L-glutamate ChEBI L-glutamate UniProt L-glutamic acid monoanion JCBN L-glutamic acid, ion(1-) ChemIDplus An alpha-amino-acid anion that is the conjugate base of D-glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-M 146.12136 146.04588 [NH3+][C@H](CCC([O-])=O)C([O-])=O CHEBI:12979 CHEBI:21022 Beilstein:8319427 MetaCyc:D-GLT D-glutamate(1-) hydrogen D-glutamate chebi_ontology (2R)-2-ammoniopentanedioate D-glutamate D-glutamic acid monoanion CHEBI:29986 D-glutamate(1-) Beilstein:8319427 Beilstein D-glutamate(1-) JCBN hydrogen D-glutamate IUPAC (2R)-2-ammoniopentanedioate IUPAC D-glutamate UniProt D-glutamic acid monoanion JCBN A dicarboxylic acid dianion that is the conjugate base of glutamate(1-). -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2 WHUUTDBJXJRKMK-UHFFFAOYSA-L 145.11342 145.03860 NC(CCC([O-])=O)C([O-])=O Beilstein:4134100 Gmelin:327903 Reaxys:4134100 2-aminopentanedioate glutamate glutamate(2-) chebi_ontology glutamic acid dianion CHEBI:29987 glutamate(2-) Beilstein:4134100 Beilstein Gmelin:327903 Gmelin Reaxys:4134100 Reaxys 2-aminopentanedioate IUPAC glutamate IUPAC glutamate(2-) JCBN glutamic acid dianion JCBN An L-alpha-amino acid anion that is the dianion obtained by the deprotonation of the both the carboxy groups of L-glutamic acid. -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-L 145.11342 145.03860 N[C@@H](CCC([O-])=O)C([O-])=O Gmelin:327905 (2S)-2-aminopentanedioate L-glutamate L-glutamate(2-) chebi_ontology L-glutamic acid dianion CHEBI:29988 L-glutamate(2-) Gmelin:327905 Gmelin (2S)-2-aminopentanedioate IUPAC L-glutamate IUPAC L-glutamate(2-) JCBN L-glutamic acid dianion JCBN -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-L 145.11342 145.03860 N[C@H](CCC([O-])=O)C([O-])=O Beilstein:8143000 Gmelin:327904 (2R)-2-aminopentanedioate D-glutamate D-glutamate(2-) chebi_ontology D-glutamic acid dianion CHEBI:29989 D-glutamate(2-) Beilstein:8143000 Beilstein Gmelin:327904 Gmelin (2R)-2-aminopentanedioate IUPAC D-glutamate IUPAC D-glutamate(2-) JCBN D-glutamic acid dianion JCBN 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 A derivative of the dimethylisoalloxazine (7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione) skeleton, with a substituent on the 10 position. 0 C12H9N4O2R 241.22550 241.07255 Cc1cc2nc3c(nc(=O)[nH]c3=O)n([*])c2cc1C CHEBI:24042 CHEBI:5073 KEGG:C00176 Flavin flavins chebi_ontology CHEBI:30527 flavin Flavin KEGG_COMPOUND flavins IUPAC A straight-chain saturated fatty acid that is butane in which one of the terminal methyl groups has been oxidised to a carboxy group. 0 C4H8O2 InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6) FERIUCNNQQJTOY-UHFFFAOYSA-N 88.10510 88.05243 CCCC(O)=O CHEBI:113450 CHEBI:22948 CHEBI:3234 CHEBI:41208 Beilstein:906770 CAS:107-92-6 DrugBank:DB03568 Gmelin:26242 HMDB:HMDB0000039 KEGG:C00246 KNApSAcK:C00001180 LIPID_MAPS_instance:LMFA01010004 MetaCyc:BUTYRIC_ACID PDBeChem:BUA PMID:10736622 PMID:10956204 PMID:11201044 PMID:11208715 PMID:11238216 PMID:11305323 PMID:12068484 PMID:13678314 PMID:14962641 PMID:1542095 PMID:15809727 PMID:15810631 PMID:15938880 PMID:19318247 PMID:19366864 PMID:19703412 PMID:21699495 PMID:22038864 PMID:22194341 PMID:22322557 PMID:22339023 PMID:22466881 Reaxys:906770 Wikipedia:Butyric_acid Butyric acid butanoic acid butyric acid chebi_ontology 1-butanoic acid 1-butyric acid 1-propanecarboxylic acid 4:0 BUTANOIC ACID Butanoate Butanoic acid Buttersaeure C4:0 CH3-[CH2]2-COOH acide butanoique acide butyrique butanic acid butoic acid ethylacetic acid n-butanoic acid n-butyric acid propanecarboxylic acid propylformic acid CHEBI:30772 butyric acid Beilstein:906770 Beilstein CAS:107-92-6 ChemIDplus CAS:107-92-6 KEGG COMPOUND CAS:107-92-6 NIST Chemistry WebBook Gmelin:26242 Gmelin LIPID_MAPS_instance:LMFA01010004 LIPID MAPS PMID:10736622 Europe PMC PMID:10956204 ChEMBL PMID:11201044 Europe PMC PMID:11208715 Europe PMC PMID:11238216 Europe PMC PMID:11305323 Europe PMC PMID:12068484 Europe PMC PMID:13678314 Europe PMC PMID:14962641 Europe PMC PMID:1542095 ChEMBL PMID:15809727 Europe PMC PMID:15810631 Europe PMC PMID:15938880 Europe PMC PMID:19318247 Europe PMC PMID:19366864 Europe PMC PMID:19703412 Europe PMC PMID:21699495 Europe PMC PMID:22038864 Europe PMC PMID:22194341 Europe PMC PMID:22322557 Europe PMC PMID:22339023 Europe PMC PMID:22466881 Europe PMC Reaxys:906770 Reaxys Butyric acid KEGG_COMPOUND butanoic acid IUPAC butyric acid IUPAC 1-butanoic acid HMDB 1-butyric acid HMDB 1-propanecarboxylic acid MetaCyc 4:0 ChEBI BUTANOIC ACID PDBeChem Butanoate KEGG_COMPOUND Butanoic acid KEGG_COMPOUND Buttersaeure ChEBI C4:0 ChEBI CH3-[CH2]2-COOH IUPAC acide butanoique IUPAC acide butyrique ChEBI butanic acid ChEBI butoic acid ChEBI ethylacetic acid NIST_Chemistry_WebBook n-butanoic acid NIST_Chemistry_WebBook n-butyric acid NIST_Chemistry_WebBook propanecarboxylic acid HMDB propylformic acid MetaCyc A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. alcohol http://langual.org 0 HOR 17.007 17.00274 O[*] CHEBI:13804 CHEBI:22288 CHEBI:2553 KEGG:C00069 http://www.langual.org/langual_thesaurus.asp?termid=B3324 Alcohol alcohols chebi_ontology an alcohol CHEBI:30879 alcohol Alcohol KEGG_COMPOUND alcohols IUPAC an alcohol UniProt 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 A short-chain fatty acid anion that is the conjugate base of valeric acid; present in ester form as component of many steroid-based pharmaceuticals. -1 C5H9O2 InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7)/p-1 NQPDZGIKBAWPEJ-UHFFFAOYSA-M 101.12376 101.06080 CCCCC([O-])=O CHEBI:14751 CHEBI:25890 Beilstein:3903735 CAS:10023-74-2 Gmelin:325619 PMID:17314444 PMID:18783570 Reaxys:3903735 pentanoate chebi_ontology CH3-[CH2]3-COO(-) n-propylacetate pentanoate pentanoic acid, ion(1-) CHEBI:31011 valerate Beilstein:3903735 Beilstein CAS:10023-74-2 ChemIDplus Gmelin:325619 Gmelin PMID:17314444 Europe PMC PMID:18783570 Europe PMC Reaxys:3903735 Reaxys pentanoate IUPAC CH3-[CH2]3-COO(-) IUPAC n-propylacetate ChEBI pentanoate UniProt pentanoic acid, ion(1-) ChemIDplus The L-enantiomer of cysteinate(1-). -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-M 120.15128 120.01247 N[C@@H](CS)C([O-])=O Beilstein:4128886 Gmelin:325857 Reaxys:4128886 L-cysteinate(1-) hydrogen L-cysteinate chebi_ontology (2R)-2-amino-3-mercaptopropanoate (2R)-2-amino-3-sulfanylpropanoate L-cysteine anion L-cysteine monoanion CHEBI:32442 L-cysteinate(1-) Beilstein:4128886 Beilstein Gmelin:325857 Gmelin Reaxys:4128886 Reaxys L-cysteinate(1-) JCBN hydrogen L-cysteinate IUPAC (2R)-2-amino-3-mercaptopropanoate ChEBI (2R)-2-amino-3-sulfanylpropanoate IUPAC L-cysteine anion NIST_Chemistry_WebBook L-cysteine monoanion JCBN The L-enantiomer of cysteinate(2-). -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-L 119.14334 119.00520 N[C@@H](C[S-])C([O-])=O Beilstein:5921923 Gmelin:325856 Reaxys:5921923 L-cysteinate L-cysteinate(2-) chebi_ontology (2R)-2-amino-3-sulfidopropanoate L-cysteine dianion CHEBI:32443 L-cysteinate(2-) Beilstein:5921923 Beilstein Gmelin:325856 Gmelin Reaxys:5921923 Reaxys L-cysteinate IUPAC L-cysteinate(2-) JCBN (2R)-2-amino-3-sulfidopropanoate IUPAC L-cysteine dianion JCBN The L-enantiomer of cysteinium. +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-O 122.16716 122.02703 [NH3+][C@@H](CS)C(O)=O Gmelin:325860 L-cysteinium chebi_ontology (1R)-1-carboxy-2-mercaptoethanaminium (1R)-1-carboxy-2-sulfanylethanaminium L-cysteine cation L-cysteinium(1+) CHEBI:32445 L-cysteinium Gmelin:325860 Gmelin L-cysteinium IUPAC (1R)-1-carboxy-2-mercaptoethanaminium ChEBI (1R)-1-carboxy-2-sulfanylethanaminium IUPAC L-cysteine cation JCBN L-cysteinium(1+) ChEBI The D-enantiomer of cysteinate(1-). -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-M 120.15128 120.01247 N[C@H](CS)C([O-])=O Gmelin:1006156 D-cysteinate(1-) hydrogen D-cysteinate chebi_ontology (2S)-2-amino-3-mercaptopropanoate (2S)-2-amino-3-sulfanylpropanoate D-cysteine monoanion CHEBI:32449 D-cysteinate(1-) Gmelin:1006156 Gmelin D-cysteinate(1-) JCBN hydrogen D-cysteinate IUPAC (2S)-2-amino-3-mercaptopropanoate ChEBI (2S)-2-amino-3-sulfanylpropanoate IUPAC D-cysteine monoanion JCBN The D-enantiomer of cysteinate(2-). -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-L 119.14334 119.00520 N[C@H](C[S-])C([O-])=O Gmelin:1342792 D-cysteinate D-cysteinate(2-) chebi_ontology (2S)-2-amino-3-sulfidopropanoate D-cysteine dianion CHEBI:32450 D-cysteinate(2-) Gmelin:1342792 Gmelin D-cysteinate IUPAC D-cysteinate(2-) JCBN (2S)-2-amino-3-sulfidopropanoate IUPAC D-cysteine dianion JCBN The D-enantiomer of cysteinium. +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-O 122.16716 122.02703 [NH3+][C@H](CS)C(O)=O Gmelin:363237 D-cysteinium chebi_ontology (1S)-1-carboxy-2-mercaptoethanaminium (1S)-1-carboxy-2-sulfanylethanaminium D-cysteine cation CHEBI:32451 D-cysteinium Gmelin:363237 Gmelin D-cysteinium IUPAC (1S)-1-carboxy-2-mercaptoethanaminium ChEBI (1S)-1-carboxy-2-sulfanylethanaminium IUPAC D-cysteine cation JCBN A sulfur-containing amino-acid anion that is the conjugate base of cysteine, obtained by deprotonation of the carboxy group. -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1 XUJNEKJLAYXESH-UHFFFAOYSA-M 120.15128 120.01247 NC(CS)C([O-])=O Beilstein:4128885 Gmelin:363235 Reaxys:4128885 cysteinate(1-) hydrogen cysteinate chebi_ontology 2-amino-3-mercaptopropanoate 2-amino-3-sulfanylpropanoate cys(-) cysteine monoanion CHEBI:32456 cysteinate(1-) Beilstein:4128885 Beilstein Gmelin:363235 Gmelin Reaxys:4128885 Reaxys cysteinate(1-) JCBN hydrogen cysteinate IUPAC 2-amino-3-mercaptopropanoate ChEBI 2-amino-3-sulfanylpropanoate IUPAC cys(-) IUPAC cysteine monoanion JCBN -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2 XUJNEKJLAYXESH-UHFFFAOYSA-L 119.14334 119.00520 NC(C[S-])C([O-])=O Gmelin:49990 cysteinate cysteinate(2-) chebi_ontology 2-amino-3-sulfidopropanoate cysteine dianion CHEBI:32457 cysteinate(2-) Gmelin:49990 Gmelin cysteinate IUPAC cysteinate(2-) JCBN 2-amino-3-sulfidopropanoate IUPAC cysteine dianion JCBN +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1 XUJNEKJLAYXESH-UHFFFAOYSA-O 122.16716 122.02703 [NH3+]C(CS)C(O)=O Gmelin:325859 1-carboxy-2-sulfanylethanaminium cysteinium chebi_ontology 1-carboxy-2-mercaptoethanaminium H2cys(+) cysteine cation CHEBI:32458 cysteinium Gmelin:325859 Gmelin 1-carboxy-2-sulfanylethanaminium IUPAC cysteinium JCBN 1-carboxy-2-mercaptoethanaminium ChEBI H2cys(+) IUPAC cysteine cation JCBN An alpha-amino-acid cation that is the conjugate acid of glycine, arising from protonation of the amino. +1 C2H6NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/p+1 DHMQDGOQFOQNFH-UHFFFAOYSA-O 76.07458 76.03930 [NH3+]CC(O)=O Gmelin:323509 glycinium chebi_ontology H2gly(+) NH3(+)-CH2-COOH carboxymethanaminium glycine cation CHEBI:32507 glycinium Gmelin:323509 Gmelin glycinium IUPAC H2gly(+) IUPAC NH3(+)-CH2-COOH IUPAC carboxymethanaminium IUPAC glycine cation JCBN An alpha-amino-acid anion that is the conjugate base of glycine, arising from deprotonation of the carboxy group. -1 C2H4NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/p-1 DHMQDGOQFOQNFH-UHFFFAOYSA-M 74.05870 74.02475 NCC([O-])=O Beilstein:1852023 Gmelin:81890 Reaxys:1852023 UM-BBD_compID:c0559 glycinate chebi_ontology H2N-CH2-COO(-) aminoacetate gly(-) glycine anion CHEBI:32508 glycinate Beilstein:1852023 Beilstein Gmelin:81890 Gmelin Reaxys:1852023 Reaxys UM-BBD_compID:c0559 UM-BBD glycinate IUPAC H2N-CH2-COO(-) IUPAC aminoacetate IUPAC gly(-) IUPAC glycine anion JCBN A sulfur-containing amino-acid anion that is the conjugate base of methionine, arising from deprotonation of the carboxy group. -1 C5H10NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p-1 FFEARJCKVFRZRR-UHFFFAOYSA-M 148.20444 148.04377 CSCCC(N)C([O-])=O Beilstein:3937270 Gmelin:326565 Reaxys:3937270 methioninate chebi_ontology 2-amino-4-(methylsulfanyl)butanoate met(-) methionine anion CHEBI:32644 methioninate Beilstein:3937270 Beilstein Gmelin:326565 Gmelin Reaxys:3937270 Reaxys methioninate IUPAC 2-amino-4-(methylsulfanyl)butanoate IUPAC met(-) IUPAC methionine anion JCBN A sulfur-containing amino-acid anion that is the conjugate acid of methionine, arising from protonation of the amino group. +1 C5H12NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p+1 FFEARJCKVFRZRR-UHFFFAOYSA-O 150.22032 150.05833 CSCCC([NH3+])C(O)=O Gmelin:326567 methioninium chebi_ontology 1-carboxy-3-(methylsulfanyl)propan-1-aminium H2met(+) methionine cation CHEBI:32646 methioninium Gmelin:326567 Gmelin methioninium IUPAC 1-carboxy-3-(methylsulfanyl)propan-1-aminium IUPAC H2met(+) IUPAC methionine cation JCBN -1 C6H13N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p-1 ODKSFYDXXFIFQN-UHFFFAOYSA-M 173.19318 173.10440 NC(CCCNC(N)=N)C([O-])=O Gmelin:603497 argininate chebi_ontology 2-amino-5-(carbamimidamido)pentanoate 2-amino-5-guanidinopentanoate arg(-) arginine anion CHEBI:32695 argininate Gmelin:603497 Gmelin argininate IUPAC 2-amino-5-(carbamimidamido)pentanoate IUPAC 2-amino-5-guanidinopentanoate JCBN arg(-) IUPAC arginine anion JCBN +1 C6H15N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1 ODKSFYDXXFIFQN-UHFFFAOYSA-O 175.20906 175.11895 NC(=[NH2+])NCCCC([NH3+])C([O-])=O Gmelin:1345599 argininium argininium(1+) chebi_ontology 2-ammonio-5-guanidiniopentanoate H2arg(+) arginine arginine monocation CHEBI:32696 argininium(1+) Gmelin:1345599 Gmelin argininium IUPAC argininium(1+) JCBN 2-ammonio-5-guanidiniopentanoate JCBN H2arg(+) IUPAC arginine UniProt arginine monocation JCBN +2 C6H16N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+2 ODKSFYDXXFIFQN-UHFFFAOYSA-P 176.21700 176.12623 NC(=[NH2+])NCCCC([NH3+])C(O)=O argininediium argininium(2+) chebi_ontology (1-carboxy-4-guanidiniobutyl)ammonium H3arg(2+) arginine dication CHEBI:32697 argininium(2+) argininediium IUPAC argininium(2+) JCBN (1-carboxy-4-guanidiniobutyl)ammonium ChEBI H3arg(2+) IUPAC arginine dication JCBN A serinate that is the conjugate base of L-serine, obtained by deprotonation of the carboxy group. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-M 104.08468 104.03532 N[C@@H](CO)C([O-])=O Beilstein:4372751 Gmelin:324693 L-serinate chebi_ontology (2S)-2-amino-3-hydroxypropanoate L-serine anion CHEBI:32836 L-serinate Beilstein:4372751 Beilstein Gmelin:324693 Gmelin L-serinate IUPAC (2S)-2-amino-3-hydroxypropanoate IUPAC L-serine anion JCBN A serinium that is the conjugate acid of L-serine, obtained by protonation of the amino group. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-O 106.10056 106.04987 [NH3+][C@@H](CO)C(O)=O L-serinium chebi_ontology (1S)-1-carboxy-2-hydroxyethanaminium L-serine cation CHEBI:32837 L-serinium L-serinium IUPAC (1S)-1-carboxy-2-hydroxyethanaminium IUPAC L-serine cation JCBN The D-enantiomer of serinate. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-M 104.08468 104.03532 N[C@H](CO)C([O-])=O Gmelin:745975 D-serinate chebi_ontology (2R)-2-amino-3-hydroxypropanoate D-serine anion CHEBI:32840 D-serinate Gmelin:745975 Gmelin D-serinate IUPAC (2R)-2-amino-3-hydroxypropanoate IUPAC D-serine anion JCBN The D-enantiomer of serinium. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-O 106.10056 106.04987 [NH3+][C@H](CO)C(O)=O D-serinium chebi_ontology (1R)-1-carboxy-2-hydroxyethanaminium D-serine cation CHEBI:32841 D-serinium D-serinium IUPAC (1R)-1-carboxy-2-hydroxyethanaminium IUPAC D-serine cation JCBN An alpha-amino-acid anion that is the conjugate base of serine. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1 MTCFGRXMJLQNBG-UHFFFAOYSA-M 104.08468 104.03532 NC(CO)C([O-])=O Gmelin:324692 serinate chebi_ontology 2-amino-3-hydroxypropanoate serine anion CHEBI:32845 serinate Gmelin:324692 Gmelin serinate IUPAC 2-amino-3-hydroxypropanoate IUPAC serine anion JCBN An alpha-amino-acid cation that is the conjugate acid of serine. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1 MTCFGRXMJLQNBG-UHFFFAOYSA-O 106.10056 106.04987 [NH3+]C(CO)C(O)=O Gmelin:1925675 serinium chebi_ontology 1-carboxy-2-hydroxyethanaminium serine cation CHEBI:32846 serinium Gmelin:1925675 Gmelin serinium IUPAC 1-carboxy-2-hydroxyethanaminium IUPAC serine cation JCBN -1 C5H11N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p-1 AHLPHDHHMVZTML-UHFFFAOYSA-M 131.15312 131.08260 NCCCC(N)C([O-])=O CHEBI:11448 CHEBI:19370 Gmelin:1242186 2,5-diaminopentanoate ornithinate chebi_ontology ornithine anion CHEBI:32964 ornithinate Gmelin:1242186 Gmelin 2,5-diaminopentanoate IUPAC ornithinate IUPAC ornithine anion JCBN 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 vitamin role Any micronutrient that is an organic compound. The term "vitamines" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines. CHEBI:10004 CHEBI:27305 Wikipedia:Vitamin Vitamin chebi_ontology vitamina vitaminas vitamine vitamines vitamins vitaminum CHEBI:33229 vitamin Vitamin ChEBI vitamina ChEBI vitaminas ChEBI vitamine ChEBI vitamines ChEBI vitamins ChEBI vitaminum ChEBI application role 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 An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands). coordination entities coordination entity chebi_ontology coordination compounds CHEBI:33240 coordination entity coordination entities IUPAC coordination entity IUPAC coordination compounds 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 A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 atom chebi_ontology atome atomo atoms atomus element elements CHEBI:33250 atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements 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 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 An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 Wikipedia:Organosulfur_compounds organosulfur compound chebi_ontology organosulfur compounds CHEBI:33261 organosulfur compound organosulfur compound ChEBI organosulfur compounds ChEBI 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 nutrient role 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 food role Any material that can be ingested by an organism. chebi_ontology food material food materials food role foods foodstuff foodstuffs CHEBI:33290 food food material ChEBI food materials ChEBI food role ChEBI foods ChEBI foodstuff ChEBI foodstuffs ChEBI An energy-rich substance that can be transformed with release of usable energy. chebi_ontology CHEBI:33292 fuel 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 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 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 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 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 serine zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-N 105.09262 105.04259 [NH3+][C@@H](CO)C([O-])=O MetaCyc:SER (2S)-2-ammonio-3-hydroxypropanoate L-serine zwitterion chebi_ontology L-serine CHEBI:33384 L-serine zwitterion (2S)-2-ammonio-3-hydroxypropanoate IUPAC L-serine zwitterion IUPAC L-serine UniProt A molecular entity containing one or more atoms of a transition element. chebi_ontology transition element molecular entities transition metal molecular entity CHEBI:33497 transition element molecular entity transition element molecular entities ChEBI transition metal molecular entity ChEBI 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 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 Any carboxylic acid having a sulfur substituent. chebi_ontology S-containing carboxylic acid S-containing carboxylic acids sulfur-containing carboxylic acids CHEBI:33576 sulfur-containing carboxylic acid S-containing carboxylic acid ChEBI S-containing carboxylic acids ChEBI sulfur-containing carboxylic acids ChEBI 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 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 chebi_ontology monocyclic compounds CHEBI:33661 monocyclic compound monocyclic compounds ChEBI heteromonocyclic compound heteromonocyclic compounds chebi_ontology CHEBI:33670 heteromonocyclic compound heteromonocyclic compound IUPAC heteromonocyclic compounds IUPAC 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 chebi_ontology zinc group molecular entities CHEBI:33673 zinc group molecular entity zinc group molecular entities ChEBI 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 chebi_ontology d-block compounds d-block molecular entities CHEBI:33676 d-block molecular entity d-block molecular entity ChEBI d-block compounds ChEBI d-block molecular entities ChEBI Hydrides are chemical compounds of hydrogen with other chemical elements. chebi_ontology CHEBI:33692 hydrides A cation consisting of more than one atom. chebi_ontology polyatomic cations CHEBI:33702 polyatomic cation polyatomic cations ChEBI amino-acid cation chebi_ontology amino acid cation amino-acid cations CHEBI:33703 amino-acid cation amino-acid cation ChEBI amino acid cation ChEBI amino-acid 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 A non-proteinogenic amino-acid in which the amino group is located on the carbon atom at the position gamma to the carboxy group. gamma-amino acid chebi_ontology gamma-amino acids CHEBI:33707 gamma-amino acid gamma-amino acid ChEBI gamma-amino acids ChEBI 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 alpha-amino-acid cation chebi_ontology alpha-amino acid cations alpha-amino-acid cations CHEBI:33719 alpha-amino-acid cation alpha-amino-acid cation ChEBI alpha-amino acid cations ChEBI alpha-amino-acid cations ChEBI cobalt group molecular entity chebi_ontology cobalt group molecular entities CHEBI:33767 cobalt group molecular entity cobalt group molecular entity ChEBI cobalt group molecular entities 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 Alkenols; the term refers specifically to vinylic alcohols, which have the structure HOCR'=CR2. Enols are tautomeric with aldehydes (R' = H) or ketones (R' =/= H). 0 C2HOR3 41.02870 41.00274 O\C([*])=C(/[*])[*] enol enols chebi_ontology alkenols enols CHEBI:33823 enol enol IUPAC enols IUPAC alkenols IUPAC enols 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 An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. 0 C5H8O3R2 116.115 116.04734 [C@H]1([C@H]([C@@H](*)[C@@H](O1)*)O)CO CHEBI:13661 CHEBI:25611 CHEBI:7647 KEGG:C00801 Nucleoside nucleosides chebi_ontology a nucleoside nucleosides CHEBI:33838 nucleoside Nucleoside KEGG_COMPOUND nucleosides IUPAC a nucleoside UniProt nucleosides ChEBI An amino compound in which the amino group is linked directly to an aromatic system. CHEBI:13827 CHEBI:22622 CHEBI:22646 CHEBI:2834 CHEBI:2863 chebi_ontology aromatic amines aryl amine aryl amines arylamine arylamines CHEBI:33860 aromatic amine aromatic amines ChEBI aryl amine ChEBI aryl amines ChEBI arylamine ChEBI arylamines ChEBI chebi_ontology transition element coordination entities transition metal coordination compounds transition metal coordination entities CHEBI:33861 transition element coordination entity transition element coordination entities ChEBI transition metal coordination compounds ChEBI transition metal coordination entities ChEBI cobalt molecular entity chebi_ontology cobalt compounds cobalt molecular entities CHEBI:33888 cobalt molecular entity cobalt molecular entity ChEBI cobalt compounds ChEBI cobalt molecular entities ChEBI cobalt coordination entity chebi_ontology cobalt coordination compounds cobalt coordination entities CHEBI:33890 cobalt coordination entity cobalt coordination entity ChEBI cobalt coordination compounds ChEBI cobalt coordination entities ChEBI 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 chebi_ontology cobalt corrinoids cobalt-corrinoids CHEBI:33906 cobalt corrinoid cobalt corrinoids ChEBI cobalt-corrinoids ChEBI chebi_ontology metal-tetrapyrrole metal-tetrapyrrole complex metallotetrapyrroles CHEBI:33909 metallotetrapyrrole metal-tetrapyrrole ChEBI metal-tetrapyrrole complex ChEBI metallotetrapyrroles ChEBI A derivative of the corrin nucleus, which contains four reduced or partly reduced pyrrole rings joined in a macrocycle by three =C- groups and one direct carbon-carbon bond linking alpha positions. 0 C19HN4R21 285.239 285.02012 CHEBI:23391 CHEBI:3890 KEGG:C06021 Corrinoid corrinoid corrinoids chebi_ontology Corrinoid protein Corrinoid protein Co+ Korrinoid corrinoide corrinoides CHEBI:33913 corrinoid Corrinoid KEGG_COMPOUND corrinoid UniProt corrinoids IUPAC Corrinoid protein KEGG_COMPOUND Corrinoid protein Co+ KEGG_COMPOUND Korrinoid ChEBI corrinoide IUPAC corrinoides IUPAC chebi_ontology CHEBI:33937 macronutrient A quaternary ammonium ion that is the the conjugate acid of carnitine. +1 C7H16NO3 InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3/p+1 PHIQHXFUZVPYII-UHFFFAOYSA-O 162.20688 162.11247 C[N+](C)(C)CC(O)CC(O)=O CAS:406-76-8 CAS:461-06-3 KEGG:C00487 3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium chebi_ontology 3-hydroxy-4-(trimethylammonio)butanoic acid Carnitine CHEBI:3424 carnitinium CAS:406-76-8 KEGG COMPOUND CAS:461-06-3 KEGG COMPOUND 3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium IUPAC 3-hydroxy-4-(trimethylammonio)butanoic acid ChEBI Carnitine KEGG_COMPOUND 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 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-N 121.15922 121.01975 [NH3+][C@@H](CS)C([O-])=O Gmelin:49993 (2R)-2-ammonio-3-sulfanylpropanoate L-cysteine zwitterion chebi_ontology (2R)-2-ammonio-3-mercaptopropanoate L-cysteine CHEBI:35235 L-cysteine zwitterion Gmelin:49993 Gmelin (2R)-2-ammonio-3-sulfanylpropanoate IUPAC L-cysteine zwitterion IUPAC (2R)-2-ammonio-3-mercaptopropanoate ChEBI L-cysteine UniProt 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-N 121.15922 121.01975 [NH3+][C@H](CS)C([O-])=O Gmelin:2352354 (2S)-2-ammonio-3-sulfanylpropanoate D-cysteine zwitterion chebi_ontology (2S)-2-ammonio-3-mercaptopropanoate D-cysteine CHEBI:35236 D-cysteine zwitterion Gmelin:2352354 Gmelin (2S)-2-ammonio-3-sulfanylpropanoate IUPAC D-cysteine zwitterion IUPAC (2S)-2-ammonio-3-mercaptopropanoate ChEBI D-cysteine UniProt 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 [NH3+]C(CS)C([O-])=O Gmelin:49992 2-ammonio-3-sulfanylpropanoate cysteine zwitterion chebi_ontology (+)H3N-CH(CH2SH)-COO(-) 2-ammonio-3-mercaptopropanoate CHEBI:35237 cysteine zwitterion Gmelin:49992 Gmelin 2-ammonio-3-sulfanylpropanoate IUPAC cysteine zwitterion IUPAC (+)H3N-CH(CH2SH)-COO(-) ChEBI 2-ammonio-3-mercaptopropanoate ChEBI 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 An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amnio group of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7) MTCFGRXMJLQNBG-UHFFFAOYSA-N 105.09262 105.04259 [NH3+]C(CO)C([O-])=O Beilstein:3935647 Gmelin:2060272 2-ammonio-3-hydroxypropanoate serine zwitterion chebi_ontology CHEBI:35243 serine zwitterion Beilstein:3935647 Beilstein Gmelin:2060272 Gmelin 2-ammonio-3-hydroxypropanoate IUPAC serine zwitterion IUPAC A serine zwitterion obtained by transfer of a proton from the carboxy to the amino group of D-serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-N 105.09262 105.04259 [NH3+][C@H](CO)C([O-])=O MetaCyc:D-SERINE (2R)-2-ammonio-3-hydroxypropanoate D-serine zwitterion chebi_ontology D-serine CHEBI:35247 D-serine zwitterion (2R)-2-ammonio-3-hydroxypropanoate IUPAC D-serine zwitterion IUPAC D-serine UniProt 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 quaternary ammonium quaternary ammonium ions CHEBI:35267 quaternary ammonium ion quaternary ammonium ion IUPAC Quaternary amine KEGG_COMPOUND 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 ammonium ions azanium ion derivative azanium ion derivatives azanium ions CHEBI:35274 ammonium ion derivative ammonium ion derivatives ChEBI ammonium ions ChEBI azanium ion derivative ChEBI azanium ion derivatives ChEBI azanium ions ChEBI Neutral molecules having charge-separated forms with an onium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. betaines chebi_ontology onium betaines CHEBI:35281 onium betaine betaines IUPAC onium betaines ChEBI Any neutral molecule having charge-separated forms with a quaternary ammonium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. chebi_ontology ammonium betaines CHEBI:35284 ammonium betaine ammonium betaines ChEBI 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, so may be considered as triterpenoids. 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 A sterol in which the hydroxy group at position 3 has beta- configuration. 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@@H](C4)O)C CHEBI:13609 CHEBI:1725 CHEBI:1726 CHEBI:20248 chebi_ontology 3beta-hydroxysteroids 3beta-sterols CHEBI:35348 3beta-sterol 3beta-hydroxysteroids ChEBI 3beta-sterols ChEBI 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 Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. fatty acids http://langual.org 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13633 CHEBI:24024 CHEBI:4984 Codex::570 Europe::570 KEGG:C00162 PMID:14287444 PMID:14300208 PMID:14328676 Wikipedia:Fatty_acid http://www.langual.org/langual_thesaurus.asp?termid=B3098 Fatty acid fatty acids chebi_ontology Fettsaeure Fettsaeuren acide gras acides gras acido graso acidos grasos fatty acids CHEBI:35366 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): antifoaming agent. foam stabilizer, glazing agent. fatty acid PMID:14287444 Europe PMC PMID:14300208 Europe PMC PMID:14328676 Europe PMC Fatty acid KEGG_COMPOUND fatty acids IUPAC Fettsaeure ChEBI Fettsaeuren ChEBI acide gras ChEBI acides gras ChemIDplus acido graso ChEBI acidos grasos ChEBI fatty acids ChEBI 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 used in the prophylaxis or therapy of infectious diseases. chebi_ontology anti-infective agents anti-infective drugs antiinfective agents antiinfective drug CHEBI:35441 antiinfective agent anti-infective agents ChEBI anti-infective drugs ChEBI antiinfective agents ChEBI antiinfective drug 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 C27H48 InChI=1S/C27H48/c1-19(2)9-8-10-20(3)23-14-15-24-22-13-12-21-11-6-7-17-26(21,4)25(22)16-18-27(23,24)5/h19-25H,6-18H2,1-5H3/t20-,21?,22+,23-,24+,25+,26+,27-/m1/s1 XIIAYQZJNBULGD-LDHZKLTISA-N 372.67002 372.37560 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCCC(C)C Beilstein:5334741 CAS:14982-53-7 LIPID_MAPS_instance:LMST01010000 Wikipedia:Cholestane cholestane chebi_ontology CHEBI:35516 cholestane Beilstein:5334741 Beilstein CAS:14982-53-7 ChemIDplus CAS:14982-53-7 NIST Chemistry WebBook LIPID_MAPS_instance:LMST01010000 LIPID MAPS cholestane IUPAC 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 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 secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it. 0 CH2OR2 30.026 30.01056 *C(*)O CHEBI:13425 CHEBI:13686 CHEBI:26617 CHEBI:58662 CHEBI:8741 CHEBI:9077 KEGG:C00432 KEGG:C01612 Secondary alcohol chebi_ontology R-CHOH-R' a secondary alcohol secondary alcohols CHEBI:35681 secondary alcohol Secondary alcohol KEGG_COMPOUND R-CHOH-R' KEGG_COMPOUND a secondary alcohol UniProt secondary alcohols 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 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 Any monocarboxylic acid which also contains a separate (alcoholic or phenolic) hydroxy substituent. chebi_ontology hydroxy acid hydroxy monocarboxylic acids CHEBI:35868 hydroxy monocarboxylic acid hydroxy acid ChEBI hydroxy monocarboxylic acids 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 A hydroxy monocarboxylic acid that has a hydroxy group beta to the carboxy group. chebi_ontology 3-hydroxy acid 3-hydroxy monocarboxylic acids beta-hydroxy acid beta-hydroxy acids beta-hydroxy carboxylic acid beta-hydroxy carboxylic acids CHEBI:35969 3-hydroxy monocarboxylic acid 3-hydroxy acid ChEBI 3-hydroxy monocarboxylic acids ChEBI beta-hydroxy acid ChEBI beta-hydroxy acids ChEBI beta-hydroxy carboxylic acid ChEBI beta-hydroxy carboxylic acids ChEBI A drug used to treat or prevent microbial infections. chebi_ontology antimicrobial drugs CHEBI:36043 antimicrobial drug antimicrobial drugs ChEBI A substance used in the prophylaxis or therapy of virus diseases. chebi_ontology anti-viral drug anti-virus drug antiviral drugs CHEBI:36044 antiviral drug anti-viral drug ChEBI anti-virus drug ChEBI antiviral drugs ChEBI Any monocarboxylic acid anion carrying at least one hydroxy substituent. chebi_ontology hydroxy monocarboxylic acid anions hydroxymonocarboxylic acid anion hydroxymonocarboxylic acid anions CHEBI:36059 hydroxy monocarboxylic acid anion hydroxy monocarboxylic acid anions ChEBI hydroxymonocarboxylic acid anion ChEBI hydroxymonocarboxylic acid anions 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 Compounds having a fully conjugated cyclic dione structure, such as that of benzoquinones, derived from aromatic compounds by conversion of an even number of -CH= groups into -C(=O)- groups with any necessary rearrangement of double bonds (polycyclic and heterocyclic analogues are included). CHEBI:13684 CHEBI:26517 Wikipedia:Quinone quinone quinones chebi_ontology Chinon quinones CHEBI:36141 quinone quinone IUPAC quinones IUPAC Chinon ChEBI quinones ChEBI Conjugate base of chenodeoxycholic acid; major species at pH 7.3. -1 C24H39O4 InChI=1S/C24H40O4/c1-14(4-7-21(27)28)17-5-6-18-22-19(9-11-24(17,18)3)23(2)10-8-16(25)12-15(23)13-20(22)26/h14-20,22,25-26H,4-13H2,1-3H3,(H,27,28)/p-1/t14-,15+,16-,17-,18+,19+,20-,22+,23+,24-/m1/s1 RUDATBOHQWOJDD-BSWAIDMHSA-M 391.56406 391.28538 [H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC([O-])=O CHEBI:13960 CHEBI:23093 CHEBI:57884 Beilstein:3703074 3alpha,7alpha-dihydroxy-5beta-cholan-24-oate chenodeoxycholate chebi_ontology chenodeoxycholate anion chenodeoxycholate(1-) CHEBI:36234 chenodeoxycholate Beilstein:3703074 Beilstein 3alpha,7alpha-dihydroxy-5beta-cholan-24-oate IUPAC chenodeoxycholate UniProt chenodeoxycholate anion ChEBI chenodeoxycholate(1-) ChEBI 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 CHEBI:23166 CHEBI:23211 chebi_ontology CHEBI:36278 cholanic acids macrocyclic tetrapyrroles chebi_ontology cyclic tetrapyrroles macrocyclic tetrapyrrole CHEBI:36309 cyclic tetrapyrrole macrocyclic tetrapyrroles IUPAC cyclic tetrapyrroles ChEBI macrocyclic tetrapyrrole ChEBI 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 A particle smaller than an atom. chebi_ontology subatomic particles CHEBI:36342 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 nucleus or any of its constituents in any of their energy states. nuclear particle chebi_ontology CHEBI:36347 nuclear particle nuclear particle IUPAC 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 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 heterotricyclic compound heterotricyclic compounds chebi_ontology heterotricyclic compounds CHEBI:36688 heterotricyclic compound heterotricyclic compound ChEBI heterotricyclic compounds IUPAC heterotricyclic compounds ChEBI Any hydroxy steroid carrying a hydroxy group at position 3. chebi_ontology 3-hydroxy steroids CHEBI:36834 3-hydroxy steroid 3-hydroxy steroids ChEBI A 3-hydroxy steroid in which the 3-hydroxy substituent is in the beta-position. 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@@H](C4)O)C CHEBI:71195 KEGG:C02945 MetaCyc:3-Beta-Hydroxysterols PMID:10535978 PMID:12829805 chebi_ontology 3beta-hydroxy steroids a 3beta-hydroxysteroid CHEBI:36836 3beta-hydroxy steroid PMID:10535978 SUBMITTER PMID:12829805 SUBMITTER 3beta-hydroxy steroids ChEBI a 3beta-hydroxysteroid UniProt 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 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 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 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:37253 elemental zinc A 7,8-dimethylbenzo[g]pteridine-2,4-dione that is isoalloxazine substituted by methyl groups at positions 7 and 8. 0 C12H10N4O2 InChI=1S/C12H10N4O2/c1-5-3-7-8(4-6(5)2)14-10-9(13-7)11(17)16-12(18)15-10/h3-4H,1-2H3,(H2,14,15,16,17,18) ZJTJUVIJVLLGSP-UHFFFAOYSA-N 242.23356 242.08038 Cc1cc2nc3c(nc(=O)[nH]c3=O)[nH]c2cc1C Beilstein:539579 PMID:16128574 Reaxys:539579 7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione chebi_ontology dimethylisoalloxazine CHEBI:37323 7,8-dimethylisoalloxazine Beilstein:539579 Beilstein PMID:16128574 Europe PMC Reaxys:539579 Reaxys 7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione IUPAC dimethylisoalloxazine IUPAC 0 C12H10N4O2 242.234 242.08038 7,8-dimethylbenzo[g]pteridine-2,4-dione chebi_ontology CHEBI:37324 7,8-dimethylbenzo[g]pteridine-2,4-dione 7,8-dimethylbenzo[g]pteridine-2,4-dione IUPAC 0 C10H6N4O2 InChI=1S/C10H6N4O2/c15-9-7-8(13-10(16)14-9)12-6-4-2-1-3-5(6)11-7/h1-4H,(H2,12,13,14,15,16) HAUGRYOERYOXHX-UHFFFAOYSA-N 214.18040 214.04908 O=c1[nH]c2nc3ccccc3nc2c(=O)[nH]1 Beilstein:85819 CAS:490-59-5 LINCS:LSM-2889 alloxazine benzo[g]pteridine-2,4(1H,3H)-dione chebi_ontology Alloxazin CHEBI:37325 alloxazine Beilstein:85819 Beilstein CAS:490-59-5 NIST Chemistry WebBook alloxazine NIST_Chemistry_WebBook benzo[g]pteridine-2,4(1H,3H)-dione IUPAC Alloxazin NIST_Chemistry_WebBook 0 C10H6N4O2 214.181 214.04908 benzo[g]pteridine-2,4-dione chebi_ontology CHEBI:37326 benzo[g]pteridine-2,4-dione benzo[g]pteridine-2,4-dione IUPAC 0 C10H6N4O2 InChI=1S/C10H6N4O2/c15-9-7-8(13-10(16)14-9)12-6-4-2-1-3-5(6)11-7/h1-4H,(H2,12,13,14,15,16) HAUGRYOERYOXHX-UHFFFAOYSA-N 214.18040 214.04908 O=c1nc2[nH]c3ccccc3nc2c(=O)[nH]1 Beilstein:991206 benzo[g]pteridine-2,4(3H,10H)-dione chebi_ontology CHEBI:37327 isoalloxazine Beilstein:991206 Beilstein benzo[g]pteridine-2,4(3H,10H)-dione IUPAC A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. CHEBI:24074 CHEBI:24076 folates chebi_ontology folate folates CHEBI:37445 folic acids folates IUPAC folate ChEBI folates ChEBI 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 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 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 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 Any organic heterocyclic compound containing at least one ring oxygen atom. PMID:17134300 chebi_ontology heterocyclic organooxygen compounds organooxygen heterocyclic compounds oxacycles CHEBI:38104 oxacycle PMID:17134300 Europe PMC heterocyclic organooxygen compounds ChEBI organooxygen heterocyclic compounds ChEBI oxacycles ChEBI chebi_ontology heterocyclic organosulfur compounds organosulfur heterocyclic compounds CHEBI:38106 organosulfur heterocyclic compound heterocyclic organosulfur compounds ChEBI organosulfur heterocyclic compounds ChEBI CHEBI:25429 CHEBI:38075 chebi_ontology organic heteropolycyclic compounds CHEBI:38166 organic heteropolycyclic compound organic heteropolycyclic compounds ChEBI chebi_ontology monocyclic heteroarenes CHEBI:38179 monocyclic heteroarene monocyclic heteroarenes ChEBI chebi_ontology azabicycloalkanes CHEBI:38295 azabicycloalkane azabicycloalkanes ChEBI chebi_ontology thiabicycloalkanes CHEBI:38297 thiabicycloalkane thiabicycloalkanes ChEBI Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). chebi_ontology CHEBI:38313 diazines A pyrimidine carrying one or more oxo substituents. chebi_ontology pyrimidones CHEBI:38337 pyrimidone pyrimidones ChEBI A member of the class of pyrimidines that is pyrimidine substituted by at least one amino group and its derivatives. chebi_ontology aminopyrimidines CHEBI:38338 aminopyrimidine aminopyrimidines ChEBI CHEBI:26949 CHEBI:38417 1,3-thiazoles chebi_ontology CHEBI:38418 1,3-thiazoles 1,3-thiazoles ChEBI 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 chebi_ontology benzopteridines CHEBI:38925 benzopteridine benzopteridines 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 Any saturated fatty acid lacking a side-chain. PMID:15644336 straight-chain saturated fatty acid chebi_ontology straight-chain saturated fatty acids CHEBI:39418 straight-chain saturated fatty acid PMID:15644336 Europe PMC straight-chain saturated fatty acid ChEBI straight-chain saturated fatty acids ChEBI CHEBI:13784 CHEBI:26445 CHEBI:7263 chebi_ontology CHEBI:39446 pyrimidine ribonucleosides Any compound having a pyrimidine as part of its structure. CHEBI:13681 CHEBI:26448 chebi_ontology CHEBI:39447 pyrimidines KEGG:C02019 Cyclic ketone cyclic ketones chebi_ontology CHEBI:3992 cyclic ketone Cyclic ketone KEGG_COMPOUND cyclic ketones 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 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 chebi_ontology CHEBI:43254 (4S)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one A ubiquinone having a side chain of 10 isoprenoid units. In the naturally occurring isomer, all isoprenyl double bonds are in the E- configuration. 0 C59H90O4 InChI=1S/C59H90O4/c1-44(2)24-15-25-45(3)26-16-27-46(4)28-17-29-47(5)30-18-31-48(6)32-19-33-49(7)34-20-35-50(8)36-21-37-51(9)38-22-39-52(10)40-23-41-53(11)42-43-55-54(12)56(60)58(62-13)59(63-14)57(55)61/h24,26,28,30,32,34,36,38,40,42H,15-23,25,27,29,31,33,35,37,39,41,43H2,1-14H3/b45-26+,46-28+,47-30+,48-32+,49-34+,50-36+,51-38+,52-40+,53-42+ ACTIUHUUMQJHFO-UPTCCGCDSA-N 863.34350 862.68391 COC1=C(OC)C(=O)C(C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)=C(C)C1=O CHEBI:46241 CHEBI:9854 Beilstein:1900141 CAS:303-98-0 Drug_Central:4607 HMDB:HMDB0001072 KEGG:C11378 KEGG:D01065 KNApSAcK:C00002866 LIPID_MAPS_instance:LMPR02010001 PDBeChem:U10 PMID:10953455 PMID:13445756 PMID:17192765 PMID:17605305 PMID:18787645 PMID:18843432 PMID:20367194 PMID:25544601 PMID:26741866 PMID:27012265 PMID:7599208 PMID:7718355 Reaxys:1900141 Wikipedia:Coenzyme_Q10 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione Coenzyme Q10 coenzyme Q10 chebi_ontology 2-((all-E)-3,7,11,15,19,23,27,31,35,39-decamethyl-2,6,10,14,18,22,26,30,34,38-tetracontadecaenyl)-5,6-dimethoxy-3-methyl-p-benzoquinone 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methyl-1,4-benzoquinone Adelir CoQ CoQ10 Q Q 199 Q10 UBIQUINONE-10 Ubidecarenone Ubiquinone-10 all-trans-ubiquinone ubiquinone ubiquinone 10 ubiquinone 50 ubiquinone-10 CHEBI:46245 coenzyme Q10 Beilstein:1900141 Beilstein CAS:303-98-0 ChemIDplus CAS:303-98-0 KEGG COMPOUND Drug_Central:4607 DrugCentral LIPID_MAPS_instance:LMPR02010001 LIPID MAPS PMID:10953455 Europe PMC PMID:13445756 Europe PMC PMID:17192765 Europe PMC PMID:17605305 Europe PMC PMID:18787645 Europe PMC PMID:18843432 Europe PMC PMID:20367194 Europe PMC PMID:25544601 Europe PMC PMID:26741866 Europe PMC PMID:27012265 Europe PMC PMID:7599208 Europe PMC PMID:7718355 Europe PMC Reaxys:1900141 Reaxys 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione IUPAC Coenzyme Q10 KEGG_COMPOUND coenzyme Q10 ChemIDplus 2-((all-E)-3,7,11,15,19,23,27,31,35,39-decamethyl-2,6,10,14,18,22,26,30,34,38-tetracontadecaenyl)-5,6-dimethoxy-3-methyl-p-benzoquinone ChemIDplus 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methyl-1,4-benzoquinone ChEBI Adelir KEGG_DRUG CoQ ChEBI CoQ10 ChEBI Q ChEBI Q 199 ChemIDplus Q10 ChEBI UBIQUINONE-10 PDBeChem Ubidecarenone KEGG_COMPOUND Ubiquinone-10 KEGG_COMPOUND all-trans-ubiquinone ChEBI ubiquinone ChEBI ubiquinone 10 ChemIDplus ubiquinone 50 ChemIDplus ubiquinone-10 UniProt 0 O 15.99940 15.99491 CHEBI:29353 CHEBI:44607 PDBeChem:O OXO GROUP oxo chebi_ontology =O CHEBI:46629 oxo group OXO GROUP PDBeChem oxo IUPAC =O IUPAC 0 C7H6O4 InChI=1S/C7H6O4/c1-3-2-4(8)6(10)7(11)5(3)9/h2,10-11H,1H3 DUPLFIFGNDSGBB-UHFFFAOYSA-N 154.12014 154.02661 CC1=CC(=O)C(O)=C(O)C1=O Beilstein:2254950 2,3-dihydroxy-5-methylcyclohexa-2,5-diene-1,4-dione chebi_ontology CHEBI:46691 2,3-dihydroxy-5-methyl-1,4-benzoquinone Beilstein:2254950 Beilstein 2,3-dihydroxy-5-methylcyclohexa-2,5-diene-1,4-dione IUPAC 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 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 +1 C5H13N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p+1 AHLPHDHHMVZTML-UHFFFAOYSA-O 133.16900 133.09715 [NH3+]CCCC([NH3+])C([O-])=O 2,5-diammoniopentanoate ornithinium ornithinium(1+) chebi_ontology ornithine monocation CHEBI:46912 ornithinium(1+) 2,5-diammoniopentanoate IUPAC ornithinium IUPAC ornithinium(1+) JCBN ornithine monocation JCBN +2 C5H14N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p+2 AHLPHDHHMVZTML-UHFFFAOYSA-P 134.17694 134.10443 [NH3+]CCCC([NH3+])C(O)=O 1-carboxybutane-1,4-diaminium ornithinediium ornithinium(2+) chebi_ontology ornithine dication CHEBI:46913 ornithinium(2+) 1-carboxybutane-1,4-diaminium IUPAC ornithinediium IUPAC ornithinium(2+) JCBN ornithine dication JCBN chebi_ontology tetrahydrofuranols CHEBI:47017 tetrahydrofuranol tetrahydrofuranols ChEBI chebi_ontology dihydroxytetrahydrofurans CHEBI:47019 dihydroxytetrahydrofuran dihydroxytetrahydrofurans ChEBI CHEBI:27220 CHEBI:36947 chebi_ontology urea derivatives CHEBI:47857 ureas urea derivatives ChEBI A chemical compound that can be excited by light of a specific wavelength and subsequently transfer energy to a chosen reactant. This is commonly molecular oxygen within a cancer tissue, which is converted to (highly rective) singlet state oxygen. This rapidly reacts with any nearby biomolecules, ultimately killing the cancer cells. chebi_ontology photosensitising agent CHEBI:47868 photosensitizing agent photosensitising agent ChEBI macrocyclic polypyrroles chebi_ontology cyclic polypyrroles polypyrrole macrocycles CHEBI:47882 cyclic polypyrrole macrocyclic polypyrroles IUPAC cyclic polypyrroles ChEBI polypyrrole macrocycles ChEBI Any steroid substituted by at least one carboxy group. chebi_ontology steroid acids CHEBI:47891 steroid acid steroid acids 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 chebi_ontology CHEBI:48359 protophilic solvent chebi_ontology CHEBI:48360 amphiprotic solvent 0 CH4N2O InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) XSQUKJJJFZCRTK-UHFFFAOYSA-N 60.05534 60.03236 NC(O)=N Beilstein:773698 CAS:4744-36-9 carbamimidic acid chebi_ontology H2N-C(=NH)-OH H2N-C(OH)=NH HO-C(=NH)-NH2 Isoharnstoff carbamimic acid carbonamidimidic acid isourea pseudourea CHEBI:48376 carbamimidic acid Beilstein:773698 Beilstein CAS:4744-36-9 ChemIDplus carbamimidic acid IUPAC H2N-C(=NH)-OH IUPAC H2N-C(OH)=NH IUPAC HO-C(=NH)-NH2 IUPAC Isoharnstoff ChEBI carbamimic acid ChemIDplus carbonamidimidic acid IUPAC isourea ChemIDplus pseudourea ChemIDplus Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing =O by =NR; thus tautomers of amides. In organic chemistry an unspecified imidic acid is generally a carboximidic acid, RC(=NR)(OH). imidic acid imidic acids chebi_ontology imidic acids imino acids CHEBI:48377 imidic acid imidic acid ChEBI imidic acids IUPAC imidic acids ChEBI imino acids IUPAC carboximidic acid carboximidic acids chebi_ontology carboximidic acids CHEBI:48378 carboximidic acid carboximidic acid ChEBI carboximidic acids IUPAC carboximidic acids ChEBI A carboximidic acid that is the imidic acid tautomer of urea, H2NC(=NH)OH, and its hydrocarbyl derivatives. isoureas chebi_ontology isoureas CHEBI:48379 isourea isoureas IUPAC isoureas ChEBI A role played by a substance that can react readily with, and thereby eliminate, radicals. chebi_ontology free radical scavengers free-radical scavenger CHEBI:48578 radical scavenger free radical scavengers ChEBI free-radical scavenger ChEBI An azole in which the five-membered heterocyclic aromatic skeleton contains a N atom and one S atom. chebi_ontology thiazole CHEBI:48901 thiazoles thiazole ChEBI Any L-alpha-amino acid carrying an N-acyl substituent. 0 C3H3NO3R2 101.061 101.01129 CHEBI:13240 CHEBI:7232 KEGG:C02850 chebi_ontology N-Acyl-L-amino acid CHEBI:48927 N-acyl-L-alpha-amino acid N-Acyl-L-amino acid KEGG_COMPOUND chebi_ontology drug metabolites CHEBI:49103 drug metabolite drug metabolites 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 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 An agent that binds to and activates excitatory amino acid receptors. chebi_ontology excitatory amino acid agonists excitatory amino acid receptor agonist excitatory amino acid receptor agonists CHEBI:50103 excitatory amino acid agonist excitatory amino acid agonists ChEBI excitatory amino acid receptor agonist ChEBI excitatory amino acid receptor agonists ChEBI 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 Any protective agent counteracting or neutralizing the action of poisons. chebi_ontology antidotes CHEBI:50247 antidote antidotes ChEBI A compound that, on administration, must undergo chemical conversion by metabolic processes before becoming the pharmacologically active drug for which it is a prodrug. PMID:23993918 PMID:23998799 PMID:24329110 PMID:24628402 PMID:24709544 PMID:25144792 PMID:25157234 PMID:25269430 PMID:25391982 PMID:25591121 PMID:25620096 PMID:25795057 PMID:26028253 PMID:26184144 PMID:28070577 PMID:28215138 PMID:28219047 PMID:28259775 PMID:28319647 PMID:28329729 PMID:28334528 Wikipedia:Prodrug chebi_ontology Prodrugs CHEBI:50266 prodrug PMID:23993918 Europe PMC PMID:23998799 Europe PMC PMID:24329110 Europe PMC PMID:24628402 Europe PMC PMID:24709544 Europe PMC PMID:25144792 Europe PMC PMID:25157234 Europe PMC PMID:25269430 Europe PMC PMID:25391982 Europe PMC PMID:25591121 Europe PMC PMID:25620096 Europe PMC PMID:25795057 Europe PMC PMID:26028253 Europe PMC PMID:26184144 Europe PMC PMID:28070577 Europe PMC PMID:28215138 Europe PMC PMID:28219047 Europe PMC PMID:28259775 Europe PMC PMID:28319647 Europe PMC PMID:28329729 Europe PMC PMID:28334528 Europe PMC Prodrugs ChEBI Synthetic or natural substance which is given to prevent a disease or disorder or are used in the process of treating a disease or injury due to a poisonous agent. chebi_ontology chemoprotectant chemoprotectants chemoprotective agent chemoprotective agents protective agents CHEBI:50267 protective agent chemoprotectant ChEBI chemoprotectants ChEBI chemoprotective agent ChEBI chemoprotective agents ChEBI protective agents 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 A univalent organyl group obtained by cleaving the bond from C-2 to the side chain of a proteinogenic amino-acid. chebi_ontology canonical amino-acid side-chain canonical amino-acid side-chains proteinogenic amino-acid side-chain proteinogenic amino-acid side-chain groups proteinogenic amino-acid side-chains CHEBI:50325 proteinogenic amino-acid side-chain group canonical amino-acid side-chain ChEBI canonical amino-acid side-chains ChEBI proteinogenic amino-acid side-chain ChEBI proteinogenic amino-acid side-chain groups ChEBI proteinogenic amino-acid side-chains ChEBI 0 CH3S 47.10052 46.99555 sulfanylmethyl chebi_ontology -CH2-SH HS-CH2- cysteine side-chain CHEBI:50326 sulfanylmethyl group sulfanylmethyl IUPAC -CH2-SH IUPAC HS-CH2- IUPAC cysteine side-chain ChEBI 0 C3H5O2 73.07060 73.02895 2-carboxyethyl chebi_ontology glutamic acid side-chain CHEBI:50329 2-carboxyethyl group 2-carboxyethyl IUPAC glutamic acid side-chain ChEBI 0 C4H10N3 100.14242 100.08747 3-carbamimidamidopropyl chebi_ontology 3-(carbamimidoylamino)propyl 3-guanidinopropyl arginine side-chain CHEBI:50340 3-carbamimidamidopropyl group 3-carbamimidamidopropyl IUPAC 3-(carbamimidoylamino)propyl IUPAC 3-guanidinopropyl ChEBI arginine side-chain ChEBI Any steroid based on a cholestane skeleton and its derivatives. chebi_ontology cholestanoids CHEBI:50401 cholestanoid cholestanoids ChEBI An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position. CHEBI:22937 CHEBI:50581 chebi_ontology alkyl alcohols hydroxyalkane hydroxyalkanes CHEBI:50584 alkyl alcohol alkyl alcohols ChEBI hydroxyalkane ChEBI hydroxyalkanes ChEBI A product in capsule, tablet or liquid form that provide essential nutrients, such as a vitamin, an essential mineral, a protein, an herb, or similar nutritional substance. chebi_ontology Dietary Supplement Food Supplementation Nutritional supplement CHEBI:50733 nutraceutical Dietary Supplement ChEBI Food Supplementation ChEBI Nutritional supplement ChEBI 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 chemical compound, or part thereof, which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy. Wikipedia:Allergen chebi_ontology alergeno allergene allergenic agent CHEBI:50904 allergen alergeno ChEBI allergene ChEBI allergenic agent ChEBI role (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 role played by the molecular entity or part thereof within a chemical context. chebi_ontology CHEBI:51086 chemical role nitrogen http://langual.org CHEBI:25556 CHEBI:7594 Codex::941 Europe::941 KEGG:C06061 http://www.langual.org/langual_thesaurus.asp?termid=B3173 chebi_ontology Nitrogenous compounds nitrogen compounds nitrogen molecular entities CHEBI:51143 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): packaging gas, propellant. 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 A carboxamide resulting from the formal condensation of a carboxylic acid with the amino group of an amino acid. CHEBI:21653 CHEBI:22226 chebi_ontology N-acyl amino acid N-acyl amino acids N-acyl-amino-acid N-acyl-amino-acids N-acylamino acid N-acylamino acids acyl-amino-acid acyl-amino-acids acylamino acids CHEBI:51569 N-acyl-amino acid N-acyl amino acid ChEBI N-acyl amino acids ChEBI N-acyl-amino-acid ChEBI N-acyl-amino-acids ChEBI N-acylamino acid ChEBI N-acylamino acids ChEBI acyl-amino-acid ChEBI acyl-amino-acids ChEBI acylamino acids ChEBI Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton. chebi_ontology CHEBI:51570 biotins chebi_ontology organic polycyclic compounds CHEBI:51958 organic polycyclic compound organic polycyclic compounds ChEBI chebi_ontology organic tricyclic compounds CHEBI:51959 organic tricyclic compound organic tricyclic compounds ChEBI An organic anion that is the conjugate base of methanol. -1 CH3O InChI=1S/CH3O/c1-2/h1H3/q-1 NBTOZLQBSIZIKS-UHFFFAOYSA-N 31.03390 31.01894 C[O-] Reaxys:1839368 chebi_ontology methoxide ion CHEBI:52090 methoxide Reaxys:1839368 Reaxys methoxide ion 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 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 amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of glycine. 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06660 75.03203 [NH3+]CC([O-])=O Gmelin:1807 MetaCyc:GLY 2-azaniumylacetate chebi_ontology glycine CHEBI:57305 glycine zwitterion Gmelin:1807 Gmelin 2-azaniumylacetate IUPAC glycine UniProt Zwitterionic form of gamma-amino-beta-hydroxybutyric acid having an anionic carboxy group and a protonated amino group. 0 C4H9NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8) YQGDEPYYFWUPGO-UHFFFAOYSA-N 119.11920 119.05824 [NH3+]CC(O)CC([O-])=O 4-azaniumyl-3-hydroxybutanoate chebi_ontology 4-amino-3-hydroxybutanoate 4-ammonio-3-hydroxybutanoate CHEBI:57630 gamma-amino-beta-hydroxybutyric acid zwitterion 4-azaniumyl-3-hydroxybutanoate IUPAC 4-amino-3-hydroxybutanoate UniProt 4-ammonio-3-hydroxybutanoate ChEBI Zwitterionic form of creatine arising from transfer of a proton from the carboxy to the guanidino group; major species at pH 7.3. 0 C4H9N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9) CVSVTCORWBXHQV-UHFFFAOYSA-N 131.13320 131.06948 CN(CC([O-])=O)C(N)=[NH2+] MetaCyc:CREATINE {[amino(iminio)methyl](methyl)amino}acetate chebi_ontology creatine CHEBI:57947 creatine zwitterion {[amino(iminio)methyl](methyl)amino}acetate IUPAC creatine UniProt The anion resulting from removal of a proton from the nitrogen at the 3 position (between the two carbonyl gropus) of riboflavin. -1 C17H19N4O6 InChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/p-1/t11-,12+,14-/m0/s1 AUNGANRZJHBGPY-SCRDCRAPSA-M 375.35600 375.13101 Cc1cc2nc3c(nc(=O)[n-]c3=O)n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C Beilstein:4924198 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-2H-benzo[g]pteridin-3-id-10(4H)-yl)-D-ribitol chebi_ontology 7,8-dimethyl-2,4-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-2H,3H,4H,10H-benzo[g]pteridin-3-ide riboflavin CHEBI:57986 riboflavin(1-) Beilstein:4924198 Beilstein 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-2H-benzo[g]pteridin-3-id-10(4H)-yl)-D-ribitol IUPAC 7,8-dimethyl-2,4-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-2H,3H,4H,10H-benzo[g]pteridin-3-ide ChEBI riboflavin UniProt The conjugate base of an N-acetyl-D-amino acid. -1 C4H5NO3R 115.08740 115.02694 CC(=O)N[C@H]([*])C([O-])=O chebi_ontology N-acetyl-D-amino acetate(1-) N-acetyl-D-amino acid anions N-acetyl-D-amino carboxylate anions an N-acetyl-D-amino acid CHEBI:58496 N-acetyl-D-amino acid anion N-acetyl-D-amino acetate(1-) ChEBI N-acetyl-D-amino acid anions ChEBI N-acetyl-D-amino carboxylate anions ChEBI an N-acetyl-D-amino acid UniProt Any fatty acid anion obtained by removal of a proton from the carboxy group of a short-chain fatty acid (chain length of less than C6). -1 CO2R 44.010 43.98983 [O-]C([*])=O chebi_ontology a short-chain fatty acid short-chain fatty acid anions CHEBI:58951 short-chain fatty acid anion a short-chain fatty acid UniProt short-chain fatty acid anions ChEBI Any fatty acid anion in which there is no C-C unsaturation. chebi_ontology saturated fatty acid anions CHEBI:58953 saturated fatty acid anion saturated fatty acid anions ChEBI Any saturated fatty acid anion lacking a carbon side-chain. chebi_ontology straight-chain saturated fatty acid anions CHEBI:58954 straight-chain saturated fatty acid anion straight-chain saturated fatty acid anions ChEBI Any substance capable of eliciting an immune response only when attached to a large carrier such as a protein. Examples include dinitrophenols; oligosaccharides; peptides; and heavy metals. PMID:17875790 PMID:17986299 PMID:19101624 PMID:291959 PMID:3782019 chebi_ontology haptens CHEBI:59174 hapten PMID:17875790 Europe PMC PMID:17986299 Europe PMC PMID:19101624 Europe PMC PMID:291959 Europe PMC PMID:3782019 Europe PMC haptens ChEBI Any fatty acid whose skeletal carbon atoms form an unbranched open chain. chebi_ontology straight-chain fatty acids CHEBI:59202 straight-chain fatty acid straight-chain fatty acids ChEBI A fatty acid anion formed by deprotonation of the carboxylic acid functional group of a straight-chain fatty acid. chebi_ontology straight-chain FA anion straight-chain FA anions straight-chain fatty acid anions CHEBI:59203 straight-chain fatty acid anion straight-chain FA anion ChEBI straight-chain FA anions ChEBI straight-chain fatty acid anions ChEBI Any member of the sub-set of polyunsaturated fatty acid for which there is an absolute dietary requirement. PMID:1745654 PMID:19034351 PMID:7609665 chebi_ontology EFA EFAs EFS acides gras indispensables acidos grasos esenciales essential fatty acids essentielle Fettsaeuren CHEBI:59549 essential fatty acid PMID:1745654 Europe PMC PMID:19034351 Europe PMC PMID:7609665 Europe PMC EFA ChEBI EFAs ChEBI EFS ChEBI acides gras indispensables ChEBI acidos grasos esenciales ChEBI essential fatty acids ChEBI essentielle Fettsaeuren ChEBI Any fatty acid with a chain length of between C6 and C12. 0 CHO2R 45.01740 44.99765 OC([*])=O chebi_ontology MCFA MCFAs medium-chain fatty acids CHEBI:59554 medium-chain fatty acid MCFA ChEBI MCFAs ChEBI medium-chain fatty acids ChEBI A fatty acid anion resulting from the deprotonation of the carboxylic acid moiety of a medium-chain fatty acid. -1 CO2R 44.010 43.98983 [O-]C([*])=O chebi_ontology MCFA anion MCFA anions a medium chain fatty acid medium-chain FA anion medium-chain FA anions medium-chain fatty acid anions CHEBI:59558 medium-chain fatty acid anion MCFA anion ChEBI MCFA anions ChEBI a medium chain fatty acid UniProt medium-chain FA anion ChEBI medium-chain FA anions ChEBI medium-chain fatty acid anions ChEBI 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 Conjugate base of an L-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C2H3NO2R 73.051 73.01638 [C@H](C(=O)[O-])(N)* chebi_ontology L-alpha-amino carboxylate CHEBI:59814 L-alpha-amino acid anion L-alpha-amino carboxylate ChEBI Zwitterionic form of an L-alpha-amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 [NH3+][C@@H]([*])C([O-])=O chebi_ontology L-alpha-amino acid zwitterions an L-alpha-amino acid CHEBI:59869 L-alpha-amino acid zwitterion L-alpha-amino acid zwitterions ChEBI an L-alpha-amino acid UniProt Zwitterionic form of a D-alpha-amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 [NH3+][C@H]([*])C([O-])=O chebi_ontology D-alpha-amino acid zwitterions a D-alpha-amino acid CHEBI:59871 D-alpha-amino acid zwitterion D-alpha-amino acid zwitterions ChEBI a D-alpha-amino acid UniProt A carboxylic acid anion that is the conjugate base of an N-acyl-L-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C3H2NO3R2 100.05290 100.00347 [O-]C(=O)[C@H]([*])NC([*])=O chebi_ontology N-acyl-L-alpha-amino acid(1-) an N-acyl-L-amino acid CHEBI:59874 N-acyl-L-alpha-amino acid anion N-acyl-L-alpha-amino acid(1-) ChEBI an N-acyl-L-amino acid UniProt The conjugate base of an N-acyl-D-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C3H2NO3R2 100.05290 100.00347 [O-]C(=O)[C@@H]([*])NC([*])=O chebi_ontology N-acyl-D-alpha-amino acid(1-) an N-acyl-D-amino acid CHEBI:59876 N-acyl-D-alpha-amino acid anion N-acyl-D-alpha-amino acid(1-) ChEBI an N-acyl-D-amino acid UniProt 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 Flavin protonated to pH 7.3 -1 C12H8N4O2R 240.21750 240.06473 Cc1cc2nc3c(nc(=O)[n-]c3=O)n([*])c2cc1C chebi_ontology an oxidized flavin CHEBI:60531 flavin(1-) an oxidized flavin UniProt Any alpha-amino acid anion in which the parent amino acid has D-configuration. -1 C2H3NO2R 73.051 73.01638 [C@@H](C(=O)[O-])(N)* chebi_ontology D-alpha-amino acid anions D-alpha-amino carboxylate CHEBI:60895 D-alpha-amino acid anion D-alpha-amino acid anions ChEBI D-alpha-amino carboxylate ChEBI An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the function of histone deacetylase (EC 3.5.1.98). Wikipedia:Histone_deacetylase_inhibitor chebi_ontology EC 3.5.1.98 (histone deacetylase) inhibitors EC 3.5.1.98 inhibitor EC 3.5.1.98 inhibitors HDAC inhibitor HDAC inhibitors HDACi HDACis HDI HDIs histone amidohydrolase inhibitor histone amidohydrolase inhibitors histone deacetylase (EC 3.5.1.98) inhibitor histone deacetylase (EC 3.5.1.98) inhibitors histone deacetylase inhibitor histone deacetylase inhibitors CHEBI:61115 EC 3.5.1.98 (histone deacetylase) inhibitor EC 3.5.1.98 (histone deacetylase) inhibitors ChEBI EC 3.5.1.98 inhibitor ChEBI EC 3.5.1.98 inhibitors ChEBI HDAC inhibitor ChEBI HDAC inhibitors ChEBI HDACi ChEBI HDACis ChEBI HDI ChEBI HDIs ChEBI histone amidohydrolase inhibitor ChEBI histone amidohydrolase inhibitors ChEBI histone deacetylase (EC 3.5.1.98) inhibitor ChEBI histone deacetylase (EC 3.5.1.98) inhibitors ChEBI histone deacetylase inhibitor ChEBI histone deacetylase inhibitors 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 Any hydroxy carboxylic acid which contains a hydroxy group located beta- to the carboxylic acid group. chebi_ontology 3-hydroxy carboxylic acids 3-hydroxycarboxylic acid 3-hydroxycarboxylic acids beta-hydroxy carboxylic acid beta-hydroxy carboxylic acids beta-hydroxycarboxylic acid beta-hydroxycarboxylic acids CHEBI:61355 3-hydroxy carboxylic acid 3-hydroxy carboxylic acids ChEBI 3-hydroxycarboxylic acid ChEBI 3-hydroxycarboxylic acids ChEBI beta-hydroxy carboxylic acid ChEBI beta-hydroxy carboxylic acids ChEBI beta-hydroxycarboxylic acid ChEBI beta-hydroxycarboxylic acids ChEBI Zwitterionic form of a polar amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 C(C([O-])=O)(*)[NH3+] MetaCyc:Polar-amino-acids chebi_ontology a polar amino acid CHEBI:62031 polar amino acid zwitterion MetaCyc:Polar-amino-acids SUBMITTER a polar amino acid UniProt Any compound that is able to prevent damage to the liver. chebi_ontology antihepatotoxic agent hepatoprotective agents CHEBI:62868 hepatoprotective agent antihepatotoxic agent ChEBI hepatoprotective agents ChEBI A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity. chebi_ontology glycosyl compounds CHEBI:63161 glycosyl compound glycosyl compounds 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 sulfur-containing amino acid whose alpha-carboxylic acid group is ionized (not protonated). chebi_ontology sulfur-containing amino-acid anions CHEBI:63470 sulfur-containing amino-acid anion sulfur-containing amino-acid anions ChEBI Any compound that can be used for the treatment of neurodegenerative disorders. chebi_ontology neuroprotectant neuroprotectants neuroprotective agents CHEBI:63726 neuroprotective agent neuroprotectant ChEBI neuroprotectants ChEBI neuroprotective agents 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 amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of methionine; major species at pH 7.3. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8) FFEARJCKVFRZRR-UHFFFAOYSA-N 149.21100 149.05105 CSCCC([NH3+])C([O-])=O 2-azaniumyl-4-(methylsulfanyl)butanoate chebi_ontology 2-ammonio-4-(methylsulfanyl)butanoate methionine CHEBI:64558 methionine zwitterion 2-azaniumyl-4-(methylsulfanyl)butanoate IUPAC 2-ammonio-4-(methylsulfanyl)butanoate IUPAC methionine UniProt An EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor that interferes with the action of glycine hydroxymethyltransferase (EC 2.1.2.1). Wikipedia:Glycine_hydroxymethyltransferase chebi_ontology 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitor 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitors EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitors EC 2.1.2.1 inhibitor EC 2.1.2.1 inhibitors L-serine hydroxymethyltransferase inhibitor L-serine hydroxymethyltransferase inhibitors L-threonine aldolase inhibitor L-threonine aldolase inhibitors allothreonine aldolase inhibitor allothreonine aldolase inhibitors glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitor glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitors glycine hydroxymethyltransferase inhibitor glycine hydroxymethyltransferase inhibitors serine aldolase inhibitor serine aldolase inhibitors serine hydroxymethylase inhibitor serine hydroxymethylase inhibitors serine hydroxymethyltransferase inhibitor serine hydroxymethyltransferase inhibitors serine transhydroxymethylase inhibitor serine transhydroxymethylase inhibitors threonine aldolase inhibitor threonine aldolase inhibitors CHEBI:64570 EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitor 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitor ChEBI 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitors ChEBI EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitors ChEBI EC 2.1.2.1 inhibitor ChEBI EC 2.1.2.1 inhibitors ChEBI L-serine hydroxymethyltransferase inhibitor ChEBI L-serine hydroxymethyltransferase inhibitors ChEBI L-threonine aldolase inhibitor ChEBI L-threonine aldolase inhibitors ChEBI allothreonine aldolase inhibitor ChEBI allothreonine aldolase inhibitors ChEBI glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitor ChEBI glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitors ChEBI glycine hydroxymethyltransferase inhibitor ChEBI glycine hydroxymethyltransferase inhibitors ChEBI serine aldolase inhibitor ChEBI serine aldolase inhibitors ChEBI serine hydroxymethylase inhibitor ChEBI serine hydroxymethylase inhibitors ChEBI serine hydroxymethyltransferase inhibitor ChEBI serine hydroxymethyltransferase inhibitors ChEBI serine transhydroxymethylase inhibitor ChEBI serine transhydroxymethylase inhibitors ChEBI threonine aldolase inhibitor ChEBI threonine aldolase inhibitors ChEBI An excitatory amino acid agonist which binds to NMDA receptors and triggers a response. chebi_ontology N-methyl-D-aspartate receptor agonist N-methyl-D-aspartate receptor agonists NMDA receptor agonists NMDAR agonist NMDAR agonists CHEBI:64571 NMDA receptor agonist N-methyl-D-aspartate receptor agonist ChEBI N-methyl-D-aspartate receptor agonists ChEBI NMDA receptor agonists ChEBI NMDAR agonist ChEBI NMDAR agonists ChEBI A food additive which is added to flour or dough to improve baking quality and/or colour. Wikipedia:Flour_treatment_agent flour treatment agent chebi_ontology dough improver dough improvers improving agent improving agents CHEBI:64577 flour treatment agent flour treatment agent ChEBI dough improver ChEBI dough improvers ChEBI improving agent ChEBI improving agents ChEBI 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 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 alpha-amino acid anion that is the conjugate base of citrulline, obtained by deprotonation of the carboxy group. -1 C6H12N3O3 InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/p-1 RHGKLRLOHDJJDR-UHFFFAOYSA-M 174.17780 174.08841 NC(CCCNC(N)=O)C([O-])=O 2-amino-5-(carbamoylamino)pentanoate chebi_ontology CHEBI:66922 citrullinate 2-amino-5-(carbamoylamino)pentanoate IUPAC A monocarboxylic acid anion that is the conjugate base of creatine, obtained by deprotonation of the carboxy group. -1 C4H8N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)/p-1 CVSVTCORWBXHQV-UHFFFAOYSA-M 130.12520 130.06220 CN(CC([O-])=O)C(N)=N {[imino(amino)methyl](methyl)amino}acetate chebi_ontology (N-methylcarbamimidamido)acetate N-[amino(imino)methyl]-N-methylglycinate CHEBI:66924 creatinate {[imino(amino)methyl](methyl)amino}acetate IUPAC (N-methylcarbamimidamido)acetate ChEBI N-[amino(imino)methyl]-N-methylglycinate ChEBI An N-acyl-L-alpha-amino acid anion obtained by deprotonation of any folic acid. chebi_ontology folate folate anion folate anions CHEBI:67011 folates folate ChEBI folate anion ChEBI folate anions ChEBI Any 1,4-benzoquinone carrying a single hydroxy substituent. 0 C6HO3R3 121.07030 120.99257 OC1=C([*])C(=O)C([*])=C([*])C1=O chebi_ontology 2-hydroxy-1,4-benzoquinones hydroxy-1,4-benzoquinone hydroxy-1,4-benzoquinones hydroxybenzoquinone hydroxybenzoquinones monohydroxybenzoquinones CHEBI:67273 monohydroxy-1,4-benzoquinones 2-hydroxy-1,4-benzoquinones ChEBI hydroxy-1,4-benzoquinone ChEBI hydroxy-1,4-benzoquinones ChEBI hydroxybenzoquinone ChEBI hydroxybenzoquinones ChEBI monohydroxybenzoquinones ChEBI Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen. Wikipedia:Azole chebi_ontology azoles CHEBI:68452 azole azoles ChEBI An enzyme inhibitor that inhibits the action of a transferase (EC 2.*) Wikipedia:Transferase chebi_ontology EC 2 inhibitor EC 2 inhibitors EC 2.* (transferase) inhibitors EC 2.* inhibitor EC 2.* inhibitors transferase inhibitor transferase inhibitors CHEBI:71300 EC 2.* (transferase) inhibitor EC 2 inhibitor ChEBI EC 2 inhibitors ChEBI EC 2.* (transferase) inhibitors ChEBI EC 2.* inhibitor ChEBI EC 2.* inhibitors ChEBI transferase inhibitor ChEBI transferase inhibitors ChEBI Benzoquinones with at least one hydroxy substituent. chebi_ontology hydroxybenzoquinones CHEBI:71648 hydroxybenzoquinone hydroxybenzoquinones ChEBI An amino-acid anion in which the amino group is situated gamma- to the carboxylate group. chebi_ontology gamma-amino acid anions CHEBI:71666 gamma-amino acid anion gamma-amino acid anions 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 drug used in treating and healing of wounds. Wikipedia:Wound_healing chebi_ontology vulneraries wound-healing agent wound-healing agents wound-healing drug wound-healing drugs CHEBI:73336 vulnerary vulneraries ChEBI wound-healing agent ChEBI wound-healing agents ChEBI wound-healing drug ChEBI wound-healing drugs ChEBI A role borne by a molecule that acts to counteract or neutralize the deleterious effects of paracetamol (acetaminophen). PMID:16354242 PMID:16573399 PMID:16575097 PMID:22348679 PMID:22352734 PMID:22353666 PMID:22835053 PMID:22998987 PMID:7112203 chebi_ontology Tylenol poisoning antidote Tylenol poisoning antidotes acetaminophen poisoning antidote acetaminophen poisoning antidotes antidote to Tylenol poisoning antidote to acetaminophen poisoning antidotes to Tylenol poisoning antidotes to acetaminophen poisoning antidotes to paracetamol poisoning paracetamol poisoning antidote paracetamol poisoning antidotes CHEBI:74529 antidote to paracetamol poisoning PMID:16354242 Europe PMC PMID:16573399 Europe PMC PMID:16575097 Europe PMC PMID:22348679 Europe PMC PMID:22352734 Europe PMC PMID:22353666 Europe PMC PMID:22835053 Europe PMC PMID:22998987 Europe PMC PMID:7112203 Europe PMC Tylenol poisoning antidote ChEBI Tylenol poisoning antidotes ChEBI acetaminophen poisoning antidote ChEBI acetaminophen poisoning antidotes ChEBI antidote to Tylenol poisoning ChEBI antidote to acetaminophen poisoning ChEBI antidotes to Tylenol poisoning ChEBI antidotes to acetaminophen poisoning ChEBI antidotes to paracetamol poisoning ChEBI paracetamol poisoning antidote ChEBI paracetamol poisoning antidotes ChEBI A ligase inhibitor that interferes with the action of a C-N bond-forming ligase (EC 6.3.*.*). chebi_ontology C--N bond-forming ligase inhibitor C--N bond-forming ligase inhibitors C-N bond-forming ligase (EC 6.3.*) inhibitor C-N bond-forming ligase (EC 6.3.*) inhibitors C-N bond-forming ligase inhibitor C-N bond-forming ligase inhibitors EC 6.3.* (C-N bond-forming ligase) inhibitorS EC 6.3.* inhibitor EC 6.3.* inhibitors EC 6.3.*.* inhibitor EC 6.3.*.* inhibitors CHEBI:75600 EC 6.3.* (C-N bond-forming ligase) inhibitor C--N bond-forming ligase inhibitor ChEBI C--N bond-forming ligase inhibitors ChEBI C-N bond-forming ligase (EC 6.3.*) inhibitor ChEBI C-N bond-forming ligase (EC 6.3.*) inhibitors ChEBI C-N bond-forming ligase inhibitor ChEBI C-N bond-forming ligase inhibitors ChEBI EC 6.3.* (C-N bond-forming ligase) inhibitorS ChEBI EC 6.3.* inhibitor ChEBI EC 6.3.* inhibitors ChEBI EC 6.3.*.* inhibitor ChEBI EC 6.3.*.* inhibitors ChEBI Any enzyme inhibitor that interferes with the action of a ligase (EC 6.*.*.*). Ligases are enzymes that catalyse the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. Wikipedia:Ligase chebi_ontology EC 6.* (ligase) inhibitors EC 6.* inhibitor EC 6.* inhibitors EC 6.*.*.* inhibitor EC 6.*.*.* inhibitors ligase inhibitor ligase inhibitors CHEBI:75603 EC 6.* (ligase) inhibitor EC 6.* (ligase) inhibitors ChEBI EC 6.* inhibitor ChEBI EC 6.* inhibitors ChEBI EC 6.*.*.* inhibitor ChEBI EC 6.*.*.* inhibitors ChEBI ligase inhibitor ChEBI ligase inhibitors 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 of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B) that play important roles in cell metabolism. The group comprises vitamin B1, B2, B3, B5, B6, B7, B9, and B12. (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such.) PMID:22743781 PMID:23093174 PMID:23238962 PMID:23449527 PMID:23462586 PMID:23690582 Wikipedia:B_vitamin chebi_ontology B vitamins B-group vitamin B-group vitamins vitamin B CHEBI:75769 B vitamin PMID:22743781 Europe PMC PMID:23093174 Europe PMC PMID:23238962 Europe PMC PMID:23449527 Europe PMC PMID:23462586 Europe PMC PMID:23690582 Europe PMC B vitamins ChEBI B-group vitamin ChEBI B-group vitamins ChEBI vitamin B 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 Any unsaturated fatty acid anion containing more than one C-C unsaturated bond. Major species at pH 7.3. chebi_ontology PUFA polyunsaturated fatty acid anions CHEBI:76567 polyunsaturated fatty acid anion PUFA SUBMITTER polyunsaturated fatty acid anions ChEBI A transferase inhibitor inhibiting the action of transferase of a one-carbon-containing group (EC 2.1.*.*). chebi_ontology C1-transferase (EC 2.1.*) inhibitor C1-transferase (EC 2.1.*) inhibitors C1-transferase inhibitor C1-transferase inhibitors EC 2.1.* (C1-transferase) inhibitors EC 2.1.* inhibitor EC 2.1.* inhibitors one-carbon-containing group transferase inhibitor one-carbon-containing group transferase inhibitors CHEBI:76655 EC 2.1.* (C1-transferase) inhibitor C1-transferase (EC 2.1.*) inhibitor ChEBI C1-transferase (EC 2.1.*) inhibitors ChEBI C1-transferase inhibitor ChEBI C1-transferase inhibitors ChEBI EC 2.1.* (C1-transferase) inhibitors ChEBI EC 2.1.* inhibitor ChEBI EC 2.1.* inhibitors ChEBI one-carbon-containing group transferase inhibitor ChEBI one-carbon-containing group transferase inhibitors ChEBI An enzyme inhibitor which interferes with the action of a lyase (EC 4.*.*.*). Lyases are enzymes cleaving C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation. Wikipedia:Lyase chebi_ontology EC 4.* (lyase) inhibitors EC 4.* inhibitor EC 4.* inhibitors EC 4.*.*.* inhibitor EC 4.*.*.* inhibitors lyase (EC 4.*) inhibitor lyase (EC 4.*) inhibitorS lyase inhibitor lyase inhibitors CHEBI:76710 EC 4.* (lyase) inhibitor EC 4.* (lyase) inhibitors ChEBI EC 4.* inhibitor ChEBI EC 4.* inhibitors ChEBI EC 4.*.*.* inhibitor ChEBI EC 4.*.*.* inhibitors ChEBI lyase (EC 4.*) inhibitor ChEBI lyase (EC 4.*) inhibitorS ChEBI lyase inhibitor ChEBI lyase inhibitors ChEBI A lyase inhibitor which inhibits the action of a C-N lyase (EC 4.3.*.*). chebi_ontology C-N lyase (EC 4.3.*) inhibitor C-N lyase (EC 4.3.*) inhibitors C-N lyase inhibitor C-N lyase inhibitors EC 4.3.* (C-N lyase) inhibitors EC 4.3.* inhibitor EC 4.3.* inhibitors CHEBI:76713 EC 4.3.* (C-N lyase) inhibitor C-N lyase (EC 4.3.*) inhibitor ChEBI C-N lyase (EC 4.3.*) inhibitors ChEBI C-N lyase inhibitor ChEBI C-N lyase inhibitors ChEBI EC 4.3.* (C-N lyase) inhibitors ChEBI EC 4.3.* inhibitor ChEBI EC 4.3.* inhibitors ChEBI 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 An EC 6.3.* (C-N bond-forming ligase) inhibitor that interferes with the action of any acid-ammonia (or amine) ligase (EC 6.3.1.*). chebi_ontology EC 6.3.1.* (acid-ammonia/amine ligase) inhibitors EC 6.3.1.* inhibitor EC 6.3.1.* inhibitors acid-ammonia (or amine) ligase inhibitor acid-ammonia (or amine) ligase inhibitors CHEBI:76823 EC 6.3.1.* (acid-ammonia/amine ligase) inhibitor EC 6.3.1.* (acid-ammonia/amine ligase) inhibitors ChEBI EC 6.3.1.* inhibitor ChEBI EC 6.3.1.* inhibitors ChEBI acid-ammonia (or amine) ligase inhibitor ChEBI acid-ammonia (or amine) ligase inhibitors ChEBI An EC 4.3.* (C-N lyase) inhibitor that interferes with the action of any ammonia-lyase (EC 4.3.1.*). chebi_ontology EC 4.3.1.* (ammonia-lyase) inhibitors EC 4.3.1.* (ammonia-lyases) inhibitor EC 4.3.1.* (ammonia-lyases) inhibitors EC 4.3.1.* inhibitor EC 4.3.1.* inhibitors ammonia-lyase (EC 4.3.1.*) inhibitor ammonia-lyase (EC 4.3.1.*) inhibitors ammonia-lyase inhibitor ammonia-lyase inhibitors CHEBI:76832 EC 4.3.1.* (ammonia-lyase) inhibitor EC 4.3.1.* (ammonia-lyase) inhibitors ChEBI EC 4.3.1.* (ammonia-lyases) inhibitor ChEBI EC 4.3.1.* (ammonia-lyases) inhibitors ChEBI EC 4.3.1.* inhibitor ChEBI EC 4.3.1.* inhibitors ChEBI ammonia-lyase (EC 4.3.1.*) inhibitor ChEBI ammonia-lyase (EC 4.3.1.*) inhibitors ChEBI ammonia-lyase inhibitor ChEBI ammonia-lyase inhibitors ChEBI An EC 2.1.* (C1-transferase) inhibitor that interferes with the action of any hydroxymethyl-, formyl- and related transferase (EC 2.1.2.*). chebi_ontology EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitors EC 2.1.2.* inhibitor EC 2.1.2.* inhibitors hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitor hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitors CHEBI:76874 EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitors ChEBI EC 2.1.2.* inhibitor ChEBI EC 2.1.2.* inhibitors ChEBI hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitor ChEBI hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) 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 compound that alters the structure of mucus so as to decrease its viscosity and thereby facilitate its removal by ciliary action and expectoration. Compare with antitussives, which suppress the cough reflex, and expectorants, which are considered to increase the volume of secretions in the respiratory tract, so facilitating their removal by ciliary action and coughing. PMID:17419975 PMID:17594730 PMID:20031934 PMID:2117172 PMID:22895919 chebi_ontology mucolytics CHEBI:77034 mucolytic PMID:17419975 Europe PMC PMID:17594730 Europe PMC PMID:20031934 Europe PMC PMID:2117172 Europe PMC PMID:22895919 Europe PMC mucolytics ChEBI A food additive that imparts colour to food. In European countries, E-numbers for permitted food colours are from E 100 to E 199, divided into yellows (E 100-109), oranges (E 110-119), reds (E 120-129), blues and violets (E 130-139), greens (E 140-149), browns and blacks (E 150-159), and others (E 160-199). Wikipedia:Food_coloring chebi_ontology food coloring food colorings food colourings CHEBI:77182 food colouring food coloring ChEBI food colorings ChEBI food colourings ChEBI An EC 4.3.1.* (ammonia-lyase) inhibitor that interferes with the action of histidine ammonia-lyase (EC 4.3.1.3). Wikipedia:Histidine_ammonia-lyase chebi_ontology EC 4.3.1.3 (histidine ammonia-lyase) inhibitors EC 4.3.1.3 inhibitor EC 4.3.1.3 inhibitors L-histidine ammonia-lyase (urocanate-forming) inhibitor L-histidine ammonia-lyase (urocanate-forming) inhibitors L-histidine ammonia-lyase inhibitor L-histidine ammonia-lyase inhibitors histidase inhibitor histidase inhibitors histidinase inhibitor histidinase inhibitors histidine alpha-deaminase inhibitor histidine alpha-deaminase inhibitors histidine ammonia-lyase (EC 4.3.1.3) inhibitor histidine ammonia-lyase (EC 4.3.1.3) inhibitors histidine ammonia-lyase inhibitor histidine ammonia-lyase inhibitors CHEBI:77703 EC 4.3.1.3 (histidine ammonia-lyase) inhibitor EC 4.3.1.3 (histidine ammonia-lyase) inhibitors ChEBI EC 4.3.1.3 inhibitor ChEBI EC 4.3.1.3 inhibitors ChEBI L-histidine ammonia-lyase (urocanate-forming) inhibitor ChEBI L-histidine ammonia-lyase (urocanate-forming) inhibitors ChEBI L-histidine ammonia-lyase inhibitor ChEBI L-histidine ammonia-lyase inhibitors ChEBI histidase inhibitor ChEBI histidase inhibitors ChEBI histidinase inhibitor ChEBI histidinase inhibitors ChEBI histidine alpha-deaminase inhibitor ChEBI histidine alpha-deaminase inhibitors ChEBI histidine ammonia-lyase (EC 4.3.1.3) inhibitor ChEBI histidine ammonia-lyase (EC 4.3.1.3) inhibitors ChEBI histidine ammonia-lyase inhibitor ChEBI histidine ammonia-lyase inhibitors ChEBI 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 Any saturated fatty acid anion containing 4 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C4H7O2 87.09718 87.04460 [O-]C([*])=O chebi_ontology fatty acid 4:0 CHEBI:78115 fatty acid anion 4:0 fatty acid 4:0 UniProt A monocarboxylic acid anion that is the conjugate base of N-acetyl-L-cysteine, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C5H8NO3S InChI=1S/C5H9NO3S/c1-3(7)6-4(2-10)5(8)9/h4,10H,2H2,1H3,(H,6,7)(H,8,9)/p-1/t4-/m0/s1 PWKSKIMOESPYIA-BYPYZUCNSA-M 162.18700 162.02304 CC(=O)N[C@@H](CS)C([O-])=O MetaCyc:CPD-9175 PMID:19268377 Reaxys:6327823 (2R)-2-acetamido-3-sulfanylpropanoate chebi_ontology N-acetyl-L-cysteine CHEBI:78236 N-acetyl-L-cysteinate MetaCyc:CPD-9175 SUBMITTER PMID:19268377 SUBMITTER Reaxys:6327823 Reaxys (2R)-2-acetamido-3-sulfanylpropanoate IUPAC N-acetyl-L-cysteine UniProt food component role 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 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 organic molecular entity that contains at least one C=C bond. chebi_ontology olefinic compounds CHEBI:78840 olefinic compound olefinic compounds 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 member of the class of monohydroxy-1,4-benzoquinones that is 2-hydroxy-1,4-benzoquinone carrying an additional methyl substituent at position 5. 0 C7H6O3 InChI=1S/C7H6O3/c1-4-2-6(9)7(10)3-5(4)8/h2-3,10H,1H3 BMBZVGUSOUAIMK-UHFFFAOYSA-N 138.121 138.03169 C=1C(C(=CC(C1C)=O)O)=O CAS:615-91-8 KEGG:C18316 MetaCyc:CPD-9135 Reaxys:1861302 2-hydroxy-5-methylcyclohexa-2,5-diene-1,4-dione chebi_ontology 2-Hydroxy-5-methyl-1,4-benzoquinone 2-Hydroxy-5-methyl-p-benzoquinone CHEBI:81667 2-hydroxy-5-methylquinone CAS:615-91-8 ChemIDplus CAS:615-91-8 KEGG COMPOUND Reaxys:1861302 Reaxys 2-hydroxy-5-methylcyclohexa-2,5-diene-1,4-dione IUPAC 2-Hydroxy-5-methyl-1,4-benzoquinone KEGG_COMPOUND 2-Hydroxy-5-methyl-p-benzoquinone ChemIDplus A Daphnia metabolite produced by the species Daphnia galeata. chebi_ontology Daphnia galeata metabolites CHEBI:83038 Daphnia galeata metabolite Daphnia galeata metabolites ChEBI 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 derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom. chebi_ontology canonical amino acid derivative canonical amino acid derivatives canonical amino-acid derivative canonical amino-acid derivatives proteinogenic amino acid derivatives proteinogenic amino-acid derivative proteinogenic amino-acid derivatives CHEBI:83811 proteinogenic amino acid derivative canonical amino acid derivative ChEBI canonical amino acid derivatives ChEBI canonical amino-acid derivative ChEBI canonical amino-acid derivatives ChEBI proteinogenic amino acid derivatives ChEBI proteinogenic amino-acid derivative ChEBI proteinogenic amino-acid derivatives ChEBI Any derivative of a non-proteinogenic amino acid resulting from reaction at an amino group or carboxy group, or from the replacement of any hydrogen by a heteroatom. chebi_ontology non-canonical amino acid derivative non-canonical amino-acid derivatives non-proteinogenic amino-acid derivatives CHEBI:83812 non-proteinogenic amino acid derivative non-canonical amino acid derivative ChEBI non-canonical amino-acid derivatives ChEBI non-proteinogenic amino-acid derivatives ChEBI Any of the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Apart from glycine, which is non-chiral, all have L configuration. Wikipedia:Proteinogenic_amino_acid chebi_ontology canonical amino acid canonical amino acids proteinogenic amino acids CHEBI:83813 proteinogenic amino acid canonical amino acid ChEBI canonical amino acids ChEBI proteinogenic amino acids ChEBI Any amino-acid that is not naturally encoded in the genetic code of any organism. Wikipedia:Non-proteinogenic_amino_acids chebi_ontology non-canonical amino acid non-canonical amino acids non-canonical amino-acid non-canonical amino-acids non-coded amino acid non-coded amino acids non-coded amino-acid non-coded amino-acids non-proteinogenic amino acids non-proteinogenic amino-acid non-proteinogenic amino-acids CHEBI:83820 non-proteinogenic amino acid non-canonical amino acid ChEBI non-canonical amino acids ChEBI non-canonical amino-acid ChEBI non-canonical amino-acids ChEBI non-coded amino acid ChEBI non-coded amino acids ChEBI non-coded amino-acid ChEBI non-coded amino-acids ChEBI non-proteinogenic amino acids ChEBI non-proteinogenic amino-acid ChEBI non-proteinogenic amino-acids ChEBI Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues. CHEBI:25359 chebi_ontology amino acid derivatives modified amino acids CHEBI:83821 amino acid derivative amino acid derivatives ChEBI modified amino acids ChEBI A proteinogenic amino acid derivative resulting from the formal reaction of L-cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of L-cysteine by a heteroatom. chebi_ontology L-cysteine derivatives CHEBI:83824 L-cysteine derivative L-cysteine derivatives ChEBI Any alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids. chebi_ontology non-proteinogenic alpha-amino acids non-proteinogenic alpha-amino-acid non-proteinogenic alpha-amino-acids CHEBI:83925 non-proteinogenic alpha-amino acid non-proteinogenic alpha-amino acids ChEBI non-proteinogenic alpha-amino-acid ChEBI non-proteinogenic alpha-amino-acids ChEBI A proteinogenic amino acid derivative resulting from reaction of L-glutamic acid at the amino group or either of the carboxy groups, or from the replacement of any hydrogen of L-glutamic acid by a heteroatom. chebi_ontology L-glutamic acid derivatives CHEBI:83982 L-glutamic acid derivative L-glutamic acid derivatives ChEBI Any metabolite (endogenous or exogenous) found in human urine samples. chebi_ontology human urinary metabolites CHEBI:84087 human urinary metabolite human urinary metabolites ChEBI 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 member of the class of cholanic acids carrying two hydroxy substituents at unspecified positions. chebi_ontology dihydroxycholanic acids CHEBI:85184 dihydroxycholanic acid dihydroxycholanic acids 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 organic anion obtained by deprotonation of the hydroxy group of 2-hydroxy-5-methylquinone. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.). -1 C7H5O3 InChI=1S/C7H6O3/c1-4-2-6(9)7(10)3-5(4)8/h2-3,10H,1H3/p-1 BMBZVGUSOUAIMK-UHFFFAOYSA-M 137.113 137.02442 C1(C=C(C(C=C1C)=O)[O-])=O MetaCyc:CPD-9135 4-methyl-3,6-dioxocyclohexa-1,4-dien-1-olate chebi_ontology 2-hydroxy-5-methylquinone 2-hydroxy-5-methylquinone(1-) CHEBI:88190 2-oxido-5-methylquinone MetaCyc:CPD-9135 SUBMITTER 4-methyl-3,6-dioxocyclohexa-1,4-dien-1-olate IUPAC 2-hydroxy-5-methylquinone UniProt 2-hydroxy-5-methylquinone(1-) ChEBI cell A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. environmental environmental material A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure. Damion Dooley https://en.wikipedia.org/wiki/Food food product The FoodOn product type class is provided as a food product category tree under which new food product categories and food products themselves can be placed. This tree has upper level categories inspired from other product type schemes like the US Code of Federal Regulations. However it has a much greater depth to it than the other product type schemes in an effort to group related products together. The basis of this tree was inherited from the environment ontology (ENVO). foodon product type A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. SUBSET_SIREN:F17332 meat food product A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. http://en.wikipedia.org/wiki/Meat This food product type includes food products which are derived from or produced by a plant. plant food product A seafood product is a vertebrate or invertibrate organism from an aquatic environment. Some of the subclasses are currently freshwater organisms. Damion Dooley seafood product fermented fish or seafood food product sea water fish food product plant fruit food product A food preserved by soaking and storing it in vinegar or brine. SUBSET_SIREN:F1302 SUBSET_SIREN:F16510 pickled subset_siren subset_siren SIREN DB annotation: * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) food (pickled) sugar condiment A food product which is derived from or produced by an animal that has a vertibrae. Damion Dooley vertebrate animal food product cereal grain food product Damion Dooley http://langual.org 2019-06-11T07:25:19Z SUBSET_SIREN:F5644 alcoholic beverage subset_siren SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) fermented beverage A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish. Damion Dooley https://en.wikipedia.org/wiki/Condiment condiment food product distilled fermented beverage A food product derived from or produced by a plant. plant root food product The default nut product is a whole, raw nut - meaning that the kernel is whole, and moderately or significantly dried, but not baked. Minimal references to nuts often leave ambiguous whether the shell is on or off. "I ate a peanut" doesn't clarify whether I ate a shell-off nut or whether I did the shelling. Damion Dooley SUBSET_SIREN:F16972 nut food product plant seed food product plant lipid food product invertebrate animal food product Damion Dooley cooked food (cooked) A product of the dry seeds of plants of the genus Pisum. Damion Dooley http://en.wikipedia.org/wiki/Legume dry pea food product PULSES are annual leguminous crops yielding from one to 12 grains or seeds of variable size, shape and colour within a pod. They are used for both food and feed. The term "pulses" is limited to crops harvested solely for dry grain, thereby excludingcrops harvested green for food (green peas, green beans, etc.) which are classified as vegetable crops. Also excluded are those crops used mainly for oil extraction (e.g.soybeand and groundnuts) and leguminous crops (e.g. seeds of clover and alfalfa) that are used exclusively for sowing purposes. Damion Dooley http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef04e.htm#4.02 pulse pulses pulse food product https://en.wikipedia.org/wiki/Legume#Classification_of_pulses A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment. Damion Dooley http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 http://www.langual.org/langual_thesaurus.asp?termid=H0151 herb and spice herb or spice spice or herb animal lipid food product A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). Damion Dooley fish food product plant derived beverage plant derived fermented beverage Are all fermented foods considered preserved to some extent? Damion Dooley food (fermented) Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food. vegetable food product Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food. http://www.fao.org/es/faodef/fdef07e.htm#7.01 Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. botanical fruit food product Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. http://eurovoc.europa.eu/drupal/?q=request&amp;uri=http://eurovoc.europa.eu/1115 http://oek1.fao.org/skosmos/agrovoc/en/page/c_3119 http://www.fao.org/pollination/resources/glossary/en/ https://en.wikipedia.org/wiki/Fruit A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995) http://www.fao.org/pollination/resources/glossary/en/ legume http://purl.obolibrary.org/obo/FOODON_03411254 http://purl.obolibrary.org/obo/FOODON_03411338 legume food product shellfish food product Damion Dooley A fermentation process in which either carbohydrates, proteins or fats are modified through microbial, enzymatic and/or other biological process. fermentation/modification process Hoi-dong is fermented sea mussel http://orcid.org/0000-0002-1816-4260 hoi-dong Fermented onions or pickled onion http://orcid.org/0000-0002-1816-4260 Hom dong Fermented meat product is any product made primarily of meat subjected to a fermentation process. Damion Dooley fermented meat product An alcoholic drink (or alcoholic beverage) is a drink that contains ethanol, a type of alcohol produced by fermentation of grains, fruits, or other sources of sugar. Damion Dooley https://en.m.wikipedia.org/wiki/Alcoholic_drink alcoholic beverage A bean vegetable food product is a human or animal food product - such as a snap, shell or dry bean product - derived from the fruit pod, seed, or leaf of one of several genera of the flowering plant family Fabaceae. Note, this was previously labelled "Bean (vegetable) food product". We have been listing both dry and freshly harvested moist beans here, so have broadened the name scope. Damion Dooley bean food product http://purl.obolibrary.org/obo/FOODON_00002428 http://www.fao.org/es/faodef/fdef04e.htm#4.02 https://oconto.extension.wisc.edu/files/2011/02/The-Importance-of-Dry-Beans-in-Your-Diet.pdf A broad bean food product is a product derived from the broad bean plant. Damion Dooley broad bean food product food component cloves clove food product crustacean food product Damion Dooley Damion Dooley's note: This category was created to organize SIREN inspired food products. It will probably get merged with the upper level 'dietary supplement' food product type items. dietary or therapeutic formulation food product A distilled spirit is an alcoholic drink produced by distillation of grains, fruit, or vegetables that have already gone through alcoholic fermentation. The distillation process purifies the liquid and removes diluting components like water, for the purpose of increasing its proportion of alcohol content (commonly expressed as alcohol by volume, ABV). Damion Dooley https://en.m.wikipedia.org/wiki/Liquor distilled drink hard alcohol hard liquor liquor spirit distilled spirit fermented cereal beverage food supplement food product fruit based alcoholic beverage gluten refined food product grain based alcoholic beverage gravy or sauce A food product made from legumes that are considered vegetables, such as immature raw legume pods or seeds. Damion Dooley leguminous vegetable food product Note american/ gb english spelling variation mollusc food product mollusk food product mussel food product onion flavouring food product onion food product A product containing primarily immature ripe pigeon peas. Damion Dooley 2019-07-14T10:26:00 pigeon pea vegetable food product plant based alcoholic beverage plant based refined or partially-refined food product plant derived distilled spirit plant fruit vegetable food product A food product harvested from underground plant parts. plant root vegetable food product plant seed vegetable food product Damion Dooley preserved food (preserved) pumpkin food product refined or partially-refined food product sesame food product sesame coated nut (snack) squash food product sugar based cacao food product sunflower food product vegetable pickle food product vitamin and mineral food supplement food product A meal type is the name of an eating occasion that may have location, food type, or other customary contextual features. (Damion's 1st draft definition) Damion Dooley food product by meal type food product by organism food food material Damion Dooley A zucchini food product is a food product deriving from either golden or green zucchini plant cultivars. zucchini food product A process involving the physical transformation of a food source or food product into some derived organic material or food product Damion Dooley food transformation process Very strange - As of 2018/11/28, unless this annotation on the subClassOf relation exists, with Makefile, the relation is removed from foodon.owl output and 'food transformation process' becomes parentless. Related to robot "WARNING: An illegal reflective access operation has occurred"??? Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snails, bivalves, squids, and octopuses), annelids (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals).[wikipedia] Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Damion Dooley https://en.wikipedia.org/wiki/Invertebrate animal invertebrate animal The food product by quality class provides descriptors for describing food visually or via other senses, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. Damion Dooley food product by quality food object quality An aquatic invertebrate may live entirely beneath the water, or may live upon its surface or on the plants surrounding it. Some breathe air, others breathe water. To move, they may walk, swim, float, skate, fly or glide on their bellies—or they may not move much at all. Because snails are members of gastropod, a subclass of molluscs, ... leading to aquatic invertebrates, we can't make aquatic invertebrates disjoint with terrestrial invertebrates. Damion Dooley https://nature.mdc.mo.gov/discover-nature/general-species-information/aquatic-invertebrate-facts 2019-04-29T19:23:38Z aquatic invertebrate Damion Dooley 2019-05-21T22:37:06Z Aves avian bird avian animal Damion Dooley 2019-05-23T23:02:07Z food product by process Damion Dooley 2019-05-25T06:43:20Z peeled food (peeled) A lipid food product is a food product made primarily of plant or animal fat or oil Damion Dooley 2019-06-11T09:18:41Z fats and oils oils and fats lipid food product A whole bean is a bean having an intact seed shape and composition. Damion Dooley's note. This could be enhanced to explicitly state the anatomical parts of a seed - seed coat, cotyledons, embryo etc. Currently the Plant Ontology is not explicit about this yet. Damion Dooley 2019-06-29T15:02:04Z bean bean (whole) Cooked bean material is the bean material output of a cooking process applied to dry, rehydrated, or raw (fresh) beans. Damion Dooley 2019-07-08T21:47:07Z bean (cooked) A bean pod is a fruit pod from a bean plant Damion Dooley 2019-07-08T23:32:17Z bean pod A pigeon pea food product is a food product derived from the pigeon pea plant Damion Dooley 2019-07-09T22:29:17Z pigeon pea food product https://en.wikipedia.org/wiki/Pigeon_pea Damion Dooley 2019-07-09T22:29:49Z pigeon pea pigeon pea (whole) Damion Dooley 2019-07-11T19:24:57Z fava bean pod broad bean pod Damion Dooley 2019-07-12T17:18:31Z pea food product 2019-08-14T18:02:36Z animal Golden zucchini is a modern hybrid summer squash (Cucurbita pepo). 2019-08-22T19:52:25Z gold gush zucchini golden delight zucchini goldfinger zucchini yellow zucchini golden zucchini plant A golden or yellow zucchini is a summer squash harvested from the golden zucchini cultivar. 2019-08-22T20:36:52Z golden zucchini yellow zucchini golden zucchini squash (whole) 2019-08-24T15:43:48Z saffron saffron food product A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). https://en.wikipedia.org/wiki/Vegetarian_cuisine 2019-09-11T21:12:43Z vegetarian food vegetarian food product "peeling" is the process of removing the outer covering, layer or skin from a fruit, vegetable, or plant or animal (such as a shrimp). Damion Dooley food peeling process The zebrafish (Danio rerio) is a tropical freshwater fish belonging to the minnow family (Cyprinidae) of the order Cypriniformes Dalia AlGhamdi https://en.wikipedia.org/wiki/Zebrafish zebrafish A broad bean is a bean harvested from a broad bean plant. http://langual.org SUBSET_SIREN:F1227 Windsor bean broad bean faba bean fava bean Horse bean field bean tic bean tick bean subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) broad bean (whole) http://langual.org SUBSET_SIREN:F1444 subset_siren SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) vegetable juice food product A bean substance is a substance made by processing seed from a bean plant. Damion Dooley's note: This class is intended to provide the most generic reference to bean, as it does not imply any more information about the state of a bean - whether it is whole or in fragments, or fragments of several beans, whether it is dry, raw, or cooked etc. Damion Dooley https://en.wikipedia.org/wiki/Bean http://langual.org SUBSET_SIREN:F1467 subset_siren SIREN DB annotation: * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) bean substance A liquid prepared for consumption, or a product that can be combined with water or milk to make one. Damion Dooley http://langual.org 2019-09-12T00:00:00 beverage food product http://langual.org SUBSET_SIREN:F2001 subset_siren SIREN DB annotation: * derives from 'part of animal' (http://purl.obolibrary.org/obo/FOODON_03420164) animal-derived food http://langual.org SUBSET_SIREN:F3588 subset_siren SIREN DB annotation: * has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'sucrose' (http://purl.obolibrary.org/obo/CHEBI_17992) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) * has substance added 'flavoring or spice extract or concentrate added' (http://purl.obolibrary.org/obo/FOODON_03460100) * has substance added 'chocolate or cocoa added' (http://purl.obolibrary.org/obo/FOODON_03460231) * has substance added 'vegetable fat or oil added' (http://purl.obolibrary.org/obo/FOODON_03460263) dark chocolate http://langual.org SUBSET_SIREN:F4497 subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) edible seed food product http://langual.org SUBSET_SIREN:F4869 sunflower seed subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) sunflower seed (whole kernel, raw) http://langual.org SUBSET_SIREN:F4870 subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) pumpkin seed (shell off) http://langual.org SUBSET_SIREN:F10006 subset_siren SIREN DB annotation: * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) fermented bean product http://langual.org SUBSET_SIREN:F10306 sesame subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) sesame seed http://langual.org SUBSET_SIREN:F10661 subset_siren SIREN DB annotation: * has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) * formed as a result of 'alcohol fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460232) * formed as a result of 'food distillation process' (http://purl.obolibrary.org/obo/FOODON_03460270) beverage alcohol Damion Dooley http://langual.org zucchini SUBSET_SIREN:F10943 green zucchini zucchini squash courgettes subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) zucchini squash (whole) http://langual.org SUBSET_SIREN:F11146 subset_siren SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) sauce http://langual.org SUBSET_SIREN:F11737 subset_siren processed food product http://langual.org SUBSET_SIREN:F15169 subset_siren SIREN DB annotation: * has substance added 'mineral added' (http://purl.obolibrary.org/obo/FOODON_03460159) * has substance added http://purl.obolibrary.org/obo/FOODON_03460163 * has substance added 'nutrient or dietary substance added' (http://purl.obolibrary.org/obo/FOODON_03460194) vitamin and mineral dietary supplement A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish. Damion Dooley http://langual.org SUBSET_SIREN:F15173 subset_siren SIREN DB annotation: * derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) fish product (unspecified species) https://en.wikipedia.org/wiki/Fish_products http://langual.org SUBSET_SIREN:F15837 subset_siren SIREN DB annotation: * has quality 'divided into pieces' (http://purl.obolibrary.org/obo/FOODON_03430152) * derives from 'peel, core or seed' (http://purl.obolibrary.org/obo/FOODON_03420110) fruit peel food product http://langual.org SUBSET_SIREN:F17197 subset_siren SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) fish sauce Seasoned product that contains multiple ingredients and that is used in limited amounts to accompany other foods; excludes flavors, spices and herbs. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0105 condiment, dressing, gravy or sauce gravy, condiment, dressing or sauce sauce, condiment, dressing or gravy dressing, condiment, gravy or sauce (us cfr) Aromatic or pungent plant product used whole or ground as a seasoning in food products. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0113 herb or spice spice or herb (us cfr) Extract, concentrate or isolate derived from a food source through one or more refining steps (see *EXTRACT, CONCENTRATE OR ISOLATE OF PLANT OR ANIMAL*) and marketed as such. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0129 refined or partially-refined food product (us cfr) Product that imparts or helps to impart a taste or aroma in food (21 CFR.170.3(n)(26). [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0133 seasoning or flavoring flavoring or seasoning (us cfr) Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0143 pie filling, fruit fruit or fruit product (us cfr) Meat (flesh and organs including blood and bone marrow) from mammals. Used for meat in all forms including cured meat, sausage or luncheon meat and meat product analogs. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0150 meat or meat product (from mammal) (us cfr) Vegetables in all forms except where a use-related product type descriptior (such as *PREPARED FOOD PRODUCT* or *SNACK FOOD*) takes precedence. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0152 vegetable or vegetable product (us cfr) Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. Prepared foods often undergo several of the processes listed in *F. EXTENT OF HEAT TREATMENT* and *H. TREATMENT APPLIED*; these factors should be carefully considered in indexing. The classification of prepared food products emphasizes consumption characteristics. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0172 prepared dish prepared food product (us cfr) Food product that is usually pungent, tart, salty, or spicy and is used to enhance the flavors of other foods; includes catsup, relish, prepared mustard, prepared horseradish, and condiment sauces. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0179 relish or condiment condiment or relish (us cfr) Products of the flesh of animals. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0217 meat, poultry, seafood or related product (us cfr) Alcoholic or nonalcoholic beverage; excludes milk and milk-based beverages, fruit juices and fruit juice drinks, and vegetable juices. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0229 beverage (us cfr) Fruits and vegetables in all forms. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0257 fruit or vegetable product (us cfr) Nuts in all forms, including nut butters and pastes. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0260 nut or nut product (us cfr) The liquid extracted or expressed from mature vegetables with or without optional ingredients such as seasoning or salt. Products prepared from vegetable juice by thickening with gelatin or pectin are indexed under the broader term *VEGETABLE OR VEGETABLE PRODUCT*. For part or portion, index the part or the plant from which the juice was extracted, rather than *PLANT EXTRACT, CONCENTRATE, OR ISOLATE*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0264 juice, vegetable vegetable juice (us cfr) Flesh from fish or shellfish. Includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0267 seafood or seafood product (us cfr) Any form of cacao, cacao product, chocolate, chocolate product or chocolate product analog except chocolate candy; includes such products as cacao beans, cacao nibs, chocolate liquor, sweet or milk chocolate, and chocolate syrup; excludes flavors and extracts derived from cacao beans and chocolate- or cacao-flavored foods (21 CFR 163). [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0272 chocolate or cacao product cacao or chocolate product (us cfr) Alcoholic beverage prepared by fermentation of grain or plant-related products and subsequent distillation (27 CFR 5.11). http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0277 hard liquor liquor, alcoholic spirits, distilled distilled spirits (us cfr) Beverage containing more than 0.5% alcohol; includes distilled spirits, malt beverage, and wine. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0278 alcoholic beverage (us cfr) Nonstandardized food product used as a meal accompaniment and consisting of a mixture of fats or oils, starch, liquid and other optional ingredients specified by the recipe; excludes condiment sauce (q.v.) and tomato or spaghetti sauce, which are vegetable products. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0286 sauce or gravy gravy or sauce (us cfr) Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0289 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. product type, USA http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0305 seed or seed product (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0306 nut or seed product (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0308 supplemental formulation (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0309 therapeutic formulation dietary or therapeutic formulation (us cfr) A food product type is a class of food products that is differentiated by its food composition, processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. Damion Dooley http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0361 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food product type Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A1270 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. product type, U.S. code of federal regulations, title 21 https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1001 pea plant edible seed cultivars http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1006 fruit used as vegetable http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1012 sugar-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1013 plant used for producing extract or concentrate http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1017 oil-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1018 vegetable-producing plant, root, tuber or bulb http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1041 LanguaL curation note: A chemical food component is a food substance derived from a nonliving source (e.g., salt, water or synthesized compounds). chemical food component http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1047 grain or seed-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1048 carbohydrate-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1057 vegetable-producing plant, above-ground parts Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. Damion Dooley https://en.wikipedia.org/wiki/Mammal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1134 mammal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1140 fruit-producing plant A legume is a plant or its fruit or seed in the family *Fabaceae* (or *Leguminosae*). Legumes are grown agriculturally, primarily for their grain seed called pulse, for livestock forage and silage, and as soil-enhancing green manure. Well-known legumes include alfalfa, clover, peas, beans, chickpeas, lentils, lupin bean, mesquite, carob, soybeans, peanuts and tamarind. [https://en.wikipedia.org/wiki/Legume] http://langual.org http://eol.org/pages/4277 http://www.langual.org/langual_thesaurus.asp?termid=B1156 fabaceae pod or seed vegetable plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1174 edible seed producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1179 flavor-producing plant herb-producing plant spice or flavor-producing plant Winter squash is an annual fruit representing several squash species within the genus Cucurbita. It differs from summer squash in that it is harvested and eaten in the mature fruit stage when the seeds within have matured fully and the skin has hardened into a tough rind. At this stage, most varieties of this fruit can be stored for use during the winter. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1189 curcurbita winter squash Cucurbita moschata Cucurbita pepo cucurbita maxima winter squash plant Californiacondor http://langual.org GRIN:12606 MANSFELD:4153 http://www.langual.org/langual_thesaurus.asp?termid=B1190 Cucurbita pepo L. cucurbita pepo yellow crookneck squash yellow squash summer squash plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1208 squash plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1213 nut producing plant Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature. Damion Dooley http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1222 fish Mussel is the common name used for members of several families of bivalve molluscs, from saltwater and freshwater habitats. These groups have in common a shell whose outline is elongated and asymmetrical compared with other edible clams, which are often more or less rounded or oval. Damion Dooley https://en.wikipedia.org/wiki/Mussel http://langual.org https://upload.wikimedia.org/wikipedia/commons/thumb/4/45/CornishMussels.JPG/640px-CornishMussels.JPG palaeoheterodonta pteriomorphia http://eol.org/pages/2235 http://www.langual.org/langual_thesaurus.asp?termid=B1223 mytilidae mussel http://langual.org DPNL 2003:13063 GRIN:33749 ITIS:505186 MANSFELD:10138 PLANTS:SEOR4 http://eol.org/pages/4428 http://www.langual.org/langual_thesaurus.asp?termid=B1226 simsim Sesamum indicum L. Sesamum orientale L. sesamum indicum sesamum orientale sesame plant http://langual.org GRIN:50069 MANSFELD:12338 http://www.langual.org/langual_thesaurus.asp?termid=B1255 Syzygium aromaticum (L.) Merr. & L.M. Perry caryophyllus eugenia aromatica syzygium aromaticum clove plant A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. Damion Dooley http://langual.org animal http://www.langual.org/langual_thesaurus.asp?termid=B1297 LanguaL curation note: For a unicellular animal, use *ALGAE OR FUNGUS USED AS FOOD SOURCE*. vertebrate animal The onion (*Allium cepa *L), also known as the bulb onion or common onion, is a vegetable that is the most widely cultivated species of the genus *Allium*. Its close relatives include the garlic, shallot, leek, chive,[2] and Chinese onion. This genus also contains several other species variously referred to as onions and cultivated for food, such as the Japanese bunching onion (*Allium fistulosum*), the tree onion (*A. ×proliferum*), and the Canada onion (*Allium canadense*). The name "wild onion" is applied to a number of *Allium* species, but *A. cepa* is exclusively known from cultivation. [https://en.wikipedia.org/wiki/Onion] http://langual.org DPNL 2003:7304 GRIN:300022 PLANTS:ALLIU http://eol.org/pages/8187 http://www.langual.org/langual_thesaurus.asp?termid=B1300 Allium Allium L. Allium sp. allium spp. bulb onion cebolla garden onion onion plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1324 grain plant http://langual.org GRIN:300472 MANSFELD:30744 http://www.langual.org/langual_thesaurus.asp?termid=B1338 Pisum sativum L. green pea plant lathyrus l. pisum l. pea plant Multicellular plants. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1347 LanguaL curation note: For unicellular plants as well as for algae, mushrooms and yeast, use the appropriate narrower term under *ALGAE OR FUNGUS USED AS FOOD SOURCE*. plant http://purl.obolibrary.org/obo/PO_0000003 http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1365 osteichthyes fish, bony *Vicia faba*, the Broad Bean, is a species of bean (*Fabaceae*) native to north Africa and southwest Asia, and extensively cultivated elsewhere. A variety is provisionally recognized: Vicia faba var. equina Pers. - Horse Bean. Although usually classified in the same genus Vicia as the vetches, some botanists treat it in a separate monotypic genus *Faba*. The term fava bean (from the Italian fava, meaning "broad bean") is usually used in English speaking countries such as the US, however the term broad bean is the most common name in the UK. WIKIPEDIA:Vicia_faba http://langual.org vicia faba DPNL 2003:13823 GRIN:300661 ITIS:26339 MANSFELD:30416 PLANTS:VIFA http://eol.org/pages/4277 http://www.langual.org/langual_thesaurus.asp?termid=B1367 faba bean plant fava bean plant horse bean plant horsebean plant Vicia faba L. Vicia faba L. (varieties for human consumption) broad bean plant Crustaceans form a large, diverse arthropod taxon which includes such familiar animals as crabs, lobsters, crayfish, shrimp, krill, woodlice, and barnacles. [https://en.wikipedia.org/wiki/Crustacean] http://langual.org http://eol.org/pages/2598871 http://www.langual.org/langual_thesaurus.asp?termid=B1374 crustacea crustacean The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. [https://en.wikipedia.org/wiki/Shellfish] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1433 Covers both freshwater and saltwater organisms shellfish http://langual.org DPNL 2003:9052 GRIN:12606 ITIS:22373 PLANTS:CUPE http://eol.org/pages/584410 http://www.langual.org/langual_thesaurus.asp?termid=B1456 Cucurbita pepo L. cucurbita pepo field pumpkin pumpkin plant http://langual.org GRIN:12265 MANSFELD:14971 http://www.langual.org/langual_thesaurus.asp?termid=B1459 Crocus sativus L. crocus sativus saffron plant The zucchini or courgette is a summer squash which can reach nearly a meter in length, but which is usually harvested at half that size or less. Along with certain other squashes, it belongs to the species Cucurbita pepo. Zucchini can be dark or light green. A related hybrid, the golden zucchini, is a deep yellow or orange color. WIKIPEDIA:Zucchini http://langual.org DPNL 2003:9052 GRIN:12606 ITIS:22373 PLANTS:CUPE http://eol.org/pages/584410 http://www.langual.org/langual_thesaurus.asp?termid=B1462 Cucurbita pepo L. courgette cucurbita pepo cucurbita pepo var. melopepo cv. zucchini zucchini plant http://langual.org DPNL 2003:10207 GRIN:27923 ITIS:36616 MANSFELD:32888 PLANTS:HEAN3 http://eol.org/pages/468106 http://www.langual.org/langual_thesaurus.asp?termid=B1547 Helianthus annuus L. giant greystripe helianthus annuus sunflower plant order= obolibrary:FOODON_03411297 # vertebrate obolibrary:FOODON_00002452 # invertebrate obolibrary:FOODON_03411347 # plant obolibrary:FOODON_03411301 # algae obolibrary:FOODON_03411261 # fungae obolibrary:FOODON_03412345 # lichen A food source is a plant or animal from which a food product or component is derived. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1564 This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995]. food source Leaf vegetables, also called leafy greens, salad greens, pot herbs, vegetable greens, or simply greens, are plant leaves eaten as a vegetable, sometimes accompanied by tender petioles and shoots. https://en.wikipedia.org/wiki/Leaf_vegetable http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1566 leafy green leafy vegetable A bean plant is one of several genera of the flowering plant family Fabaceae, which has seed pods, seeds, and/or leaf material used for human or animal food. https://en.wikipedia.org/wiki/Bean http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1567 bean plant bean plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1579 vegetable-producing plant Cypriniformes is an order of ray-finned fish, including the carps, minnows, loaches and relatives. This order contains 11-12 families, over 400 genera, and more than 4,250 species, with new species being described every few months or so, and new genera being recognized frequently. They are most diverse in southeastern Asia, and are entirely absent from Australia and South America. [https://en.wikipedia.org/wiki/Cypriniformes] http://langual.org http://eol.org/pages/3194 http://www.langual.org/langual_thesaurus.asp?termid=B1594 cypriniformes minnow sucker fish, cypriniform http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1607 nut or edible seed producing plant The *Cyprinidae* are the family of freshwater fishes, collectively called cyprinids, that includes the carps, the true minnows, and their relatives (for example, the barbs and barbels). Also commonly called the "carp family", or "minnow family", Cyprinidae is the largest known fish family and the largest vertebrate animal family in general, with about 3,000 living and extinct species in about 370 genera. The family belongs to the ostariophysian order Cypriniformes, of whose genera and species the cyprinids make more than two-thirds.. [https://en.wikipedia.org/wiki/Cyprinidae] http://langual.org http://eol.org/pages/3198 http://www.langual.org/langual_thesaurus.asp?termid=B1921 barbs cyprinidae minnow family carp or minnow family The pigeon pea (Cajanus cajan) is a perennial legume from the family Fabaceae. Since its domestication in the Indian subcontinent at least 3,500 years ago, its seeds have become a common food in Asia, Africa, and Latin America. https://en.wikipedia.org/wiki/Pigeon_pea http://langual.org GRIN:8319 MANSFELD:27597 http://www.langual.org/langual_thesaurus.asp?termid=B2010 cajanus cajan catjang pea red gram Cajanus cajan (L.) Huth gandules pigeon pea plant Mustards are several plant species in the genera *Brassica* and *Sinapis* whose small mustard seeds are used as a spice and, by grinding and mixing them with water, vinegar or other liquids, are turned into the condiment known as mustard or prepared mustard. The seeds are also pressed to make mustard oil, and the edible leaves can be eaten as mustard greens. WIKIPEDIA:Mustard_plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B2069 brassica spp. sinapis spp. mustard plant Cucurbita (Latin for gourd) is a genus of herbaceous vines in the gourd family, Cucurbitaceae, also known as cucurbits, native to the Andes and Mesoamerica. Five species are grown worldwide for their edible fruit, variously known as squash, pumpkin, or gourd depending on species, variety, and local parlance, and for their seeds. http://langual.org GRIN:12957 MANSFELD:4048 http://www.langual.org/langual_thesaurus.asp?termid=B2091 Cucurbita maxima L. (Duch.) pumpkin plant cucurbita spp. pumpkin, squash or gourd squash, gourd or pumpkin plant *Mollusca* is a large phylum of invertebrate animals whose members are known as molluscs or mollusks. Molluscs are the largest marine phylum, comprising about 23% of all the named marine organisms. Numerous molluscs also live in freshwater and terrestrial habitats. [https://en.wikipedia.org/wiki/Mollusca] http://langual.org EC:No 216/2009 MOL FAO ASFIS:MOL http://eol.org/pages/2195 http://www.langual.org/langual_thesaurus.asp?termid=B2112 Mollusca mollusks mollusk mollusc *Bivalvia*, in previous centuries referred to as the *Lamellibranchiata* and *Pelecypoda*, is a class of marine and freshwater molluscs that have laterally compressed bodies enclosed by a shell consisting of two hinged parts. Bivalves as a group have no head and they lack some usual molluscan organs like the radula and the odontophore. They include the clams, oysters, cockles, mussels, scallops, and numerous other families that live in saltwater, as well as a number of families that live in freshwater.[https://en.wikipedia.org/wiki/Bivalvia] http://langual.org http://eol.org/pages/2215 http://www.langual.org/langual_thesaurus.asp?termid=B2113 bivalvia lamellibranchiata pelecypod pelecypoda bivalve A type of winter squash that grows on a vine. It has a sweet, nutty taste similar to that of a pumpkin. It has tan-yellow skin and orange fleshy pulp with a compartment of seeds in the bottom. When ripe, it turns increasingly deep orange, and becomes sweeter and richer. http://langual.org DPNL 2003:9051 GRIN:12601 ITIS:22370 MANSFELD:4090 PLANTS:CUMO http://eol.org/pages/584408 http://www.langual.org/langual_thesaurus.asp?termid=B2509 butternut pumpkin cucurbita moschata cucurbita moschata var. butternut gramma Cucurbita moschata Duch. Cucurbita moschata Duchesne butternut squash plant This section and its narrover terms refer to the European Commission food additive regulation according to COMMISSION REGULATION (EU) No 1129/2011 of 11 November 2011 amending Annex II to Regulation (EC) No 1333/2008 of the European Parliament and of the Council by establishing a Union list of food additives [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2011:295:0001:0177:EN:PDF] and its basis, the four Food Additive Directives: the EEC Framework Directive on Food Additives (89/107/EEC), the Directive on colours (94/36/EC), the Directive on sweeteners (94/35/EC) and the 'miscellaneous' Directive (95/2/EC) plus amendments [http://ec.europa.eu/food/fs/sfp/flav_index_en.html] and/or Codex Alimentarius Commission General Standard for Food Additives (CODEX STAN 192, revised 2011) [http://www.codexalimentarius.net/download/standards/4/CXS_192e.pdf]. If used for food supplement substances, thissection and its narrover terms refer to the European Commission regulation in general [http://ec.europa.eu/food/food/labellingnutrition/supplements/index_en.htm] and specifically to the EC Directive on the approximation of the laws of the Members States relating to food supplements (2002/46/EC) [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B2972 Damion Dooley's note: manysubclasses here are currently originating from LanguaL additives that have not yet been matched to CHEBI ontology terms. If matches are possible they will be implemented over time, at which point the corresponding FoodOn id's will be deprecated. food additive http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B2974 liquid http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3357 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. plant according to family http://langual.org CCPR: DPNL 2003:8093 GRIN:30008 GRIN:300085 PLANTS:BRASS2 http://eol.org/pages/4219 http://www.langual.org/langual_thesaurus.asp?termid=B3372 Brassica Brassica L. Brassica sp. Brassica spp. brassica spp. brassica species This section list vitamins and mineral substances which may be used in the manufacture of food supplements. DIRECTIVE 2002/46/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 10 June 2002 on the approximation of the laws of the Member States relating to food supplements [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. This section list vitamins and mineral substances which may be used in the manufacture of food supplements. DIRECTIVE 2002/46/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 10 June 2002 on the approximation of the laws of the Member States relating to food supplements [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3749 food supplements, vitamin and mineral substances (ec) DIRECTIVE 2002/46/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 10 June 2002 on the approximation of the laws of the Member States relating to food supplements [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF] and its amendments COMMISSION DIRECTIVE 2006/37/EC [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2006:094:0032:0033:EN:PDF] and COMMISSION REGULATION (EC) No 1170/2009 [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2009:314:0036:0042:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3751 food supplements, vitamin substances (ec) DIRECTIVE 2002/46/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 10 June 2002 on the approximation of the laws of the Member States relating to food supplements [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3761 vitamin b12 *Allium* is a genus of monocotyledonous flowering plants that includes hundreds of species, including the cultivated onion, garlic, scallion, shallot, leek, and chives. [https://en.wikipedia.org/wiki/Allium] http://langual.org http://eol.org/pages/8187 http://www.langual.org/langual_thesaurus.asp?termid=B4302 allium onion wild onion allium species The *Cucurbitaceae*, also called cucurbits and the gourd family, are a plant family consisting of about 965 species in around 95 genera, the most important of which are: *Cucurbita* - squash, pumpkin, zucchini, some gourds; *Lagenaria* - calabash, and others that are inedible; *Citrullus* - watermelon (*C. lanatus, C. colocynthis*) and others; *Cucumis* - cucumber (*C. sativus*), various melons; *Luffa* - luffa, loofah http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B4460 cucurbitaceae gourd/squash family gourd/squash family Edible flesh of any type of animal, including poultry and seafood. Excludes parts containing only animal fat, which is indexed under *FAT OR OIL* or under *FAT, TRIM*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0103 Damion Dooley Feb 6, 2017: Good meat cut resources to incorporate for Canada: The CFIA Meat Cuts Manual http://www.inspection.gc.ca/food/labelling/meat-cuts/eng/1300126276015/1300126372856 meat part of animal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0106 organ meat, digestive system http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0110 core, seed, or peel seed, peel or core LanguaL curation note: Used for a fruit byproduct consisting of peel, core or seed (with adjacent tissue) or of fruit from which the juice has been extracted or expressed. peel, core or seed Anatomical part of the plant or animal from which the food product or its major ingredient is derived, e.g., *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0116 part of plant or animal Bone, feathers, shell, skin or trim fat. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0122 LanguaL curation note: *BLOOD* AND *INK, AQUATIC ANIMAL* are now listed under organism substance. nonmeat part of animal Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0127 LanguaL curation note: Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. animal body or body part http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0129 organ meat, cardiovascular system http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0145 organ meat, urogenital system The parts of a plant that are not fruit or seed. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0148 flower, root, stem or leaf leaf, flower, root or stem stem, leaf, flower or root root, stem, leaf or flower Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0152 carbohydrate extract, concentrate, or isolate The main propagative part of a plant, especially the kernel of a grain or nut. The bulk of the seed is formed by the endosperm, which encloses the germ and is covered by skin (bran). http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0155 seed dehulled seed kernel kernel or seed nut, shelled (part or portion) seed or kernel, skin undetermined seed without shell or hull shelled seed LanguaL curation note: The factor values under *SEED* are arrayed so that the indexer can check first whether the skin is present, removed or undetermined and then check the same information for the germ. Renamed from *SEED OR KERNEL* in LanguaL 2008. seed (anatomical part) Anatomical part of an animal; includes eggs and milk that, although separated from the animal, are prouced as integral parts and are affected by the animal's food intake and metabolism. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0164 part of animal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0165 fruit or seed The fleshy fruit of any plant. *FRUIT* includes vegetables berries and pods as well. The bulk of a fruit is its fleshy part, which is covered by a peel (skin) and which encloses a core, pit or seeds. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0167 berry berry or fruit (anatomical part) fruit or berry, peel undetermined hip (fruit) infructescence LanguaL curation note: The descriptors under *FRUIT* are arrayed so that the indexer can check first whether the peel is present, removed or undetermined; then check the same informationfor the core, pit or seeds. For juices, beverages or jellies made from fruit, Index the entire part from which the product is derived. Renamed from *FRUIT OR BERRY* in LanguaL 2008. fruit part Bone (endoskeleton) or shell (exoskeleton) of animals, or any part thereof. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0168 shell (animal) bone or shell Anatomical part of a plant, such as fruit, seed, pod, leaf, stem or flower as well as the whole plant. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0174 part of plant Carcass meat from any type of animal including poultry and seafood. Includes retail and wholesale cuts other than organ meat. Refers to the whole carcass or parts. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0175 skeletal meat part Extract, concentrate or isolate high in gluten, the predominant protein of wheat or corn. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0177 gluten Food substance or component consisting predominantly of mixed glycerol esters of fatty acids and, in far lesser amounts, of fatty acids, sterols and pigments. A fat is a solid at room temperature, an oil is a liquid at room temperature (20 degrees C.). Excludes essential oils. Damion Dooley http://langual.org 2019-06-20T05:09:36Z SUBSET_SIREN:F15008 http://www.langual.org/langual_thesaurus.asp?termid=C0190 http://www.langual.org/langual_thesaurus.asp?termid=H0221 oil or fat subset_siren SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) fat or oil Edible organ meat, including blood and bone marrow. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0218 variety meat organ meat A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0228 Damion Dooley's note: Items in this branch will be merged into foodon food product branch. extract, concentrate or isolate of plant or animal Extract, concentrate or isolate high in protein; may contain amino acids, polypeptides and enzymes. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0236 http://www.langual.org/langual_thesaurus.asp?termid=H0164 protein extract, concentrate or isolate http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0238 bulb, root or tuber tuber, bulb or root root, tuber or bulb Meat from organs that do not belong to the cardiovascular, digestive or urogenital system. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0255 organ meat, other systems The hard, central part of an apple, pear, etc., that contains the seeds (Source: Webster's) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0293 LanguaL curation note: Renamed from *FRUIT OR BERRY, CORE ONLY* in LanguaL 2008. fruit core (anatomical part) The rind or skin of fruit (Source: Webster's) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0294 LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL ONLY* in LanguaL 2008. fruit peel (anatomical part) The part of a flowering plant that typically contains the embryo with its protective coat and stored food and that can develop into a new plant under the proper conditions; fertilised and mature ovule (Source: Webster's). .Seeds and fruits commonly called seeds include: grain, kernel, berry, ear, corn, nut. (Source: Webster's Thesaurus). http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0295 LanguaL curation note: Renamed from *FRUIT OR BERRY, SEED ONLY in LanguaL 2008. fruit seed (anatomical part) A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. http://langual.org SUBSET_SIREN:F5105 http://www.langual.org/langual_thesaurus.asp?termid=E0130 fluid SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) food (liquid) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=G0002 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food cooking process Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. Multiple values can be assigned. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0111 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food treatment process Modified by microbial or enzymatic action resulting in molecular changes in any food component. If salt, sugar or other food additive is used to aid in the modification process, index it by the appropriate term under *INGREDIENT ADDED*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0119 fermented, unspecified microbial/enzymatic modification process http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0130 LanguaL curation note: Used when physical or chemical changes are effected in any food ingredient through a physical or non-enzymatic chemical process. physical/chemical modification process http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0141 LanguaL curation note: Used when the food product underwent mechanical, chemical or enzymatic modification that has affected the texture, flavor or other characteristic of the product. food modification process This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred. nut or seed added http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0177 LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance. plant seed or nut food product Treated with acid that may be produced by fermentation or added and/or with salt brine, often in the presence of spices or herbs, producing changes in flavor and texture. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0190 LanguaL curation note: Also index by other applicable terms from *MICROBIALLY/ ENZYMATICALLY MODIFIED*. pickling process http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0216 vitamin B The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=J0107 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food preservation process 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. 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 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. 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 true Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. receptor binding Wikipedia:Ligand_(biochemistry) receptor ligand molecular_function receptor-associated protein activity GO:0005102 Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'. signaling receptor binding Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GOC:bf GOC:ceb ISBN:0198506732 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function GO:0005488 Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. GOC:ceb GOC:mah ISBN:0198506732 Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GO:0001948 GO:0045308 MIPS_funcat:16.01 MIPS_funcat:18.01.07 Reactome:R-HSA-170835 Reactome:R-HSA-170846 protein amino acid binding glycoprotein binding molecular_function GO:0005515 protein binding Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GOC:go_curators Reactome:R-HSA-170835 An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3 Reactome:R-HSA-170846 TGFBR2 recruits TGFBR1 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). 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 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 subcellular entity NIF_Subcellular:nlx_subcell_100315 The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. Wikipedia:Intracellular internal to cell protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. 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. MIPS_funcat:70.10 NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus 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 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. MIPS_funcat:01.04 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 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 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:0023033 MIPS_funcat:30 Wikipedia:Signal_transduction 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 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. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 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 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 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. 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. janelomax 2012-10-17T15:46:40Z GO:0044236 GO:0044710 MIPS_funcat:01 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 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 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. janelomax 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 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 Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. regulation of receptor activity biological_process GO:0010469 regulation of signaling receptor activity Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. 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 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 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 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-6787403 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-6787403 GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA 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 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 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. janelomax 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 function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. MIPS_funcat:18.02.07 molecular_function GO:0030545 receptor regulator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. GOC:ceb The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. receptor activator activity molecular_function GO:0030546 signaling receptor activator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. GOC:ceb 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 stops, prevents, or reduces the frequency, rate or extent of protein binding. down regulation of protein binding down-regulation of protein binding downregulation of protein binding inhibition of protein binding biological_process GO:0032091 negative regulation of protein binding Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. GOC:mah Any process that activates or increases the frequency, rate or extent of protein binding. up regulation of protein binding up-regulation of protein binding upregulation of protein binding activation of protein binding stimulation of protein binding biological_process GO:0032092 positive regulation of protein binding Any process that activates or increases the frequency, rate or extent of protein binding. 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 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. rfoulger 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 Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. rfoulger 2011-08-01T02:45:27Z GO:0004872 GO:0019041 receptor activity receptor activity involved in signal transduction molecular_function GO:0038023 signaling receptor activity Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. GOC:bf GOC:signaling receptor activity involved in signal transduction GOC:bf 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 activates or increases the activity of an enzyme. GO:0048554 MIPS_funcat:18.02.01.01 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 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, 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, 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 Any process that modulates the frequency, rate or extent of protein binding. biological_process GO:0043393 regulation of protein binding Any process that modulates the frequency, rate or extent of protein binding. GOC:go_curators 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 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. jane 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. jane 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 The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms. CL:0000000 NIF_Subcellular:sao628508602 cellular subcomponent cellular_component protoplast GO:0044464 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. cell part obsolete cell part true OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms. GOC:jl cellular subcomponent NIF_Subcellular:sao628508602 protoplast GOC:mah 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 The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). midori 2010-09-13T04:51:59Z GO:0071884 receptor agonist activity signaling molecule signaling receptor ligand activity vitamin D receptor activator activity molecular_function GO:0048018 Definition discussed in https://github.com/geneontology/go-ontology/issues/14220 receptor ligand activity The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). GOC:kv GOC:molecular_function_refactoring GOC:pdt receptor agonist activity GOC:molecular_function_refactoring 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 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 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 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 MIPS_funcat:18.02.01 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 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 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 MIPS_funcat:34.11 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 that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. biological_process GO:0051098 regulation of binding Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. up regulation of binding up-regulation of binding upregulation of binding activation of binding stimulation of binding biological_process GO:0051099 positive regulation of binding Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. down regulation of binding down-regulation of binding downregulation of binding inhibition of binding biological_process GO:0051100 negative regulation of binding Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai 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 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. EC:2.-.-.- 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 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 A compound molecular function in which an effector function is controlled by one or more regulatory components. molecular_function GO:0060089 molecular transducer activity A compound molecular function in which an effector function is controlled by one or more regulatory components. GOC:dos GOC:pdt 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 A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. molecular_function GO:0098772 molecular function regulator A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. GOC:dos GOC:pt 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. 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 Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:40:53Z regulation of receptor ligand biological_process GO:1900120 regulation of receptor binding Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling regulation of receptor ligand GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:40:57Z down regulation of receptor binding down-regulation of receptor binding downregulation of receptor binding inhibition of receptor binding inhibition of receptor ligand biological_process down regulation of receptor-associated protein activity GO:1900121 negative regulation of receptor binding Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling down regulation of receptor binding GOC:TermGenie down-regulation of receptor binding GOC:TermGenie downregulation of receptor binding GOC:TermGenie inhibition of receptor binding GOC:TermGenie inhibition of receptor ligand GOC:TermGenie down regulation of receptor-associated protein activity GOC:TermGenie Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:41:00Z up regulation of receptor binding upregulation of receptor binding activation of receptor binding biological_process GO:1900122 positive regulation of receptor binding Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling up regulation of receptor binding GOC:TermGenie upregulation of receptor binding GOC:TermGenie activation of receptor binding 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 Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity. rfoulger 2010-12-02T09:28:47Z negative regulation of receptor activity biological_process GO:2000272 negative regulation of signaling receptor activity Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity. GOC:obol Any process that activates or increases the frequency, rate or extent of signaling receptor activity. rfoulger 2010-12-02T09:28:50Z biological_process GO:2000273 positive regulation of signaling receptor activity Any process that activates or increases the frequency, rate or extent of signaling receptor activity. GOC:obol data item Data items include counts of things, analyte concentrations, and statistical summaries. 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 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol 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. 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. PERSON: Chris Stoeckert OBI_0000142 information content entity 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 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 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 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 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 centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry A clinically prescribed procedure, therapy, intervention, or recommendation. 2018-11-16T20:07:28Z OGMS:0000096 health care process medical action health care process OGMS:0000096 All manners of treatment, be they pharmaceuticals, invasive procedures, etc. to relieve illness and injury in attempts to bring the body back to its normal state. 2018-11-16T20:08:29Z medical procedure NCIT:C25218 NCIT:C49236 OAE:0000094 OGMS:0000112 SIO:001024 clinical procedure treatment An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process. therapeutic procedure All manners of treatment, be they pharmaceuticals, invasive procedures, etc. to relieve illness and injury in attempts to bring the body back to its normal state. ISBN-10:0124105165 An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process. NCIT:C49236 Any procedure or test to diagnose a disease or disorder. 2018-11-16T20:10:20Z NCIT:C18020 OGMS:0000104 diagnostic technique diagnostic test diagnostic procedure Any procedure or test to diagnose a disease or disorder. NCIT:C18020 A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. 2018-11-16T20:10:35Z ERO:0000378 NCIT:C15329 NCIT:C17173 NCRO:0000228 OAE:0000067 SCDO:1000017 operation surgery surgical intervention surgical operation surgical procedure A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. NCIT:C15329 Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy. 2018-11-16T20:10:50Z NCIT:C17369 imaging procedure imaging technique medical imaging therapeutic imaging technique therapeutic imaging procedure Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy. NCIT:C17369 Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting for diagnosis, treatment, or therapy. 2018-11-16T20:11:26Z NCIT:C25294 clinical lab tests clinical laboratory tests clinical test lab test clinical laboratory procedure Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting for diagnosis, treatment, or therapy. NCIT_C25294 http://orcid.org/0000-0001-7941-2961 obsolete therapeutic intervention false Behavioral or regulatory nutritional interventions aim at modifying nutritional intake which have an impact on health outcomes. 2018-11-16T20:12:00Z nutritional intervention nutrition intervention Behavioral or regulatory nutritional interventions aim at modifying nutritional intake which have an impact on health outcomes. http://orcid.org/0000-0001-7941-2961 Cognitive and behavioral interventions are therapies that are designed to decrease symptoms and foster the belief that one has control over thoughts, beliefs, attitudes, and skills to facilitate coping. 2018-11-16T20:12:16Z NCIT:C116519 NCIT:C15184 NCIT:C64345 cognitive and behavioral therapies cognitive and behavioral therapy cognitive and behavioural intervention cognitive behavior therapy cognitive behavioral therapy cognitive behaviour therapy cognitive behavioural therapy cognitive and behavioral intervention Cognitive and behavioral interventions are therapies that are designed to decrease symptoms and foster the belief that one has control over thoughts, beliefs, attitudes, and skills to facilitate coping. PMID:22796302 https://orcid.org/0000-0002-7463-6306 The treatment of deformity or disease through mechanical force and movement, including both active and passive exercises, intended to ameliorate injury, increase mobility, and improve overall function. 2018-11-16T20:12:31Z NCIT:C15302 OGMS:0000115 PT physiatric procedure physical medicine procedure physical therapeutics physical therapy procedure physiotherapy physiotherapy procedure physical therapy The treatment of deformity or disease through mechanical force and movement, including both active and passive exercises, intended to ameliorate injury, increase mobility, and improve overall function. NCIT:C15302 PT Complementary and alternative medicine (CAM) or “complementary health approaches” are a group of diverse medical and health care practices and products that are not presently considered to be part of conventional medicine. 2019-01-07T19:24:28Z NCIT:C51976 SCDO:0000271 CAM therapy complementary or alternative medical procedure complementary medicine complementary therapy complementary and alternative medical therapy Complementary and alternative medicine (CAM) or “complementary health approaches” are a group of diverse medical and health care practices and products that are not presently considered to be part of conventional medicine. NCCIH Treatment of a disease by means of exposure of the target or the whole body to radiation. Radiation therapy is often used as part of curative therapy and occasionally as a component of palliative treatment for cancer. Other uses include total body irradiation prior to transplantation. 2018-11-16T20:20:38Z NCIT:C15313 OGMS:0000116 RT radiation radiation therapy procedure radiotherapeutics radiotherapy radiation therapy Treatment of a disease by means of exposure of the target or the whole body to radiation. Radiation therapy is often used as part of curative therapy and occasionally as a component of palliative treatment for cancer. Other uses include total body irradiation prior to transplantation. NCIT:C15313 RT A type of treatment that uses substances derived from or made by living organisms to treat disease; this includes both naturally occurring and synthetic products. 2018-11-16T20:20:54Z NCIT:C15187 BRM therapy biologic therapies biological response modifier therapy biological therapy biotheraphy biologic therapy A type of treatment that uses substances derived from or made by living organisms to treat disease; this includes both naturally occurring and synthetic products. NCIT:C15187 BRM therapy Cell therapy is therapy in which cellular material is injected into a patient. 2018-11-16T20:21:19Z NCIT:C70601 cell therapy cellular therapies cellular therapy Cell therapy is therapy in which cellular material is injected into a patient. PMID:24471045 A therapy or action designed to prevent disease or ailment. 2018-11-16T20:21:49Z preventative clinical measures preventative medical actions preventative medical measures preventative therapies preventative therapy preventive medical actions preventive medical measures preventive therapeutics preventative therapeutics A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly. 2018-11-16T20:22:04Z NCIT:C63333 biomarker analysis A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly. PMID:20978388 A behavioral modification or implementation of a behavior designed to prevent disease or ailment. 2018-11-16T20:22:48Z behavioral preventative therapeutics behavioral preventive care behavioral preventive therapy preventative behavior therapy preventative behavioral therapy behavioral preventative care An approach that improves the quality of life of patients and their families facing the problems associated with life-threatening illness, through the prevention and relief of suffering by means of early identification and impeccable assessment and treatment of pain and other problems, physical, psychosocial, and spiritual’. 2018-11-16T20:23:01Z NCIT:C101516 NCIT:C15747 comfort care symptom management supportive care palliative therapeutics An approach that improves the quality of life of patients and their families facing the problems associated with life-threatening illness, through the prevention and relief of suffering by means of early identification and impeccable assessment and treatment of pain and other problems, physical, psychosocial, and spiritual’. PMID:27162584 A service delivery system that provides palliative care/medicine when life expectancy is 6 months or less and when curative or life-prolonging therapy is no longer indicated. 2018-11-16T20:23:10Z NCIT:C15252 hospice care A service delivery system that provides palliative care/medicine when life expectancy is 6 months or less and when curative or life-prolonging therapy is no longer indicated. PMID:22190887 Care for patients with a progressive life-limiting disease with a prognosis of months or less. 2019-01-09T20:15:05Z NCIT:C67359 end-of-life treatment management end-of life care Care for patients with a progressive life-limiting disease with a prognosis of months or less. PMID:23796586 Any medical procedure used to sustain the life of a patient in critical condition. 2019-01-09T20:25:04Z NCIT:C95171 OMIT:0009105 life support care Any medical procedure used to sustain the life of a patient in critical condition. NCIT:C95171 obsolete therapeutic avoidance of behavior false obsolete therapeutic mental or psychological behavior avoidance false obsolete stress avoidance false obsolete smoking avoidance false 2019-01-11T19:39:19Z therapeutic disease avoidance 2019-01-11T19:39:37Z communicable disease avoidance 2019-01-11T19:59:24Z physiologic state avoidance 2019-01-11T19:59:44Z dehydration avoidance 2019-01-11T19:59:54Z hypertension avoidance 2019-01-11T20:01:31Z obesity avoidance 2019-01-11T20:03:43Z skin abrasion avoidance 2019-01-11T20:11:57Z therapeutic avoidance of physical activity 2019-01-11T20:12:16Z impact sports avoidance therapeutic impact activities avoidance 2019-01-11T20:13:10Z therapeutic isometric exercise avoidance A clinical recommendation to avoid or refrain from certain environmental exposures in order to maintain health or ameliorate symptoms. 2019-01-11T20:50:37Z therapeutic avoidance of environmental exposure 2019-01-11T20:50:51Z radiation exposure avoidance 2019-01-11T20:56:19Z sunlight avoidance 2019-01-11T20:56:39Z food consumption avoidance nutrition intake avoidance Any substance introduced into a living organism with therapeutic or diagnostic purpose. 2019-01-15T18:20:06Z CHEBI:52217 drug therapy drug treatment medication therapy pharmaceutical drug pharmaceutical treatment pharmacological treatment Medical treatment by means of drugs. pharmacotherapy Any substance introduced into a living organism with therapeutic or diagnostic purpose. CHEBI:52217  Medical treatment by means of drugs. http://orcid.org/0000-0001-7941-2961 A drug used to treat or prevent bacterial infections. 2019-01-15T18:59:44Z CHEBI:36047 antibacterial drug therapy antibacterial treatment antibacterial agent therapy A drug used to treat or prevent bacterial infections. CHEBI:36047 A substance that inhibits or prevents the proliferation of neoplasms. 2019-01-15T19:01:01Z anticancer agent therapy antineoplastic drug therapy CHEBI:35610 antineoplastic drug therapy cytostatic agent therapy cytostatic drug therapy antineoplastic agent therapy A substance that inhibits or prevents the proliferation of neoplasms. CHEBI:35610 A medical recommendation of sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. 2019-01-15T19:02:35Z NCIT:C39774 aerobic activity aerobic exercise aerobic exercise therapy A medical recommendation of sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. NCIT:C39774 http://orcid.org/0000-0001-7941-2961 The administration of oxygen to an individual, usually to aid in respiration. 2019-01-15T19:14:17Z MeSH:D010102 NCIT:C94624 oxygen inhalation therapy Inhalation of oxygen aimed at restoring toward normal any pathophysiologic alterations of gas exchange in the cardiopulmonary system, as by the use of a respirator, nasal catheter, tent, chamber, or mask. (From Dorland, 27th ed & Stedman, 25th ed) supplemental oxygen therapy The administration of oxygen to an individual, usually to aid in respiration. NCIT:C94624 Inhalation of oxygen aimed at restoring toward normal any pathophysiologic alterations of gas exchange in the cardiopulmonary system, as by the use of a respirator, nasal catheter, tent, chamber, or mask. (From Dorland, 27th ed & Stedman, 25th ed) MeSH:D010102 2019-01-15T19:14:42Z lung volume reduction surgery Transference of a tissue or organ within an individual, between individuals of the same species, or between individuals of different species. 2019-01-15T19:15:04Z NCIT:C15342 OBI:0000105 transplant procedure transplantation transplantation surgery grafting procedure transplantation surgical procedure Transference of a tissue or organ within an individual, between individuals of the same species, or between individuals of different species. NCIT:C15342 The surgical transfer of one or both lungs from one individual to another. 2019-01-15T19:15:13Z NCIT:C15274 lung grafting lung transplantation lung transplantation surgery transplantation of lung transplantation of the lung lung transplantation surgical procedure The surgical transfer of one or both lungs from one individual to another. NCIT:C15274 The transfer of a healthy liver allograft from a donor to a patient. 2019-01-15T19:15:21Z NCIT:C15271 hepatic transplantation liver grafting liver transplantation surgical transplantation of the liver transplantation of liver liver transplantation surgical procedure The transfer of a healthy liver allograft from a donor to a patient. NCIT:C15271 2019-01-15T19:31:56Z chemical exposure avoidance The use of ultrasound to produce images of structures in the human body. 2019-01-15T19:32:35Z ERO:0001325 NCIT:C17230 sonography ultrasound procedure ultrasonography procedure 2019-01-15T19:32:45Z liver ultrasound procedure 2019-01-15T19:35:19Z NCIT:C97101 pancreatic function test 2019-01-15T19:35:36Z digestive system test The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase. 2019-01-15T19:35:59Z NCIT:C74954 liver function test The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase. NCIT:C74954 The act of receiving professional guidance in resolving personal conflicts and emotional problems. 2019-01-19T19:44:32Z NCIT:C15308 NCIT:C61547 NCIT:C63474 behaviour therapy behavioural counseling counseling intervention psychotherapy behavioral counseling The act of receiving professional guidance in resolving personal conflicts and emotional problems. NCIT:C61547 counseling intervention NCIT:C61547 Counseling designed to guide and support an individual to overcome alcohol dependence. 2019-01-19T19:46:47Z NCIT:C150658 alcoholism counseling Counseling designed to guide and support an individual to overcome alcohol dependence. NCIT:C150658 The process whereby an expert in hereditary disorders provides information about risk and clinical burden of a disorder or disorders to patients or relatives in families with genetic disorders as an aid to making informed and responsible decisions about marriage, children, early diagnosis, and handling disability. 2019-01-19T19:48:00Z NCIT:C15240 SCDO:0000443 genetic counseling The process whereby an expert in hereditary disorders provides information about risk and clinical burden of a disorder or disorders to patients or relatives in families with genetic disorders as an aid to making informed and responsible decisions about marriage, children, early diagnosis, and handling disability. NCIT:C15240 2019-01-19T19:49:24Z NCIT:C67032 stress management stress management therapy A process by which a health professional provides education, recommendations, or interventions to help clients stop using tobacco products. 2019-01-19T19:51:07Z NCIT:C101244 smoking cessation counseling smoking cessation tobacco cessation counseling A process by which a health professional provides education, recommendations, or interventions to help clients stop using tobacco products. NCIT:C101244 smoking cessation http://orcid.org/0000-0001-7941-2961 The practice of piercing specific points on the body with very thin sterile needles in order to relieve pain or induce regional anesthesia. 2019-01-19T20:30:57Z NCIT:C15176 acupuncture therapy The practice of piercing specific points on the body with very thin sterile needles in order to relieve pain or induce regional anesthesia. NCIT:C15176 Continuous and profound contemplation or musing on a subject or series of subjects of a deep or abstruse nature; contemplation of spiritual matters. 2019-01-19T20:32:30Z NCIT:C51975 SCDO:0000741 meditation therapy Continuous and profound contemplation or musing on a subject or series of subjects of a deep or abstruse nature; contemplation of spiritual matters. NCIT:C51975 An ancient system of practices used to balance the mind and body through exercise, meditation (focusing thoughts), and control of breathing and emotions. Yoga is being studied as a way to relieve stress and treat sleep problems. 2019-01-19T20:34:15Z NCIT:C64897 yoga therapy An ancient system of practices used to balance the mind and body through exercise, meditation (focusing thoughts), and control of breathing and emotions. Yoga is being studied as a way to relieve stress and treat sleep problems. NCIT:C64897 An alternative medical system that focuses on the relationship between bodily structure (primarily that of the spine) and function, and how that relationship affects the preservation and restoration of health. Chiropractors use manipulative therapy as an integral treatment tool. 2019-01-19T20:35:28Z NCIT:C15204 chiropractic therapies chiropractic treatment chiropratic medicine chiropractic therapy An alternative medical system that focuses on the relationship between bodily structure (primarily that of the spine) and function, and how that relationship affects the preservation and restoration of health. Chiropractors use manipulative therapy as an integral treatment tool. NCIT:C15204 A therapeutic method of manipulation, methodical pressure, friction, and kneading of the body. 2019-01-19T20:36:55Z NCIT:C15276 massage massage and body work massage therapy A therapeutic method of manipulation, methodical pressure, friction, and kneading of the body. NCIT:C15276 Any alteration or treatment in an individual's diet with a planned goal, usually designed to improve the individual's overall health. 2019-01-19T20:39:14Z NCIT:C15447 diet behavioral nutritional intervention dietary intervention Any alteration or treatment in an individual's diet with a planned goal, usually designed to improve the individual's overall health. NCIT:C15447 The restriction of energy (calorie) intake below the amount required for weight maintenance. 2019-01-19T20:39:29Z LCD intake calorie restricted food intake carorie restriction in food intake low calorie diet intake primarily food‐based low‐calorie diet intake calorie restrictive diet intake The restriction of energy (calorie) intake below the amount required for weight maintenance. PMID:23748374 LCD intake Delivery of enteral nutrition via a tube placed into the stomach, duodenum, or jejunum. 2019-01-19T20:40:39Z NCIT:C93322 EN intake enteral nutrition support intake enteral tube feeding nutrition intake tube feeding nutrition intake enteral nutrition intake Delivery of enteral nutrition via a tube placed into the stomach, duodenum, or jejunum. NCIT:C93322 EN intake obsolete alcohol intake avoidance false 2019-01-19T20:54:50Z excessive alcohol avoidance 2019-01-19T20:55:05Z Some processed foods and soy contain large amounts of estrogen. estrogen-containing food avoidance 2019-01-19T20:59:49Z Some foods, particularly red meat, have high amounts of iron. excessive iron consumption avoidance 2019-01-19T21:00:36Z excessive protein consumption avoidance 2019-01-19T21:01:13Z fasting avoidance Abstinence from all or some kinds of food or drink, particularly for religious observance, medical nutrition therapy, or prior to a medical procedure. 2019-01-19T21:01:21Z NCIT:C63663 NPO fasting nil per os therapeutic fasting intermittant fasting fasting intervention Abstinence from all or some kinds of food or drink, particularly for religious observance, medical nutrition therapy, or prior to a medical procedure. PMID:16630428 PMID:27499591 https://orcid.org/0000-0002-7463-6306 NPO obsolete food consumption avoidance false obsolete meat consumption avoidance false obsolete nut consumption avoidance false obsolete seafood consumption avoidance false obsolete mussel consumption avoidance false 2019-01-19T21:05:54Z dietary iron supplementation avoidance obsolete saffron consumption avoidance false The addition of one or more elements and/or chemical compounds that are either absent or deficient in an individual's daily diet. 2019-01-19T21:07:25Z NCIT:C15425 nutritional supplementation The addition of one or more elements and/or chemical compounds that are either absent or deficient in an individual's daily diet. NCIT:C15425 A dietary supplement containing all or most of the vitamins that may not be readily available in the diet. Vitamins may be classified according to their solubility either in lipids (vitamins A, D, E, K, F) or in water (vitamins C, B-complex). Present in minute amounts in various foods, vitamins are essential to maintaining normal metabolism and biochemical functions. 2019-01-19T21:08:59Z NCIT:C1654 multivitamin supplementation A dietary supplement containing all or most of the vitamins that may not be readily available in the diet. Vitamins may be classified according to their solubility either in lipids (vitamins A, D, E, K, F) or in water (vitamins C, B-complex). Present in minute amounts in various foods, vitamins are essential to maintaining normal metabolism and biochemical functions. NCIT:C1654 Oral iron supplementation is an effective and well‐studied option to replenish iron stores. 2019-01-19T21:09:25Z oral iron supplementation iron replacement therapy iron supplementation Oral iron supplementation is an effective and well‐studied option to replenish iron stores. PMID:28328083 2019-01-19T21:09:48Z vitamin C supplementation 2019-01-19T21:09:59Z vitamin D supplementation obsolete amino acid supplementation false Treatment with antioxidants in order to protect cells against damage caused by oxygen-free radicals. 2019-01-19T21:12:19Z NCIT:C67025 antioxidant therapy Treatment with antioxidants in order to protect cells against damage caused by oxygen-free radicals. NCIT:C67025 Administration of nutritional support by means of a tube passed into the stomach. 2019-01-19T21:13:59Z NCIT:C73430 gastrogavage nutrition intake gavage nutrition intake Administration of nutritional support by means of a tube passed into the stomach. NCIT:C73430 Total parenteral nutrition formulated for intravenous administration in patients who cannot eat or cannot get enough nutrients from the foods they eat. It is a liquid mixture of proteins, carbohydrates, fats, vitamins, minerals and other nutrients. 2019-01-19T21:16:22Z NCIT:C29484 TPN intake hyperalimentation total parenteral nutrition intake Total parenteral nutrition formulated for intravenous administration in patients who cannot eat or cannot get enough nutrients from the foods they eat. It is a liquid mixture of proteins, carbohydrates, fats, vitamins, minerals and other nutrients. NCIT:C29484 TPN intake Any action taken for the purpose of improving or maintaining an individual's memory. 2019-01-19T21:26:54Z NCIT:C116526 working memory interventions memory aids memory intervention A behavioral modification or implementation of a behavior designed to prevent smoking. 2019-01-19T21:33:17Z NCIT:C16114 prevent smoking smoking prevention A behavioral modification or implementation of a behavior designed to prevent smoking. https://orcid.org/0000-0002-7463-6306 The prevention of conception or impregnation by the use of devices or drugs or surgery. 2019-01-19T21:34:14Z NCIT:C37932 birth control conception prevention contraceptive management pregnancy prevention contraceptive pregnancy prevention The prevention of conception or impregnation by the use of devices or drugs or surgery. NCIT:C37932 birth control NCIT:C37932 Immunization is the process whereby a person is made immune or resistant to an infectious disease, typically by the administration of a vaccine. 2019-01-19T21:36:12Z NCIT:C15258 OBI:1110094 immunization preventive immunization preventative immunization Immunization is the process whereby a person is made immune or resistant to an infectious disease, typically by the administration of a vaccine. WHO immunization NCIT:C15258 OBI:1110094 Active immunity refers to the process of exposing the body to an antigen to generate an adaptive immune response: the response takes days/weeks to develop but may be long lasting—even lifelong. 2019-01-20T00:31:42Z IDO:0000498 NCIT:C15416 VO:0000491 active immunization Active immunity refers to the process of exposing the body to an antigen to generate an adaptive immune response: the response takes days/weeks to develop but may be long lasting—even lifelong. PMID:18045976 Passive immunity refers to the process of providing IgG antibodies to protect against infection; it gives immediate, but short-lived protection. 2019-01-20T00:31:52Z NCIT:C15259 OBI:0001174 VO:0000492 passive immunization Passive immunity refers to the process of providing IgG antibodies to protect against infection; it gives immediate, but short-lived protection. PMID:18045976 2019-01-20T00:36:49Z disease exposure immunization The use of any device, marker, or other means for the purpose of detecting the presence of disease, usually in asymptomatic individuals. 2019-01-20T00:39:19Z NCIT:C15419 disease screening The use of any device, marker, or other means for the purpose of detecting the presence of disease, usually in asymptomatic individuals. NCIT:C15419 Testing conducted utilizing a manual or microprocessor audiometer to test for hearing loss. 2019-01-20T00:42:26Z NCIT:C38036 hearing exam procedure hearing testing procedure audiometric testing Testing conducted utilizing a manual or microprocessor audiometer to test for hearing loss. NCIT:C38036 The use of any device, marker, or other means for the purpose of detecting the presence of a tumor, usually before there are any symptoms. 2019-01-20T00:45:24Z NCIT:C15406 cancer screening The use of any device, marker, or other means for the purpose of detecting the presence of a tumor, usually before there are any symptoms. NCIT:C15406 The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder. 2019-01-20T00:46:22Z NCIT:C15709 genetic analysis genetic testing The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder. NCIT:C15709 Any test performed during pregnancy to assess fetal health and to detect for genetic abnormalities and various disorders. 2019-01-20T00:51:25Z pregnancy related screening pregnancy related screening test prenatal screening Any test performed during pregnancy to assess fetal health and to detect for genetic abnormalities and various disorders. NCIT:C92721 An examination of tissue removed from the body to assess the presence, cause, or extent of a disease. 2019-01-20T00:52:34Z NCIT:C15189 OPMI:0000274 biopsy biopsy procedure A diagnostic or therapeutic procedure in which an endoscope is inserted in a tubular organ to examine the structural architecture and/or remove abnormal tissues. 2019-01-20T01:01:22Z NCIT:C16546 endoscopic exam endoscopy endoscopic procedure A diagnostic or therapeutic procedure in which an endoscope is inserted in a tubular organ to examine the structural architecture and/or remove abnormal tissues. NCIT:C16546 endoscopy NCIT:C16546 2019-01-20T01:03:18Z endoscopy by site location specific endoscopy 2019-01-20T01:03:28Z endoscopy by type specific type endoscopy specific technique endoscopy An endoscopic technique that allows deep intubation of the small intestine while using a standard endoscope. An inflatable balloon attached to the endoscope's tip acts as a stabilizer and a second balloon that is advanced ahead of the endoscope acts as a pulling device. 2019-01-20T18:48:29Z NCIT:C64865 balloon-guided endoscopy balloon-guided endoscopic procedure An endoscopic technique that allows deep intubation of the small intestine while using a standard endoscope. An inflatable balloon attached to the endoscope's tip acts as a stabilizer and a second balloon that is advanced ahead of the endoscope acts as a pulling device. NCIT:C64865 Endoscopy that employs the use of tissue stains to increase tissue contrast, and enhance the ability to identify various tissue dysplasia and other abnormalities. 2019-01-20T18:51:12Z NCIT:C116476 chromoendoscopy Endoscopy that employs the use of tissue stains to increase tissue contrast, and enhance the ability to identify various tissue dysplasia and other abnormalities. NCIT:C116476 A low-cost, high-resolution imaging tool consisting of a 1-mm diameter fiber-optic bundle that produces subcellular imaging at 1,000x magnification and 4 micrometer resolution, allowing for minimally invasive bioimaging. 2019-01-20T19:03:17Z NCIT:C116480 HRME high-resolution microendoscopy A low-cost, high-resolution imaging tool consisting of a 1-mm diameter fiber-optic bundle that produces subcellular imaging at 1,000x magnification and 4 micrometer resolution, allowing for minimally invasive bioimaging. NCIT:C116480 HRME A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. 2019-01-20T19:19:15Z NCIT:C17007 PET scan positron emission tomography procedure A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. NCIT:C17007 PET scan NCIT:C17007 Ultrasound imaging following the administration of a microbubble contrast agent. 2019-01-21T20:17:52Z NCIT:C148281 CEUS contrast-enhanced ultrasound procedure Ultrasound imaging following the administration of a microbubble contrast agent. NCIT:C148281 CEUS A postmortem examination of the body that includes an examination of the internal organs and structures after dissection to determine the cause of death and the nature of pathological changes. 2019-01-21T20:33:46Z NCIT:C25153 autopsy autopsy procedure A postmortem examination of the body that includes an examination of the internal organs and structures after dissection to determine the cause of death and the nature of pathological changes. NCIT:C25153 A diagnostic test utilized to examine and define cellular anatomy or function. The test results are often used by a clinician to diagnose disease or disordered function. 2019-01-21T20:36:01Z diagnostic cytological test A diagnostic test utilized to examine and define cellular anatomy or function. The test results are often used by a clinician to diagnose disease or disordered function. NCIT:C49132 The collecting of secretions and superficial cells of the body of uterus, cervix, and ovaries; examined with a microscope to detect any abnormal cells. 2019-01-21T20:38:23Z Papanicolaou smear procedure cervical smear procedure pap test pap smear The collecting of secretions and superficial cells of the body of uterus, cervix, and ovaries; examined with a microscope to detect any abnormal cells. NCIT:C17348 Papanicolaou smear procedure NCIT:C17348 cervical smear procedure NCIT:C17348 pap test NCIT:C17348 Examination under a microscope of cells found in sputum (mucus and other matter brought up from the lungs by coughing). The test checks for abnormal cells, such as lung cancer cells. 2019-01-21T20:45:16Z NCIT:C16192 sputum cytology Examination under a microscope of cells found in sputum (mucus and other matter brought up from the lungs by coughing). The test checks for abnormal cells, such as lung cancer cells. NCIT:C16192 Examination of the cells in urine. 2019-01-21T20:47:27Z urine cytology Examination of the cells in urine. NCIT:C94473 Technique or procedure used for the study of the microanatomy of tissues and their cellular structure for the diagnosis or treatment of a disease. 2019-01-21T21:04:01Z NCIT:C16680 histological test histological procedure Technique or procedure used for the study of the microanatomy of tissues and their cellular structure for the diagnosis or treatment of a disease. NCIT:C16680 http://orcid.org/0000-0001-7941-2961 A laboratory procedure that involves the examination of blood, urine, other fluids, and stool for diagnostic or research purposes. 2019-01-21T21:12:21Z NCIT:C74944 clinical pathology procedure A laboratory procedure that involves the examination of blood, urine, other fluids, and stool for diagnostic or research purposes. NCIT:C74944 A procedure to determine the number of cells in a clinical sample. 2019-01-21T21:16:16Z NCIT:C48938 cell count clinical pathology cell count A procedure to determine the number of cells in a clinical sample. NCIT:C48938 http://orcid.org/0000-0001-7941-2961 A laboratory test to measure hematopoietic components and investigate hematologic disorders in a blood sample. 2019-01-21T21:22:45Z NCIT:C49286 hematology test A laboratory test to measure hematopoietic components and investigate hematologic disorders in a blood sample. NCIT:C49286 The determination of the maximum amount of oxygen that can be combined chemically with hemoglobin in a volume of blood. 2019-01-21T21:29:03Z NCIT:C96614 OXYCAP oxygen capacity measurement oxygen capacity test oxygen capacity measurement test The determination of the maximum amount of oxygen that can be combined chemically with hemoglobin in a volume of blood. NCIT:C96614 OXYCAP A measure of the volume of red blood cells expressed as a percentage of the total blood volume. Normal in males is 43-49%, in females 37-43%. 2019-01-21T21:32:32Z NCIT:C64796 EVF HCT PCV erythrocyte volume fraction packed cell volume hematocrit measurement test A measure of the volume of red blood cells expressed as a percentage of the total blood volume. Normal in males is 43-49%, in females 37-43%. NCIT:C64796 EVF HCT PCV erythrocyte volume fraction NCIT:C64796 packed cell volume NCIT:C64796 A medical recommendation to avoid a particular therapy, intervention, medication, or procedure. 2019-01-07T19:23:10Z avoid procedure avoid therapy avoid activity avoid drug avoid medication therapeutic avoidance intervention A medical recommendation to avoid a particular therapy, intervention, medication, or procedure. http://orcid.org/0000-0001-7941-2961 Administration of intravenous infusions of alpha-1 proteinase inhibitor at regular schedules is a specific therapy for individuals with alpha-1 antitrypsin deficiency (AATD) with pulmonary involvement. 2019-01-22T17:27:25Z augmentation therapy Administration of intravenous infusions of alpha-1 proteinase inhibitor at regular schedules is a specific therapy for individuals with alpha-1 antitrypsin deficiency (AATD) with pulmonary involvement. PMID:28752465 obsolete antispastic agents false A drug used in the treatment of Parkinson's disease. 2019-01-22T17:52:48Z CHEBI:48407 NCIT:C38149 antiparkinson agent treatment antiparkinson drug therapy antiparkinson drug treatment antiparkinsonian agent therapy antiparkisonian agent treatment antiparkisonian drug treatment antiparkinson agent therapy A drug used in the treatment of Parkinson's disease. CHEBI:48407 A substance used to treat or prevent parasitic infections. 2019-01-22T17:53:06Z CHEBI:35442 NCIT:C276 antiparasitic drug therapy antiparasitics therapy antiparisitics drug treatment antiparasitic agent therapy A substance used to treat or prevent parasitic infections. CHEBI:35442 An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms. 2019-01-22T17:53:16Z CHEBI:35480 NCIT_C241 Analgesics therapy analgesic therapy analgesic pharmacotherapeutic agent therapy An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms. CHEBI:35480 Antidepressants are mood-stimulating drugs used primarily in the treatment of affective disorders and related conditions. 2019-01-22T17:53:33Z CHEBI:35469 antidepressant drug therapy antidepressants treatment thymoanaleptics treatment thymoleptic agent therapy thymoleptic drug treatment therapy thymoleptics drug therapy antidepressant agent therapy Antidepressants are mood-stimulating drugs used primarily in the treatment of affective disorders and related conditions. CHEBI:35469 2019-01-22T17:54:06Z NCIT:C69308 receptor antagonist therapy 2019-01-22T17:54:15Z adrenal-modifying, hormonal agent therapy Anxiolytic drugs are agents that alleviate anxiety, tension, and anxiety disorders, promote sedation, and have a calming effect without affecting clarity of consciousness or neurologic conditions. 2019-01-22T17:54:43Z CHEBI:35474 anti-anxiety agent therapy anti-anxiety drug treatment anxiolytic agent drug treatment anxiolytics drug therapies minor tranquiliser therapy minor tranquilizer treatment minor tranquilizing agent treatment minor tranquilizing drug therapy anxiolytic agent therapy Anxiolytic drugs are agents that alleviate anxiety, tension, and anxiety disorders, promote sedation, and have a calming effect without affecting clarity of consciousness or neurologic conditions. CHEBI:35474 Substance that may reduce inflammation, stimulate elimination of uric acid, or increase production of uric acid. 2019-01-22T17:55:18Z NCIT:C29733 anti-gout agent therapy anti-gout combination medicine therapy anti-gout drug therapy anti-gout preparation therapy antigout agent therapy antigout combination medicine therapy antigout drug therapy antigout preparation therapy antigout agent therapy Substance that may reduce inflammation, stimulate elimination of uric acid, or increase production of uric acid. NCIT:C29733 An agent that promotes the excretion of urine through its effects on kidney function 2019-01-22T17:55:27Z CHEBI:35498 NCIT:C448 diuretic agent drug treatment therapy diuretic drug therapy diuretic drugs therapy diuretics therapy diuretic agent therapy An agent that promotes the excretion of urine through its effects on kidney function CHEBI:35498 Antipsychotic drugs are agents that control agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect. 2019-01-22T17:57:29Z CHEBI:35476 antipsychotic drug treatment antipsychotic therapy major tranquilizer drug treatment neuroleptic agent treatment neuroleptic therapies antipsychotic agent therapy Antipsychotic drugs are agents that control agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect. CHEBI:35476 A drug used to prevent seizures or reduce their severity. 2019-01-22T17:57:37Z CHEBI:35623 NCIT:C264 anti-convulsant therapy anti-convulsive agent therapy anticonvulsant drug therapy anticonvulsant therapy anticonvulsive agent therapy antiepileptic therapy anticonvulsant agent therapy A drug used to prevent seizures or reduce their severity. CHEBI:35623 A substance used in the prophylaxis or therapy of virus diseases. 2019-01-22T17:57:52Z CHEBI:36044 anti-viral drug therapy anti-virus drug treatment antiviral drug therapy antiviral agent therapy A substance used in the prophylaxis or therapy of virus diseases. CHEBI:36044 Any compound that has anti-inflammatory effects. 2019-01-22T17:58:04Z CHEBI:67079 anti-inflammatory agent treatment therapy anti-inflammatory drug therapy antiinflammatory agent therapy antiinflammatory drug therapy anti-inflammatory agent therapy Any compound that has anti-inflammatory effects. CHEBI:67079 Substance which produces loss of feeling or sensation. 2019-01-22T17:59:57Z CHEBI:38867 NCIT:C245 anaesthesia therapy anaesthetic therapy anaesthetics therapy anesthesia therapy anesthetic drug therapy anesthetic agent therapy Substance which produces loss of feeling or sensation. CHEBI:38867 Treatment with medications to improve cognition and function for patients with dementia. 2019-01-22T18:00:43Z antidementia drug therapy antidementia medication treatment antidementia agent therapy Treatment with medications to improve cognition and function for patients with dementia. PMID:31517030 2019-01-22T18:01:36Z therapeutic antidotes, deterrents, and toxicologic agent therapy 2019-01-22T18:01:53Z CHEBI:50919 NCIT:C267 A drug used to prevent nausea or vomiting. An antiemetic may act by a wide range of mechanisms: it might affect the medullary control centres (the vomiting centre and the chemoreceptive trigger zone) or affect the peripheral receptors. anti-emetic agent therapy anti-emetic drug therapy anti-emetics therapy antiemetic drug therapy antiemetic therapy antiemetics agent therapy A drug used to prevent nausea or vomiting. An antiemetic may act by a wide range of mechanisms: it might affect the medullary control centres (the vomiting centre and the chemoreceptive trigger zone) or affect the peripheral receptors. CHEBI:50919 Any antifungal drug used to prevent or treat fungal infections in humans or animals. 2019-01-22T18:02:00Z CHEBI:86327 anti-fungal drug therapy anti-fungal medication therapy antifungal drug therapy antifungal treatment antifungals therapy pharmaceutical fungicide therapy antifungal agent therapy Any antifungal drug used to prevent or treat fungal infections in humans or animals. CHEBI:86327 2019-01-22T18:11:18Z blood glucose regulator drug treatment blood glucose regulator therapy Drug that acts on blood and blood-forming organs and those that affect the hemostatic system. 2019-01-22T18:11:44Z CHEBI:50248 https://www.drugbank.ca/categories/DBCAT000008 blood modifier treatment therapy blood modifying agent treatment hematologic agent treatment therapy hematologic agent therapy Drug that acts on blood and blood-forming organs and those that affect the hemostatic system. CHEBI:50248 2019-01-22T18:11:58Z coagulant treatment therapy coagulant agent therapy An agent that prevents blood clotting. 2019-01-22T18:12:06Z CHEBI:50249 anticoagulant agent treatment anticoagulant drug treatment anticoagulant therapy anticoagulant agent therapy An agent that prevents blood clotting. CHEBI:50249 2019-01-22T18:12:20Z blood formation agent therapy A drug or agent which antagonizes or impairs any mechanism leading to blood platelet aggregation, whether during the phases of activation and shape change or following the dense-granule release reaction and stimulation of the prostaglandin-thromboxane system. 2019-01-22T18:12:39Z CHEBI:50427 platelet aggregation inhibitor agent treatment platelet aggregation inhibitor therapy platelet aggregation inhibitor agent therapy A drug or agent which antagonizes or impairs any mechanism leading to blood platelet aggregation, whether during the phases of activation and shape change or following the dense-granule release reaction and stimulation of the prostaglandin-thromboxane system. CHEBI:50427 A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. 2019-01-22T18:13:06Z CHEBI:35554 NCIT:C78274 agent affecting cardiovascular system therapy cardiovascular agent drug treatment cardiovascular drug therapy cardiovascular drug treatment therapy cardiovascular system agent therapy cardiovascular system drug therapy cardiovascular agent therapy A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. CHEBI:35554 Any drug that acts on an alpha-adrenergic receptor. 2019-01-22T18:14:42Z CHEBI:48539 a-adrenergic agent therapy a-adrenergic drug therapy a-adrenergic receptor agent therapy a-adrenergic receptor drug therapy alpha adrenergic drug therapy alpha adrenergic receptor agent therapy alpha adrenergic receptor drug treatment alpha adrenergics drug therapy alpha-adrenergic agent treatment alpha-adrenergic drug therapy alpha-adrenergic drug treatment therapy alpha-adrenergic modifier therapy alpha-adrenergic modifying agent therapy alpha-adrenergic receptor agent therapy alpha-adrenergic receptor drug therapy alpha-adrenergic receptor drug treatment alpha-adrenergic agent therapy Any drug that acts on an alpha-adrenergic receptor. CHEBI:48539 An agent that selectively binds to and activates alpha-adrenergic receptors. 2019-01-22T18:15:26Z CHEBI:48539 a-adrenergic agonist drug treatment a-adrenergic agonist therapy a-adrenergic receptor agonist therapy alpha adrenergic agonist agent drug treatment alpha adrenergic agonist drug therapy alpha adrenergic agonist treatment alpha adrenergic receptor agonist therapy alpha adrentergic receptor agonist agent therapy alpha-adrenergic agonist therapy alpha-adrenergic receptor agonist drug therapy alpha-adrenergic receptor agonist treatment alpha-adrenoceptor agonist agent therapy alpha-adrenoceptor agonist drug therapy alpha-adrenoceptor agonist therapy alpha-adrenergic agonist agent therapy An agent that selectively binds to and activates alpha-adrenergic receptors. CHEBI:48539 An agent that binds to but does not activate alpha-adrenergic receptors thereby blocking the actions of endogenous or exogenous alpha-adrenergic agonists. 2019-01-22T18:15:59Z CHEBI:37890 a-adrenergic antagonist agent therapy a-adrenergic antagonist therapy a-adrenergic receptor antagonist drug treatment alpha adrenergic antagonist drug therapy alpha blocker therapy alpha-adrenergic antagonist agent treatment alpha-adrenergic antagonist drug therapy alpha-adrenergic antagonist drug treatment alpha-adrenergic blockader therapy alpha-adrenergic blocker therapy alpha-adrenergic blocking agent therapy alpha-adrenergic receptor antagonist agent therapy alpha-adrenergic receptor antagonist drug therapy alpha-adrenergic receptor blockader therapy alpha-adrenergic receptor blocker therapy alpha-adrenoceptor antagonist therapy alpha-adrenergic antagonist agent therapy An agent that binds to but does not activate alpha-adrenergic receptors thereby blocking the actions of endogenous or exogenous alpha-adrenergic agonists. CHEBI:37890 A drug used for the treatment or prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres. 2019-01-22T18:17:04Z CHEBI:38070 NCIT:C47793 anti-arrhythmic agent therapy anti-arrhythmic drug treatment therapy antiarrhythmic agent therapy antiarrhythmic drug therapy antiarrhythmic drug treatment antiarrythmic agent therapy A drug used for the treatment or prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres. CHEBI:38070 Any of the drugs that act on beta-adrenergic receptors. 2019-01-22T18:17:27Z CHEBI:48540 b-adrenergic drug treatment beta adrenergic receptor agent treatment beta adrenergic receptor drug therapy beta-adrenergic agent treatment beta-adrenergic drug therapy beta-adrenergic drug treatment beta-adrenergic modifier therapy beta-adrenergic modifying agent therapy beta-adrenergic modifying drug treatment beta-adrenergics therapy beta-adrenergic agent therapy Any of the drugs that act on beta-adrenergic receptors. CHEBI:48540 An agent that binds to but does not activate beta-adrenergic receptors thereby blocking the actions of endogenous or exogenous beta-adrenergic agonists. 2019-01-22T18:17:55Z CHEBI:35530 Beta blocker therapy Beta-adrenergic blocking agent therapy b-adrenergic antagonist therapy b-adrenergic receptor antagonist therapy beta adrenergic antagonist agent treatment beta adrenergic antagonist drug treatment beta adrenergic receptor antagonist therapy beta-adrenergic antagonist agent treatment beta-adrenergic receptor antagonist agents beta-adrenergic receptor antagonist drug treatment beta-adrenergic receptor antagonist therapy beta-adrenergic receptor blockader therapy beta-adrenoceptor antagonist therapy beta-adrenergic antagonist agent therapy An agent that binds to but does not activate beta-adrenergic receptors thereby blocking the actions of endogenous or exogenous beta-adrenergic agonists. CHEBI:35530 obsolete calcium channel blocker agent therapy false An agent that reduces plasma lipids, such as cholesterol or low density lipoproteins (LDL), acting systemically or locally (intestines) to decrease fat digestion, absorption, production, and accumulation in the plasma and reducing pathogenic atherosclerosis and thrombosis. 2019-01-22T18:19:20Z NCIT:C29703 anti-lipidemic agent therapy antilipidemic agent therapy antilipidemic drug treatment therapy dyslipidemia agent therapy dyslipidemia drug treatment therapy dyslipidemic agent drug treatment dyslipidemic drug therapy dyslipidemic drugs therapy dyslipidemic agent therapy An agent that reduces plasma lipids, such as cholesterol or low density lipoproteins (LDL), acting systemically or locally (intestines) to decrease fat digestion, absorption, production, and accumulation in the plasma and reducing pathogenic atherosclerosis and thrombosis. NCIT:C29703 2019-01-22T18:19:47Z renin-angiotensin-aldosterone system inhibitor therapy A drug used to cause dilation of the blood vessels. 2019-01-22T18:20:06Z CHEBI:35620 NCIT:C29707 vasodilating agent therapy vasodilating drug treatment therapy vasodilator agent therapy vasodilator drug therapies vasodilator drug therapy vasodilator drug treatment therapy vasodilator therapies vasodilator agent therapy A drug used to cause dilation of the blood vessels. CHEBI:35620 obsolete other cardiovascular agent therapy false A drug that has principally analgesic, antipyretic and anti-inflammatory actions. Non-narcotic analgesics do not bind to opioid receptors 2019-01-22T18:22:25Z CHEBI:35481 non-narcotic analgesic agent therapy non-narcotic analgesic therapy non-opioid analgesics therapy non-opioid analgesics agent therapy A drug that has principally analgesic, antipyretic and anti-inflammatory actions. Non-narcotic analgesics do not bind to opioid receptors CHEBI:35481 A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. 2019-01-22T18:22:42Z narcotic therapy CHEBI:35482 narcotic analgesic therapy opioid analgesics opioid therapy opioid analgesics agent therapy A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. CHEBI:35482 Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block. 2019-01-22T18:24:45Z CHEBI:36333 local anaesthesia therapy local anaesthetics therapy local anesthesia therapy local anesthetics therapy epidural therapy spinal block therapy topical anesthesia therapy topical anesthetic therapy local anesthetic agent therapy Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block. CHEBI:36333 An antibacterial substance with aminoglycoside structure. 2019-01-22T18:25:15Z CHEBI:47779 aminoglycoside drug therapy aminoglycoside drug treatment aminoglycosides therapy aminoglycoside agent therapy An antibacterial substance with aminoglycoside structure. A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. 2019-01-22T18:25:44Z CHEBI:23066 cephalosporin antibacterial agent therapy cephalosporin beta-lactam therapy cephalosporin drug therapy cephalosporin drug treatment cephalosporin therapies cephalosporin treatment cephalosporins therapy cephalosporin agent therapy A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. CHEBI:23066 An antibacterial substance with penicillin structure. 2019-01-22T18:26:03Z CHEBI:17334 penicillin antibacterial therapy penicillin antibacterial treatment penicillin beta-lactam therapy penicillin drug therapy penicillin drug treatment penicillin treatment penicillins penicillin agent therapy An antibacterial substance with penicillin structure. obsolete other beta-lactams false A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity. 2019-01-22T18:26:31Z macrolides CHEBI:25105 macrolide antibacterial drug therapy macrolide antibacterial therapy macrolide drug therapy macrolide drug treatment macrolide antibacterial agent therapy A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity. CHEBI:25105 An organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton. 2019-01-22T18:26:50Z quinolones CHEBI:86324 quinolone antibacterials quinolone antibiotic agents quinolone antibiotics quinolone antibacterial agent therapy An organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton. CHEBI:86324 A class of sulfonamides whose members generally have bacteriostatic antibiotic properties. 2019-01-22T18:27:30Z sulfonamides therapy CHEBI:87228 sulfonamide antibacterial drug therapy sulfonamide antibacterial therapy sulfonamide antibiotic therapy sulfonamide drug therapy sulfonamide drug treatment sulfonamide antibacterial agent therapy A class of sulfonamides whose members generally have bacteriostatic antibiotic properties. CHEBI:87228 A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. 2019-01-22T18:28:05Z CHEBI:27902 tetracycline antibiotic therapy tetracycline drug therapy tetracycline drug treatment tetracycline therapy A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. CHEBI:27902 obsolete other antibacterial agents false 2019-01-22T18:28:49Z CHEBI:38808 calcium channel modifier drug therapy calcium channel modifying agent therapy A substance, such as agonists, antagonists, degradation or uptake inhibitors, depleters, precursors, and modulators of receptor function, used for its pharmacological actions on GABAergic systems. 2019-01-22T18:29:21Z CHEBI:51374 GABA augmenting agent therapy GABA augmenting therapy gamma-aminobutyric acid drug therapy gamma-aminobutyric acid modulating agent therapy gamma-aminobutyric acid augmenting agent therapy A substance, such as agonists, antagonists, degradation or uptake inhibitors, depleters, precursors, and modulators of receptor function, used for its pharmacological actions on GABAergic systems. CHEBI:51374 2019-01-22T18:29:56Z glutamate reducing agent therapy An agent that inhibits sodium influx through cell membranes. 2019-01-22T18:30:15Z CHEBI:38633 Na+ channel blocker therapy Na+ channel inhibitor drug therapy sodium channel blocker drug therapy sodium channel blocker therapy sodium channel inhibitor drug therapy sodium channel inhibitor therapy An agent that inhibits sodium influx through cell membranes. CHEBI:38633 obsolete anticonvulsants, other false They are a group of drugs that block the normal breakdown of acetylcholine (ACh) into acetate and choline and thereby increase both the levels and duration of actions of acetylcholine found in the central and peripheral nervous system. 2019-01-22T18:32:56Z CHEBI:37733 cholinesterase inhibitor drug treatment cholinesterase inhibitor medication therapy AChE inhibitor therapy acetylcholinesterase inhibitor therapy Neurogenerative diseases such as Alzheimer disease, Parkinson disease, and Lewy body dementia are indications for cholinesterase inhibitor therapy. cholinesterase inhibitor therapy They are a group of drugs that block the normal breakdown of acetylcholine (ACh) into acetate and choline and thereby increase both the levels and duration of actions of acetylcholine found in the central and peripheral nervous system. PMID:31335056 AChE inhibitor therapy Neurogenerative diseases such as Alzheimer disease, Parkinson disease, and Lewy body dementia are indications for cholinesterase inhibitor therapy. PMID:31335056 2019-01-22T18:33:33Z glutamate modulator therapy glutamate pathway modifying drug treatment glutamatergic drug therapy glutamatergic drug treatment glutamatergic pathway modifying agent therapy obsolete antidementia agents, other false Any substance that inhibits monoamine oxidase (MAO), an enzyme that catalyzes the oxidative deamination of monoamines and plays a role in the inactivation of neurotransmitters. 2019-01-22T18:36:08Z CHEBI:38623 NCIT:C667 MAO drug therapy MAO drug treatment MAO inhibitor therapy MAOI therapy inhibitors of MAO therapy inhibitors of monoamine oxidase therapy A type of drug used to treat depression. It stops the breakdown of certain chemicals in the brain that help improve a person's mood. A monoamine oxidase inhibitor is a type of antidepressant. monoamine oxidase inhibitor agent therapy Any substance that inhibits monoamine oxidase (MAO), an enzyme that catalyzes the oxidative deamination of monoamines and plays a role in the inactivation of neurotransmitters. NCIT:C667 MAO inhibitor therapy MAOI therapy A type of drug used to treat depression. It stops the breakdown of certain chemicals in the brain that help improve a person's mood. A monoamine oxidase inhibitor is a type of antidepressant. NCIT:C667 Treatment with a medication that increases the extracellular level of the neurotransmitter serotonin (5-HT) and norepinephrine by inhibiting their reuptake into the presynaptic cell. 2019-01-22T18:40:17Z OMIT:0001323 SNRI agent therapy SNRI drug therapy SNRI drug treatment serotonin and noradrenaline reuptake inhibitor agent therapy serotonin and noradrenaline reuptake inhibitor drug therapy serotonin and noradrenaline reuptake inhibitor drug treatment serotonin and norepinephrine reuptake inhibitor therapy serotonin-noradrenaline reuptake inhibitor agent therapy serotonin-noradrenaline reuptake inhibitor drug treatment serotonin-norepinephrine reuptake inhibitor drug treatment serotonin-norepinephrine reuptake inhibitor agent therapy Mood-stimulating agents which contain a tricyclic structure and are used primarily in the treatment of affective disorders and related conditions. This group of agents appear to act through brain catecholamine systems. 2019-01-22T18:41:18Z NCIT:C94727 tricyclic antidepressant drug therapy tricyclic antidepressant drug treatment tricyclic antidepressant agent therapy Mood-stimulating agents which contain a tricyclic structure and are used primarily in the treatment of affective disorders and related conditions. This group of agents appear to act through brain catecholamine systems. NCIT:C94727 obsolete antidepressants, other false Treatment with a therapeutic substance used to counteract the toxic action(s) of a specified xenobiotic. 2019-01-22T18:41:49Z CHEBI:50247 antidote drug therapy antidote agent therapy Treatment with a therapeutic substance used to counteract the toxic action(s) of a specified xenobiotic. PMID:9079217 Medication given to prevent or deter a patient from using a substance. 2019-01-22T18:42:02Z abuse deterrent drug treatment abuse deterrent agent therapy 2019-01-22T18:42:18Z toxicologic drug therapy toxicologic agent therapy Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. 2019-01-22T18:44:08Z CHEBI:24261 glucocorticoid therapy glucocorticoid agent therapy Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. CHEBI:24261 An anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins. 2019-01-22T18:44:26Z CHEBI:35475 NSAID therapy NSAIDs therapy non-steroidal anti-inflammatory drug therapy nonsteroidal anti-inflammatory agent therapy An anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins. CHEBI:35475 NSAID therapy NSAIDs therapy Treatment with medications to alleviate symptoms and occurance of migraine headaches. 2019-01-22T18:45:01Z anti migraine drug therapy anti-migraine drug therapy anti-migraine medication therapy migraine headache therapy migraine medication treatment migraine treatment standard migraine therapies treatment of migraine antimigraine agent therapy Treatment with medications to alleviate symptoms and occurance of migraine headaches. http://orcid.org/0000-0001-7941-2961 Use of medication to treat migraine headache symptoms acutely. 2019-01-22T18:45:12Z abortive anti migraine medication therapy abortive anti-migraine drug therapy abortive migraine headache treatment abortive migraine medication therapy abortive migraine treatment abortive therapy for migraine headache abortive treatment of migraine standard migraine abortive therapies symptomatic treatment of migraine abortive antimigraine agent therapy Use of medication to treat migraine headache symptoms acutely. http://orcid.org/0000-0001-7941-2961 Use of medication to decrease the occurence of migraine headaches. 2019-01-22T18:45:30Z prophylactic migraine headache treatment prophylactic migraine therapy prophylactic migraine treatment prophylactic treament of migraine headache prophylactic treatment of migraine prophylactic antimigraine agent therapy Use of medication to decrease the occurence of migraine headaches. http://orcid.org/0000-0001-7941-2961 2019-01-22T18:47:33Z antimyasthenic agent therapy 2019-01-22T18:47:49Z parasympathomimetic therapy A drug used to treat or prevent infections caused by Mycobacteria, a genus of actinobacteria. Aerobic and nonmotile, members of the genus include the pathogens responsible for causing tuberculosis and leprosy. 2019-01-22T18:48:12Z CHEBI:64912 antimycobacterial drug therapy antimycobacterial drug treatment antimycobacterials therapy antimycobacterium therapy antimycobacterial agent therapy A drug used to treat or prevent infections caused by Mycobacteria, a genus of actinobacteria. Aerobic and nonmotile, members of the genus include the pathogens responsible for causing tuberculosis and leprosy. CHEBI:64912 A substance that kills or slows the growth of Mycobacterium tuberculosis and is used in the treatment of tuberculosis. 2019-01-22T18:49:27Z CHEBI:33231 antitubercular drug therapy antitubercular drug treatment antituberculosis agent therapy tuberculostatic agent therapy antitubercular agent therapy A substance that kills or slows the growth of Mycobacterium tuberculosis and is used in the treatment of tuberculosis. CHEBI:33231 A substance that suppresses Mycobacterium leprae, ameliorates the clinical manifestations of leprosy, and/or reduces the incidence and severity of leprous reactions. 2019-01-22T18:49:45Z CHEBI:35816 leprostatic drug therapy leprostatic drug treatment leprostatic agent therapy A substance that suppresses Mycobacterium leprae, ameliorates the clinical manifestations of leprosy, and/or reduces the incidence and severity of leprous reactions. CHEBI:35816 An antineoplastic agent that replaces hydrogen atom(s) in nucleophilic moieties with alky radical(s), hindering proper function. Alkylating agents exhibit cytotoxic effects through the alkylation of DNA, resulting in strand cross-linking, ultimately inhibiting DNA replication and cancer cell growth. 2019-01-22T18:50:33Z CHEBI:22333 NCIT:C1590 NCIT:C223 alkylating agent therapy An antineoplastic agent that replaces hydrogen atom(s) in nucleophilic moieties with alky radical(s), hindering proper function. Alkylating agents exhibit cytotoxic effects through the alkylation of DNA, resulting in strand cross-linking, ultimately inhibiting DNA replication and cancer cell growth. NCIT:C1590 An agent or endogenous substance that inhibits the formation of capillaries from existing blood vessels. In cancer therapy, angiogenesis inhibitors preferentially target the new blood vessels that tumors require for oxygen and nutrition, thereby inhibiting the growth and spread of these tumors. 2019-01-22T18:50:46Z CHEBI:48422 NCIT:C1742 angiogenesis antagonist therapy angiogenesis blocker therapy angiogenesis inhibitor therapy anti-angiogenic agent therapy antiangiogenesis agent therapy antiangiogenic agent drug treatment angiostatic agent therapy antiangiogenic agent therapy An agent or endogenous substance that inhibits the formation of capillaries from existing blood vessels. In cancer therapy, angiogenesis inhibitors preferentially target the new blood vessels that tumors require for oxygen and nutrition, thereby inhibiting the growth and spread of these tumors. NCIT:C1742 A drug which acts to reduce estrogenic activity in the body, either by reducing the amount of estrogen or by reducing the activity of whatever estrogen is present. 2019-01-22T18:51:20Z CHEBI:50751 anti-oestrogenic agent therapy anti-oestrogenic drug therapy antiestrogen agent drug therapy antiestrogen drug therapy antiestrogen modifier therapy antiestrogenic drug therapy antioestrogenic agent therapy antiestrogen agent therapy A drug which acts to reduce estrogenic activity in the body, either by reducing the amount of estrogen or by reducing the activity of whatever estrogen is present. CHEBI:50751 2019-01-22T18:51:33Z antimetabolite agent drug treatment antimetabolites therapy antimetabolite agent therapy 2019-01-22T18:54:45Z aromatase inhibitor drug therapy aromatase inhibitor drug treatment aromatase inhibitor agent therapy 2019-01-22T18:55:15Z antineoplastic molecular target inhibitor drug treatment antineoplastic molecular target inhibitor agent therapy 2019-01-22T18:55:45Z antineoplastic monoclonal antibodies therapy antineoplastic monoclonal antibody drug treatment antineoplastic monoclonal antibody agent therapy 2019-01-22T18:56:30Z retinoid drug therapy retinoid drug treatment retinoid agent therapy Substance intended to kill parasitic worms (helminths). 2019-01-22T18:57:26Z CHEBI:35443 anthelminitic agent drug therapy anthelmintic drug therapy anthelmintic drug treatment antihelminthics vermifuge therapy vermicide therapy anthelmintic agent therapy Substance intended to kill parasitic worms (helminths). CHEBI:35443 Any antimicrobial drug which is used to treat or prevent protozoal infections. 2019-01-22T18:57:54Z CHEBI:35820 antiprotozoal drug therapy antiprotozoal drug treatment antiprotozoals therapy protozoan drug treatment antiprotozoal agent therapy Any antimicrobial drug which is used to treat or prevent protozoal infections. CHEBI:35820 An agent used to as a treament of ectoparasitic infestations. 2019-01-22T18:58:53Z CHEBI:38956 ectoparasiticide therapy ectoparasiticidic drug therapy ectoparasiticidic drug treatment ectoparasiticidic drugs treatment ectoparasiticidic agent therapy An agent used to as a treament of ectoparasitic infestations. http://orcid.org/0000-0001-7941-2961 An antiviral drug used for treatment of cytomegalovirus infection. 2019-01-22T18:59:18Z Anti-CMV agent therapy anti-cmv drug therapy anti-cmv therapy anti-cytomegalovirus drug therapy anti-cytomegalovirus drug treatment antiviral treatment of cytomegalovirus therapy cytomegalovirus drug treatment therapy anti-cytomegalovirus agent therapy An antiviral drug used for treatment of cytomegalovirus infection. PMID:21827432 Antipsychotic drugs which can have different modes of action but which tend to be less likely than first generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements. 2019-01-22T19:00:47Z CHEBI:65191 atypical antipsychotic agent treatment atypical antipsychotic drug therapies atypical antipsychotic drug treatment atypical antipsychotic therapies second generation antipsychotic agent therapy second generation antipsychotic drug treatment second generation antipsychotic therapy atypical antipsychotic agent therapy Antipsychotic drugs which can have different modes of action but which tend to be less likely than first generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements. CHEBI:65191 Antipsychotic drugs which can have different modes of action but which tend to be more likely than second generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements; such body movements can become permanent even after treatment has ceased. 2019-01-22T19:01:06Z CHEBI:65190 conventional antipsychotic drug treatment conventional antipsychotic therapies first generation antipsychotic agent treatment first generation antipsychotic drug treatment first generation antipsychotic therapy typical antipsychotic agent therapy typical antipsychotic drug treatment typical antipsychotic therapy conventional antipsychotic agent therapy Antipsychotic drugs which can have different modes of action but which tend to be more likely than second generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements; such body movements can become permanent even after treatment has ceased. CHEBI:65190 2019-01-22T19:02:05Z anti-spasticity agent therapy antispastic agent therapy antispastic drug treatment antispasticity agent drug treatment antispasticity agent therapy 2019-01-22T20:15:16Z antihepatitis drug therapy antihepatitis drug treatment antihepatitis agent therapy 2019-01-22T20:15:33Z antiherpetic agent drug therapy antiherpetic agent drug treatment antiherpetic agent therapy An antiviral agent that destroys or inhibits the replication of the human immunodeficiency virus. 2019-01-22T20:16:07Z CHEBI:64946 NCIT:C1660 anti-HIV agent therapy anti-HIV drug treatment anti-human immunodeficiency virus agent therapy An antiviral agent that destroys or inhibits the replication of the human immunodeficiency virus. CHEBI:64946 A drug which interferes with the binding, fusion and entry of an HIV virion to a human cell. By blocking this step in HIV's replication cycle, such agents slow the progression from HIV infection to AIDS. 2019-01-22T20:18:25Z CHEBI:59886 anti-HIV fusion inhibitor drug therapy anti-HIV fusion inhibitor drug treatment anti-HIV fusion inhibitor therapy A drug which interferes with the binding, fusion and entry of an HIV virion to a human cell. By blocking this step in HIV's replication cycle, such agents slow the progression from HIV infection to AIDS. CHEBI:59886 2019-01-22T20:18:58Z anti-HIV non-nucleoside reverse transcriptase inhibitor drug therapy anti-HIV non-nucleoside reverse transcriptase inhibitor drug treatment anti-HIV non-nucleoside reverse transcriptase inhibitor therapy 2019-01-22T20:20:58Z anti-HIV nucleoside and nucleotide reverse transcriptase inhibitor drug therapy anti-HIV nucleoside and nucleotide reverse transcriptase inhibitor drug treatment anti-HIV nucleoside and nucleotide reverse transcriptase inhibitor therapy 2019-01-22T20:21:25Z anti-HIV protease inhibitor drug therapy anti-HIV protease inhibitor drug treatment anti-HIV protease inhibitor therapy 2019-01-22T20:21:48Z anti-influenza drug therapy anti-influenza drug treatment flu shot therapy anti-influenza agent therapy obsolete anxiolytics, other false 2019-01-22T20:32:25Z antidepressant anxiolytics Antimanic drugs are agents used to treat bipolar disorders or mania associated with other affective disorders. 2019-01-22T20:33:05Z CHEBI:35477 antimanic agent drug treatment antimanic agent treatment therapy antimanic drug therapies antimanic drug therapy antimanics bipolar agent drug therapy bipolar agent drug treatment bipolar disorder agent therapy antimanic agent therapy Antimanic drugs are agents used to treat bipolar disorders or mania associated with other affective disorders. CHEBI:35477 2019-01-22T20:33:31Z anti-diabetic therapy antidiabetic agent drug treatment antidiabetic therapy antidiabetic agent therapy 2019-01-22T20:33:43Z glycemic agent drug therapy glycemic regulation agent therapy glycemic regulation drug treatment glycemic regulator agent therapy glycemic agent therapy 2019-01-22T20:33:51Z insulin drug treatment insulin therapy A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. 2019-01-22T20:34:31Z CHEBI:35470 CNS agent therapy CNS drug therapy central nervous system drug therapy central nervous system agent therapy A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. CHEBI:35470 CNS agent therapy CNS drug therapy Amines that constitute a class of central nervous system stimulants based on the structure of the parent amphetamine 1-phenylpropan-2-amine. 2019-01-22T20:35:07Z CHEBI:35338 NCIT:C62006 amphetamine drug intake amphetamine drug therapy amphetamines therapy amphetamine agent therapy Amines that constitute a class of central nervous system stimulants based on the structure of the parent amphetamine 1-phenylpropan-2-amine. CHEBI:35338 Use of non-stimulant (non-amphetamine) medication for treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-01-22T20:35:24Z non-amphetamine ADHD agent therapy non-amphetamine ADHD drug therapy non-stimulant ADHD treatment non-stimulant Attention Deficient Hyperactivity Disorder agent therapy non-stimulant ADHD agent therapy Use of non-stimulant (non-amphetamine) medication for treatment of Attention Deficit Hyperactivity Disorder (ADHD). http://orcid.org/0000-0001-7941-2961 obsolete non-amphetamines, other false 2019-01-22T20:35:53Z dental and oral agent therapy A drug used to treat or prevent skin disorders or for the routine care of skin. 2019-01-22T20:36:09Z CHEBI:50177 dermatologic agent therapy dermatologic drug therapy dermatologic drug treatment dermatological agent therapy A drug used to treat or prevent skin disorders or for the routine care of skin. CHEBI:50177 2019-01-22T20:36:28Z enzyme therapies enzyme therapy NCIT:C71592 enzyme drug therapy enzyme replacement and modifier drug treatment enzyme replacement and modifying agent therapy enzyme replacement and modifying drug treatment enzyme replacements and modifier treatment therapy enzyme modifier agent therapy enzyme modifying agent therapy enzyme modifying drug treatment enzyme replacement agent treatment enzyme replacement therapies enzyme replacement therapy enzyme replacements enzyme replacements and modifier agent therapy A drug used for its effects on the gastrointestinal system, e.g. controlling gastric acidity, regulating gastrointestinal motility and water flow, and improving digestion. 2019-01-22T20:36:38Z CHEBI:55324 gastrointestinal agent treatment gastrointestinal drug treatment gastrointestinal drug treatment therapy gastrointestinal agent therapy A drug used for its effects on the gastrointestinal system, e.g. controlling gastric acidity, regulating gastrointestinal motility and water flow, and improving digestion. CHEBI:55324 2019-01-22T20:37:00Z gastrointestinal anti-spasmodic agent therapy gastrointestinal antispasmodic agent therapy gastrointestinal antispasmodic drug treatment gastrointestinal antispasmodic treatment therapy gastrointestinal antispasmodics agent therapy H2-receptor antagonists are the drugs that selectively bind to but do not activate histamine H2 receptors, thereby blocking the actions of endogenous histamine. 2019-01-22T20:37:14Z CHEBI:37961 H2 blocker treatment therapy H2 blocking agent treatment therapy H2 receptor antagonist treatment therapy H2 receptor blockader treatment H2-receptor blocker therapy Histamine2 antagonist therapy histamine H2 receptor antagonist therapy histamine H2 receptor antagonist treatment histamine2 blocking agent therapy H2-receptor antagonist agent therapy H2-receptor antagonists are the drugs that selectively bind to but do not activate histamine H2 receptors, thereby blocking the actions of endogenous histamine. CHEBI:37961 2019-01-22T20:37:54Z irritable bowel syndrome agent therapy 2019-01-22T20:38:16Z gastrointestinal protectant drug treatment gastrointestinal protectant treatment therapy gastrointestinal protectant agent therapy Any one of the substituted benzimidazole compounds with anti-ulcer activity. A proton pump inhibitor is orally administered in the neutrally charged, inactive form and, upon entering the acidic environment of the parietal cell, gets protonated and converted into its active form. The active form will covalently and irreversibly bind to the proton pump, the H+/K+-ATPase, located on the surface of parietal cells. This leads to an inhibition of the transport of hydrogen ions, in exchange for potassium ions, into the gastric lumen and results in an inhibition of gastric acid secretion. 2019-01-22T20:38:35Z NCIT:C29723 PPI agent therapy PPI drug therapy PPI treatment therapy proton pump inhibitor drug treatment proton pump inhibitor treatment therapy proton pump inhibitor agent therapy Any one of the substituted benzimidazole compounds with anti-ulcer activity. A proton pump inhibitor is orally administered in the neutrally charged, inactive form and, upon entering the acidic environment of the parietal cell, gets protonated and converted into its active form. The active form will covalently and irreversibly bind to the proton pump, the H+/K+-ATPase, located on the surface of parietal cells. This leads to an inhibition of the transport of hydrogen ions, in exchange for potassium ions, into the gastric lumen and results in an inhibition of gastric acid secretion. NCIT:C29723 PPI agent therapy PPI drug therapy PPI treatment therapy obsolete Gastrointestinal agents, other true 2019-01-22T20:39:18Z genitourinary agent therapy 2019-01-22T20:39:46Z urinary antispasmodic agent therapy 2019-01-22T20:40:09Z benign prostate hypertrophy agent therapy 2019-01-22T20:40:24Z phosphate binders agent therapy obsolete genitourinary agents, other false 2019-01-22T20:42:45Z Glucocorticoids/ Mineralocorticoids 2019-01-22T20:44:06Z pituitary-modifying, hormonal agent therapy 2019-01-22T20:45:21Z prostaglandin-modifying, hormonal agent therapy 2019-01-22T20:46:02Z sex hormone modifying drug treatment sex hormone modifying agent therapy Any agent that can alter hormone levels or modulate hormone effects. 2019-01-22T20:49:54Z NCIT:C147908 hormone modifiers hormone modifying agent hormone modifying drug hormone modifying drugs hormone therapies hormone therapy hormone therapy agents hormone therapy drugs hormone modifying therapy Any agent that can alter hormone levels or modulate hormone effects. NCIT:C147908 2019-01-22T20:51:04Z thyroid-modifying hormonal agent therapy 2019-01-22T20:51:34Z anabolic steroid modifying drug treatment anabolic steroid modifying agent therapy 2019-01-22T20:51:44Z androgen modifying agent therapy 2019-01-22T20:52:07Z estrogen modifying agent therapy 2019-01-22T20:52:15Z progestin modifying drug treatment progestin modifying agent therapy 2019-01-22T20:52:46Z selective-estrogen receptor modifying agent therapy 2019-01-22T20:53:28Z parathyroid-suppressant hormonal agent therapy 2019-01-22T20:54:46Z androgen stimulant agent therapy 2019-01-22T20:55:10Z androgen suppressant agent therapy 2019-01-22T20:59:15Z thyroid-stimulating hormonal agent therapy 2019-01-22T20:59:33Z anti-thyroid drug treatment antithyroid agent therapy Any substance that induces, enhances, restores or suppresses the host's immune system, or an agent that utilizes or is derived from a component of the immune system. 2019-01-22T21:00:01Z CHEBI:50846 NCIT:C308 immune factor therapy immune mediator treatment therapy immune modulator therapy immune regulator therapy immunological agent treatment therapy immunomodulating agent treatment therapy immunomodulator treatment therapy immunomodulatory agent treatment therapy immunotherapeutic agent treatment therapy immunotherapy agent immunotherapy treatment immunological agent therapy Any substance that induces, enhances, restores or suppresses the host's immune system, or an agent that utilizes or is derived from a component of the immune system. NCIT:C308 A substance that augments, stimulates, activates, potentiates, or modulates the immune response at either the cellular or humoral level. A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity. 2019-01-22T21:00:13Z CHEBI:50847 immune stimulant agent therapy immunoactivator treatment therapy immunoadjuvant treatment therapy immunologic adjuvant treatment therapy immunological adjuvant treatment therapy immunopotentiator treatment therapy immunostimulant treatment therapy immune stimulant agent therapy A substance that augments, stimulates, activates, potentiates, or modulates the immune response at either the cellular or humoral level. A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity. CHEBI:50847 An agent that suppresses immune function by one of several mechanisms of action. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response. 2019-01-22T21:00:25Z CHEBI:35705 NCIT:C574 immune suppressant agent treatment immunosuppressant agent therapy immunosuppressant treatment therapy immunosuppressive agent treatment therapy immunosuppressor agent therapy immune suppressant agent therapy An agent that suppresses immune function by one of several mechanisms of action. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response. CHEBI:35705 2019-01-22T21:00:40Z passive immunizing agent therapy The drug treatment of inflammatory bowel disease (IBD), which may include the use of anti-inflammatory agents and agents that reduce the symptoms associated with IBD. 2019-01-22T21:01:33Z PMID:21857074 anti-IBD drug treatment therapy anti-inflammatory bowel disease drug treatment anti-inflammatory bowel disease therapy inflammatory bowel disease agent therapy The drug treatment of inflammatory bowel disease (IBD), which may include the use of anti-inflammatory agents and agents that reduce the symptoms associated with IBD. PMID:21857074 The salts or esters of salicylic acids, or salicylate esters of an organic acid. Some of these have analgesic, antipyretic, and anti-inflammatory activities by inhibiting prostaglandin synthesis. 2019-01-22T21:02:35Z CHEBI:30762 https://www.drugbank.ca/categories/DBCAT000579 salicylate agent therapy The salts or esters of salicylic acids, or salicylate esters of an organic acid. Some of these have analgesic, antipyretic, and anti-inflammatory activities by inhibiting prostaglandin synthesis. https://www.drugbank.ca/categories/DBCAT000579 2019-01-22T21:04:21Z metabolic bone disease drug treatment metabolic bone disease agent therapy Any compound used for the treatment of eye conditions or eye diseases. 2019-01-22T21:04:40Z CHEBI:66981 ophthalmic agent therapy ophthalmic drug treatment ophthalmics drug treatment ophthalmological agent treatment ophthalmologicals therapy ophthalmology agent therapy ophthalmology agent treatment therapy ophthalmology drug therapy ophthalmic agent therapy Any compound used for the treatment of eye conditions or eye diseases. CHEBI:66981 2019-01-22T21:04:55Z ophthalmic anti-allergy agent therapy 2019-01-22T21:05:20Z ophthalmic antiglaucoma agent therapy 2019-01-22T21:05:47Z ophthalmic anti-inflammatory agent therapy 2019-01-22T21:06:19Z ophthalmic prostaglandin and prostamide agent therapy obsolete ophthalmic agents, other false 2019-01-22T21:08:34Z otic agent therapy An agent that exerts a physiologic effect on any anatomic entity that is part of the respiratory tract and airways. 2019-01-22T21:08:56Z NCIT:C78273 agent affecting respiratory system treatment respiratory tract agent treatment respiratory tract drug treatment therapy respiratory tract agent therapy An agent that exerts a physiologic effect on any anatomic entity that is part of the respiratory tract and airways. NCIT:C78273 Histamine antagonists are the drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. 2019-01-22T21:09:06Z CHEBI:37956 antihistamine drug treatment antihistimine drug therapy histamine antagonist therapy histamine receptor blocker drug treatment histamine receptor blocker therapy antihistamine agent therapy Histamine antagonists are the drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. CHEBI:37956 2019-01-22T21:09:38Z inhaled corticosteroid drug treatment inhaled corticosteroid agent therapy 2019-01-22T21:09:53Z antileukotriene drug treatment antileukotriene agent therapy An agent that causes an increase in the expansion of a bronchus or bronchial tubes. 2019-01-22T21:10:11Z CHEBI:35523 NCIT:C319 bronchodilator agent treatment bronchodilator drug treatment broncholytic agent therapy bronchodilator agent therapy An agent that causes an increase in the expansion of a bronchus or bronchial tubes. CHEBI:35523 2019-01-22T21:10:37Z anticholinergic bronchodilator drug treatment anticholinergic bronchodilator agent therapy 2019-01-22T21:11:08Z phosphodiesterase inhibitor bronchodilator drug treatment phosphodiesterase inhibitor bronchodilator agent therapy 2019-01-22T21:11:37Z sympathomimetic bronchodilator drug therapy sympathomimetic bronchodilator agent therapy 2019-01-22T21:12:02Z NCIT:C29714 mast cell stabiliser agent therapy mast cell stabiliser drug treatment mast cell stabilizer drug treatment mast cell stabilizer agent therapy 2019-01-22T21:12:15Z pulmonary antihypertensive drug treatment pulmonary antihypertensive agent therapy obsolete respiratory tract agents, other false Treatment with a central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. 2019-01-22T21:14:36Z CHEBI:35717 NCIT:C29756 hypnotic agent therapy hypnotic drug therapy hypnotics agent therapy sedative agent drug therapy sedative agent drug treatment sedative and hypnotic drug treatment sedative drug therapy sedative drug treatment sedative treatment therapy sedative-hypnotic drug treatment sedatives and hypnotic drug therapy sedatives/hypnotic drug treatment sedatives and hypnotic agent therapy Treatment with a central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. CHEBI:35717 A drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis. 2019-01-22T21:14:48Z CHEBI:51371 NCIT:C29696 muscle relaxant agent therapy skeletal muscle relaxant drug treatment skeletal muscle relaxant agent therapy A drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis. CHEBI:51371 A substance used in the prophylaxis or therapy of infectious diseases. 2019-04-10T19:56:29Z CHEBI:35441 anti-infective drug therapy anti-infectives antiinfective agents antiinfective drug anti-infectives agent therapy A substance used in the prophylaxis or therapy of infectious diseases. CHEBI:35441 Removal of tissue from the head. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 head biopsy biopsy of head Removal of tissue from the abdomen. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 abdomen biopsy biopsy of abdomen Removal of tissue from the adipose tissue. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 adipose tissue biopsy biopsy of adipose tissue Removal of tissue from the adrenal cortex. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 adrenal cortex biopsy biopsy of adrenal cortex Removal of tissue from the adrenal gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 adrenal gland biopsy biopsy of adrenal gland Removal of tissue from the anal canal. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 anal canal biopsy biopsy of anal canal Removal of tissue from the anus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 anus biopsy biopsy of anus Removal of tissue from the aorta. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 aorta biopsy biopsy of aorta Removal of tissue from the body of uterus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 body of uterus biopsy biopsy of body of uterus Removal of tissue from the bone element. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 bone element biopsy biopsy of bone element Removal of tissue from the bone marrow. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 bone marrow biopsy biopsy of bone marrow Removal of tissue from the bone tissue. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 bone tissue biopsy biopsy of bone tissue Removal of tissue from the brain. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 brain biopsy biopsy of brain Removal of tissue from the brainstem. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 brainstem biopsy biopsy of brainstem Removal of tissue from the breast. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 breast biopsy biopsy of breast Removal of tissue from the bronchus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 bronchus biopsy biopsy of bronchus Removal of tissue from the caecum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 caecum biopsy biopsy of caecum Removal of tissue from the cardiac ventricle. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 cardiac ventricle biopsy biopsy of cardiac ventricle Removal of tissue from the cerebellum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 cerebellum biopsy biopsy of cerebellum Removal of tissue from the cerebral cortex. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 cerebral cortex biopsy biopsy of cerebral cortex Removal of tissue from the chest wall. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 chest wall biopsy biopsy of chest wall Removal of tissue from the chordate pharynx. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 chordate pharynx biopsy biopsy of chordate pharynx Removal of tissue from the choroid plexus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 choroid plexus biopsy biopsy of choroid plexus Removal of tissue from the cochlea. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 cochlea biopsy biopsy of cochlea Removal of tissue from the colon. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 colon biopsy biopsy of colon Removal of tissue from the colorectum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 colorectum biopsy biopsy of colorectum Removal of tissue from the dermis. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 dermis biopsy biopsy of dermis Removal of tissue from the diaphragm. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 diaphragm biopsy biopsy of diaphragm Removal of tissue from the dorsal plus ventral thalamus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 dorsal plus ventral thalamus biopsy biopsy of dorsal plus ventral thalamus Removal of tissue from the duodenum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 duodenum biopsy biopsy of duodenum Removal of tissue from the endocardium. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 endocardium biopsy biopsy of endocardium Removal of tissue from the endocrine pancreas. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 endocrine pancreas biopsy biopsy of endocrine pancreas Removal of tissue from the endometrium. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 endometrium biopsy biopsy of endometrium Removal of tissue from the esophagus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 esophagus biopsy biopsy of esophagus Removal of tissue from the eye. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 eye biopsy biopsy of eye Removal of tissue from the fallopian tube. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 fallopian tube biopsy biopsy of fallopian tube Removal of tissue from the frontal lobe. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 frontal lobe biopsy biopsy of frontal lobe Removal of tissue from the gall bladder. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 gall bladder biopsy biopsy of gall bladder Removal of tissue from the genitourinary system. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 genitourinary system biopsy biopsy of genitourinary system Removal of tissue from the gonad. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 gonad biopsy biopsy of gonad Removal of tissue from the heart. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 heart biopsy biopsy of heart Removal of tissue from the hypopharynx. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 hypopharynx biopsy biopsy of hypopharynx Removal of tissue from the hypothalamus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 hypothalamus biopsy biopsy of hypothalamus Removal of tissue from the intestine. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 intestine biopsy biopsy of intestine Removal of tissue from the jaw skeleton. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 jaw skeleton biopsy biopsy of jaw skeleton Removal of tissue from the lacrimal apparatus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lacrimal apparatus biopsy biopsy of lacrimal apparatus Removal of tissue from the large intestine. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 large intestine biopsy biopsy of large intestine Removal of tissue from the larynx. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2962 larynx biopsy biopsy of larynx Removal of tissue from the limb. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2963 limb biopsy biopsy of limb Removal of tissue from the lip. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2964 lip biopsy biopsy of lip Removal of tissue from the liver. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2965 liver biopsy biopsy of liver Removal of tissue from the lower respiratory tract. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2966 lower respiratory tract biopsy biopsy of lower respiratory tract Removal of tissue from the lower urinary tract. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2967 lower urinary tract biopsy biopsy of lower urinary tract Removal of tissue from the lumbar region of vertebral column. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2968 lumbar region of vertebral column biopsy biopsy of lumbar region of vertebral column Removal of tissue from the lung. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2969 lung biopsy biopsy of lung Removal of tissue from the lymph node. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2970 lymph node biopsy biopsy of lymph node Removal of tissue from the lymphatic part of lymphoid system. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2971 lymphatic part of lymphoid system biopsy biopsy of lymphatic part of lymphoid system Removal of tissue from the mammalian vulva. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2972 mammalian vulva biopsy vulva biopsy Removal of tissue from the medulla oblongata. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2973 medulla oblongata biopsy biopsy of medulla oblongata Removal of tissue from the mouth. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2974 mouth biopsy biopsy of mouth Removal of tissue from the muscle organ. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2975 muscle organ biopsy muscle biopsy Removal of tissue from the muscle tissue. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2976 muscle tissue biopsy biopsy of muscle tissue Removal of tissue from the nasolacrimal duct. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2977 nasolacrimal duct biopsy biopsy of nasolacrimal duct Removal of tissue from the nasopharynx. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2978 nasopharynx biopsy biopsy of nasopharynx Removal of tissue from the neck. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2979 neck biopsy biopsy of neck Removal of tissue from the ovary. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2980 ovary biopsy biopsy of ovary Removal of tissue from the pancreas. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2981 pancreas biopsy biopsy of pancreas Removal of tissue from the penis. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2982 penis biopsy biopsy of penis Removal of tissue from the perianal skin. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2983 perianal skin biopsy biopsy of perianal skin Removal of tissue from the peritoneum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2984 peritoneum biopsy biopsy of peritoneum Removal of tissue from the pituitary gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2985 pituitary gland biopsy biopsy of pituitary gland Removal of tissue from the pleura. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2986 pleura biopsy biopsy of pleura Removal of tissue from the rectum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2987 rectum biopsy biopsy of rectum Removal of tissue from the retina. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2988 retina biopsy biopsy of retina Removal of tissue from the saliva-secreting gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2989 saliva-secreting gland biopsy biopsy of saliva-secreting gland Removal of tissue from the scrotum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2990 scrotum biopsy biopsy of scrotum Removal of tissue from the sebaceous gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2991 sebaceous gland biopsy biopsy of sebaceous gland Removal of tissue from the small intestine. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2992 small intestine biopsy biopsy of small intestine Removal of tissue from the spinal cord. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2993 spinal cord biopsy biopsy of spinal cord Removal of tissue from the spleen. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2994 spleen biopsy biopsy of spleen Removal of tissue from the stomach. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2995 stomach biopsy biopsy of stomach Removal of tissue from the subglottis. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2996 subglottis biopsy biopsy of subglottis Removal of tissue from the submandibular gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2997 submandibular gland biopsy biopsy of submandibular gland Removal of tissue from the testis. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2998 testis biopsy biopsy of testis Removal of tissue from the thymus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2999 thymus biopsy biopsy of thymus Removal of tissue from the thyroid gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3000 thyroid gland biopsy biopsy of thyroid gland Removal of tissue from the tongue. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3001 tongue biopsy biopsy of tongue Removal of tissue from the tonsil. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3002 tonsil biopsy biopsy of tonsil Removal of tissue from the trachea. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3003 trachea biopsy biopsy of trachea Removal of tissue from the upper digestive tract. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3004 upper digestive tract biopsy biopsy of upper digestive tract Removal of tissue from the upper respiratory tract. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3005 upper respiratory tract biopsy biopsy of upper respiratory tract Removal of tissue from the ureter. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3006 ureter biopsy biopsy of ureter Removal of tissue from the urethra. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3007 urethra biopsy biopsy of urethra Removal of tissue from the urinary bladder. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3008 urinary bladder biopsy biopsy of urinary bladder Removal of tissue from the uterine cervix. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3009 uterine cervix biopsy biopsy of uterine cervix Removal of tissue from the vagina. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3010 vagina biopsy biopsy of vagina Removal of tissue from the vermiform appendix. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3011 vermiform appendix biopsy biopsy of vermiform appendix Removal of tissue from the zone of skin. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-3012 zone of skin biopsy skin biopsy Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. 2019-04-26T17:25:14Z NCIT:C16809 MRI scan for therapeutics NMRI nuclear magnetic resonance imaging for medical therapy therapeutic MRI medical magnetic resonance imaging procedure Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. NCIT:C16809 MRI scan for therapeutics NMRI therapeutic MRI Magnetic resonance imaging of the head. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the head head MRI head magnetic resonance imaging MRI of the head Magnetic resonance imaging of the abdomen. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the abdomen abdomen MRI abdomen magnetic resonance imaging MRI of the abdomen Magnetic resonance imaging of the brain. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the brain brain MRI brain magnetic resonance imaging MRI of the brain Magnetic resonance imaging of the chest. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the chest chest MRI chest magnetic resonance imaging MRI of the chest Radiation therapy in which high-energy beams are delivered to the tumor from outside of the body. 2019-04-26T19:28:21Z NCIT:C15751 EBRT external beam RT external beam radiotherapeutics external beam radiotherapy external-beam radiation External radiation therapy external beam radiation therapy Radiation therapy in which high-energy beams are delivered to the tumor from outside of the body. NCIT:C15751 EBRT external beam RT A type of radiation therapy in which radioactive material is placed inside the body, into a tumor or body cavity. 2019-04-26T19:28:57Z NCIT:C15195 Brachytherapy Internal radiation brachytherapy internal radiation radiation brachytherapy internal radiation therapy A type of radiation therapy in which radioactive material is placed inside the body, into a tumor or body cavity. NCIT:C15195 Magnetic resonance imaging of the breast. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the breast breast MRI breast magnetic resonance imaging MRI of the breast An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. 2019-08-29T18:00:40Z beta-lactams therapy CHEBI:27933 beta-lactam antibacterial drug therapy beta-lactam antibacterial drug treatment beta-lactam antibiotic agent therapy beta-lactam antibacterial agent therapy An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. CHEBI:27933 A pharmaceutical agent that inhibits the movement of calcium across through calcium channels in the cell membrane, preventing or decreasing the amount of calcium able to enter the cell. These drugs are used for their chronotropic, antihypertensive and vasodilatory effects. 2019-09-27T19:41:29Z CHEBI:38215 NCIT:C333 Ca2+ channel antagonist therapy Ca2+ channel blocker therapy calcium channel antagonist drug therapy calcium channel antagonist therapy calcium channel blocker drug therapy One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools. calcium channel blocking agent therapy A pharmaceutical agent that inhibits the movement of calcium across through calcium channels in the cell membrane, preventing or decreasing the amount of calcium able to enter the cell. These drugs are used for their chronotropic, antihypertensive and vasodilatory effects. NCIT:C333 Ca2+ channel antagonist therapy Ca2+ channel blocker therapy One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools. CHEBI:38215 Any substance that inhibits the action of N-methyl-D-aspartate (NMDA) receptors. 2019-10-01T19:23:17Z CHEBI:60643 NMDA receptor antagonist drug therapy NMDA receptor antagonist drug treatment NMDA receptor antagonist treatment NMDA receptor blocker therapy They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs. N-methyl-D-aspartate receptor antagonist therapy Any substance that inhibits the action of N-methyl-D-aspartate (NMDA) receptors. CHEBI:60643 They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs. CHEBI:60643 Use of medication for the treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-10-02T15:59:55Z ADHD drug therapy ADHD drug treatment Attention Deficit Hyperactivity Disorder drug therapy Attention Deficit Hyperactivity Disorder drug treatment drug therapy for ADHD ADHD agent therapy Use of medication for the treatment of Attention Deficit Hyperactivity Disorder (ADHD). http://orcid.org/0000-0001-7941-2961 Use of stimulant medication (usually amphetamines) for treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-10-02T16:01:46Z stimulant ADHD drug treatment stimulant Attention Deficit Hyperactivity Disorder agent therapy stimulant Attention Deficit Hyperactivity Disorder drug treatment stimulant drug therapy for ADHD stimulant drug treatment for ADHD stimulant ADHD agent therapy Use of stimulant medication (usually amphetamines) for treatment of Attention Deficit Hyperactivity Disorder (ADHD). http://orcid.org/0000-0001-7941-2961 Treatment with a medication that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. 2019-10-02T18:41:07Z CHEBI:50949 NCIT:C94725 SSRI drug therapy SSRI drug treatment selective serotonin reuptake inhbitor drug treatment selective serotonin reuptake inhibitor drug therapy Any agent that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. Increased level in the synaptic cleft prolongs the action of 5-HT on the postsynaptic receptor. This type of agent is typically used as an antidepressant and in the treatment of anxiety disorders and some personality disorders. They are also typically effective and used in treating some cases of insomnia. selective serotonin reuptake inhibitor agent therapy Treatment with a medication that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. NCIT:C94725 Any agent that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. Increased level in the synaptic cleft prolongs the action of 5-HT on the postsynaptic receptor. This type of agent is typically used as an antidepressant and in the treatment of anxiety disorders and some personality disorders. They are also typically effective and used in treating some cases of insomnia. NCIT:C94725 Treatment with colony-stimulating factors (CSF) can help the blood-forming tissue recover from the effects of chemotherapy and radiation therapy. These factors include interleukin-3 (IL-3), granulocyte colony-stimulating factor (G-CSF), macrophage colony-stimulating factor (M-CSF), and granulocyte-macrophage colony-stimulating factor (GM-CSF). 2019-10-08T17:41:54Z NCIT:C387 CSF agent therapy recombinant colony stimulating factor drug therapy recombinant colony-stimulating factor treatment recombinant hematopoietic colony-stimulating factor drug treatment colony stimulating factor agent therapy Treatment with colony-stimulating factors (CSF) can help the blood-forming tissue recover from the effects of chemotherapy and radiation therapy. These factors include interleukin-3 (IL-3), granulocyte colony-stimulating factor (G-CSF), macrophage colony-stimulating factor (M-CSF), and granulocyte-macrophage colony-stimulating factor (GM-CSF). NCIT:C387 CSF agent therapy 2019-10-08T18:06:31Z NCIT:C1287 G-CSF treatment granulocyte-colony stimulating factor treatment therapy recombinant colony-stimulating factor 3 treatment therapy recombinant granulocyte colony stimulating factor agent therapy recombinant granulocyte colony-stimulating factor drug treatment rhG-CSF therapy granulocyte colony stimulating factor agent therapy G-CSF treatment rhG-CSF therapy 2019-10-08T18:37:29Z erythropoietin modulating treatment erythropoietin regulating agent therapy A recombinant therapeutic agent which is chemically identical to or similar to the endogenous glycoprotein erythropoietin (Epo). Epo promotes the differentiation and maturation of hematopoietic progenitors into erythrocytes; is a mitogen and a chemoattractant for endothelial cells; stimulates activated and differentiated B-cells and enhances B-cell immunoglobulin production and proliferation; and is hypoxia-inducible. 2019-10-08T18:38:34Z erythrocyte colony stimulating factor agent therapy erythropoietin therapy CHEBI:81579 NCIT:C477 ESA therapy hematopoietin treatment therapy recombinant EPO treatment recombinant erythropoietin drug therapy recombinant erythropoietin treatment erythropoietin stimulating agent therapy ESA therapy recombinant EPO treatment Any inhibitor of erythropoietin, a glycoprotein hormone that controls erythropoiesis (red blood cell production). 2019-10-08T18:49:31Z CHEBI:91025 EPO inhibitor agent therapy EPO inhibitor drug treatment erythropoietin inhibitor drug treatment erythropoietin inhibitor agent therapy Any inhibitor of erythropoietin, a glycoprotein hormone that controls erythropoiesis (red blood cell production). CHEBI:91025 EPO inhibitor agent therapy EPO inhibitor drug treatment A drug that prevent fibrinolysis or lysis of a blood clot or thrombus. 2019-10-08T19:21:34Z CHEBI:48675 antifibrinolytic drug treatment antifibrinolytic agent therapy A drug that prevent fibrinolysis or lysis of a blood clot or thrombus. CHEBI:48675 A synthetic analogue of vasopressin in which 3-mercaptopropionic acid replaces the cysteine residue at position 1 and D-arginine replaces the residue at position 8. An antidiuretic, it increases urine concentration and decreases urine production, and is used (usually as the trihydrate of the acetic acid salt) to prevent and control excessive thirst, urination, and dehydration caused by injury, surgery, and certain medical conditions. It is also used in the diagnosis and treatment of cranial diabetes insipidus and in tests of renal function. 2019-10-08T19:26:15Z CHEBI:4450 NCIT:C61701 1-(3-mercaptopropionic acid)-8-D-arginine-vasopressin, 1-deamino-8-D-arginine vasopressin drug treatment 1-deamino-8-D-arginine vasopressin agent therapy 1-desamino-8-D-arginine vasopressin agent therapy DDAVP agent therapy desmopresina agent therapy desmopressin drug treatment desmopressine agent therapy desmopressinum agent therapy desmopressin agent therapy A synthetic analogue of vasopressin in which 3-mercaptopropionic acid replaces the cysteine residue at position 1 and D-arginine replaces the residue at position 8. An antidiuretic, it increases urine concentration and decreases urine production, and is used (usually as the trihydrate of the acetic acid salt) to prevent and control excessive thirst, urination, and dehydration caused by injury, surgery, and certain medical conditions. It is also used in the diagnosis and treatment of cranial diabetes insipidus and in tests of renal function. CHEBI:4450 The surgical removal (cutting out) of part or all of a structure or organ. 2019-12-27T17:21:50Z excision NCIT:C15232 abscission surgical removal surgical excision Surgical removal (cutting out or off) without replacement of all of a body part or structure. 2019-12-27T17:45:26Z resection surgical resection Taking or cutting out solid matter from a body part. The solid matter contained in the definition may be an abnormal byproduct of a biological function or a foreign body. It may be imbedded in a body part, or in the lumen of a tubular body part. The solid matter may or may not have been previously broken into pieces. 2020-01-02T19:00:34Z extirpation surgical extirpation Taking or cutting out solid matter from a body part. The solid matter contained in the definition may be an abnormal byproduct of a biological function or a foreign body. It may be imbedded in a body part, or in the lumen of a tubular body part. The solid matter may or may not have been previously broken into pieces. ICD-10-PCS A surgical procedure by which tissue or an organ (usually containing a tumor) is removed without rupture from a specific anatomic site. 2020-01-06T16:44:59Z enucleation surgical enucleation A surgical procedure by which tissue or an organ (usually containing a tumor) is removed without rupture from a specific anatomic site. NCIT:C48601 A surgical procedure that places something in the human body. 2020-01-06T18:21:08Z NCIT:C51982 implantation A surgical procedure that places something in the human body. NCIT:C51982 The removal of material from the surface of an object by vaporization, chipping, or other erosive process. 2020-01-06T19:26:24Z NCIT:C20985 https://doi.org/10.1016/B978-0-12-370610-2.50011-8 ablation therapy The removal of material from the surface of an object by vaporization, chipping, or other erosive process. https://doi.org/10.1016/B978-0-12-370610-2.50011-8 Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by light amplification by stimulated emission of radiation. 2020-01-06T19:30:40Z NCIT:C111241 photoablation therapy laser ablation therapy Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by light amplification by stimulated emission of radiation. NCIT:C111241 Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by chemical means. 2020-01-06T19:35:01Z NCIT:C111157 chemical ablation Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by chemical means. NCIT:C111157 The use of extreme cold to damage or destroy a body part, pathway, or function. The procedure is performed using small cryogenic probes during surgery, and has recently been applied to solitary sporadic renal tumor lesions. 2020-01-06T19:45:30Z NCIT:C15215 cryoablation therapy cryosurgical ablation therapy cryosurgery The use of extreme cold to damage or destroy a body part, pathway, or function. The procedure is performed using small cryogenic probes during surgery, and has recently been applied to solitary sporadic renal tumor lesions. NCIT:C15215 Thermal ablation refers to the destruction of tissue by extreme hyperthermia or hypothermia. 2020-01-06T19:50:11Z NCIT:C15670 thermal ablation therapy Thermal ablation refers to the destruction of tissue by extreme hyperthermia or hypothermia. NCIT:C15670 2020-01-08T17:26:31Z pain management Hydrotherapy is the external or internal use of water in any of its forms (water, ice, steam) for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. 2020-01-08T17:32:42Z OMIT:0008013 PMID:24926444 hydropathy hydrotherapy treatment water therapy water cure hydrotherapy Hydrotherapy is the external or internal use of water in any of its forms (water, ice, steam) for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. PMID:24926444 Thermal hydrotherapy uses external or internal use of water in any of its forms (water, ice, steam) at temperatures above or below room temperature for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. 2020-01-08T17:39:29Z hydro-thermal therapy hydrothermal therapy thermal water therapy bathing in thermal waters thermal hydrotherapy Washing out a hollow organ by flushing with a fluid. 2020-01-08T17:42:19Z NCIT:C38068 OMIT:0008013 lavage therapeutic irrigation Washing out a hollow organ by flushing with a fluid. NCIT:C38068 Therapy where a substantial part of the body is immersed in warm water to produce a variety of therapeutic effects. 2020-01-08T18:05:56Z hot bath therapy warm water bath therapy hyperthermic immersion therapy warm water shower therapy warm water immersion therapy Therapy where a substantial part of the body is immersed in warm water to produce a variety of therapeutic effects. PMID:24926444 Therapy where a substantial part of the body is immersed in cold water to produce a variety of therapeutic effects. 2020-01-08T18:06:06Z CWI therapy ice bath therapy cold water immersion therapy CWI therapy A form of treatment where a limb or significant portion of the body is immersed in hot water immediately followed by the immersion into cold water. This procedure is repeated several times. 2020-01-08T18:06:31Z contrast water therapy 2020-01-08T18:07:42Z aquatic exercise therapy A minimally-invasive procedure that permits sampling of breast ductal fluids for cytopathologic analysis. 2020-01-08T19:03:16Z NCIT:C51969 breast duct lavage A minimally-invasive procedure that permits sampling of breast ductal fluids for cytopathologic analysis. NCIT:C51969 Washing out the bronchi and alveoli by flushing with a fluid. 2020-01-08T19:03:33Z NCIT:C51913 bronchoaveolar lavage Washing out the bronchi and alveoli by flushing with a fluid. NCIT:C51913 A minimally invasive procedure that permits sampling of peritoneal fluid for cytopathologic analysis. 2020-01-08T19:03:46Z NCIT:C159340 peritoneal washing peritoneal lavage A minimally invasive procedure that permits sampling of peritoneal fluid for cytopathologic analysis. NCIT:C159340 The process in which the nasal cavity is washed to flush out mucus and debrise from the nose and sinuses with water or saline. 2020-01-08T19:04:02Z nasal irrigation nasal washing nasal lavage Avoid the administration or use of therapeutic procedure. 2020-01-12T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid therapeutic procedure avoiding therapeutic procedure therapeutic procedure avoidance Avoid the administration or use of diagnostic procedure. 2020-01-12T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid diagnostic procedure avoiding diagnostic procedure diagnostic procedure avoidance Avoid the administration or use of preventative therapeutics. 2020-01-12T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid preventative therapeutics avoiding preventative therapeutics preventative therapeutics avoidance The implantation of a piece of mechanical or electronic equipment that is useful for prevention, diagnosis, monitoring, or treatment of disease or other conditions. 2020-01-20T14:58:18Z ERO:0001092 NCIT:C16830 implantation of a medical device medical instrument implantation medical machine implantation medical device implantation Implantation of a battery-powered device that is placed under the skin (typically in the left upper chest) with electrode wires that lead into the heart (typically lodging in the apex or septum of the right ventricle). The device can detect abnormal heart rhythms and deliver low-energy or high-energy shocks to interrupt malignant arrhythmia and thereby prevent sudden death. 2020-01-20T16:54:00Z NCIt:C93238 UMLS_CUI:C0162589 ICD placement automated implantable cardioverter defibrillator placement implantable cardioverter-defibrillator implantation implantable cardioverter-defibrillator placement ICD placement The resection or complete surgical removal of a nerve. 2020-01-20T17:09:07Z surgical denervation Left cardiac sympathetic denervation (LCSD) is a surgical antiadrenergic intervention with a strong antiarrhythmic effect. LCSD consists in the removal of the left thoracic sympathetic chain and paravertebral ganglia from T1 to T4. 2020-01-20T17:11:04Z PMID:30972341 LCSD left cardiac sympathetic denervation Left cardiac sympathetic denervation (LCSD) is a surgical antiadrenergic intervention with a strong antiarrhythmic effect. LCSD consists in the removal of the left thoracic sympathetic chain and paravertebral ganglia from T1 to T4. PMID:30972341 LCSD 2020-01-20T17:50:35Z MeSH:D019637 Any procedure relating to the branch of medicine dealing with the correction of deformities of bones or muscles. orthopaedic procedure orthopedic procedure Any consultation with an orthopedics professional relating the correction of deformities of bones or muscles. 2020-01-20T17:50:52Z orthopaedic consult orthopedic consult orthopedic consultation A surgical procedure to treat and correct deformities, diseases, and injuries to the skeletal system, its articulations, and associated structures. 2020-01-20T17:51:02Z NCIT:C16186 orthopedic surgical procedure orthopedic surgery A surgical procedure to treat and correct deformities, diseases, and injuries to the skeletal system, its articulations, and associated structures. NCIT:C16186 obsolete orthopedic consultation false Orthotic services provide prescription insoles, braces, splints, callipers, footwear, spinal jackets and helmets which help people recover from or avoid injury, or live with lifelong conditions. 2020-01-20T18:01:00Z orthotic services The recommendation of the use of an orthosis or multiple orthoses, which are externally applied device used to modify the structural and functional characteristics of the neuromuscular and skeletal system. 2020-01-20T18:02:48Z PMID:26835739 orthoses usage orthotic device usage The recommendation of the use of an orthosis or multiple orthoses, which are externally applied device used to modify the structural and functional characteristics of the neuromuscular and skeletal system. PMID:26835739 2020-01-20T18:30:15Z medical professional consultation Increase in the longest dimension of a bone to correct anatomical deficiencies, congenital, traumatic, or as a result of disease. The lengthening is not restricted to long bones. The usual surgical methods are internal fixation and distraction. 2020-01-21T19:47:30Z MeSH:D001852 OMIT:0003210 limb lengthening procedure leg lengthening bone lengthening procedure Increase in the longest dimension of a bone to correct anatomical deficiencies, congenital, traumatic, or as a result of disease. The lengthening is not restricted to long bones. The usual surgical methods are internal fixation and distraction. MeSH:D001852 A bone fixation technique using an external fixator for lengthening limbs, correcting pseudarthroses and other deformities, and assisting the healing of otherwise hopeless traumatic or pathological fractures and infections, such as chronic osteomyelitis. 2020-01-21T19:52:10Z MeSH:D018889 Ilizarov technique Ilizarov procedure A bone fixation technique using an external fixator for lengthening limbs, correcting pseudarthroses and other deformities, and assisting the healing of otherwise hopeless traumatic or pathological fractures and infections, such as chronic osteomyelitis. MeSH:D018889 Bone lengthening by gradual mechanical distraction. An external fixation device produces the distraction across the bone plate. The technique was originally applied to long bones but in recent years the method has been adapted for use with mandibular implants in maxillofacial surgery. 2020-01-21T20:01:15Z MeSH:D019857 distraction osteogenesis Bone lengthening by gradual mechanical distraction. An external fixation device produces the distraction across the bone plate. The technique was originally applied to long bones but in recent years the method has been adapted for use with mandibular implants in maxillofacial surgery. MeSH:D019857 A measurement performed in a clinical setting using clinician's observations and instrument data to inform patient care and research. 2020-01-21T20:29:43Z CMO:0000000 PMID:2647562 clinical assessment clinical measurement A measurement performed in a clinical setting using clinician's observations and instrument data to inform patient care and research. PMID:2647562 An assessment of body temperature. 2020-01-21T20:35:51Z CMO:0000015 GeneReviews:NBK331 body temperature measurement The act of assessing an individual's current temperature, heart rate, respiratory rate, pulse oxygenation, and blood pressure. 2020-01-21T20:43:33Z NCIT:C49672 VSTEST vital signs measurement The act of assessing an individual's current temperature, heart rate, respiratory rate, pulse oxygenation, and blood pressure. NCIT:C49672 VSTEST An assessment of the number of heartbeats per unit time, usually expressed as beats per minute. 2020-01-21T20:47:05Z CMO:0000002 NCIT:C49677 HR measurement heart rate measurement HR measurement Assessment and recording of arterial pulses in any of a number of locations. The observer should note its intensity, rate, rhythm, and if any blood vessel tenderness, tortuosity, or nodularity exists. 2020-01-21T20:59:19Z GeneReveiws:NBK350 pulse assessment The rate of breathing (inhalation and exhalation) measured within in a unit time, usually expressed as breaths per minute. 2020-01-21T21:04:00Z CMO:0000289 NCIT:C49678 respiratory rate assessment The rate of breathing (inhalation and exhalation) measured within in a unit time, usually expressed as breaths per minute. NCIT:C49678 Procedure to evaluate the structure and/or function of the cardiovascular system. 2020-01-21T21:09:50Z CMO:0000001 NCIT:C100084 cardiovascular measurement cardiovascular diagnostic procedure Measurement of the pressure on the walls of the vessels as blood moves around the body. Systolic blood pressure is the pressure when the heart beats – while the heart muscle is contracting (squeezing) and pumping oxygen-rich blood into the blood vessels. Diastolic blood pressure is the pressure on the blood vessels when the heart muscle relaxes. The diastolic pressure is always lower than the systolic pressure. 2020-01-21T21:13:22Z CMO:0000003 https://www.ncbi.nlm.nih.gov/books/NBK279251 blood pressure assessment blood pressure monitoring blood pressure measurement Monitoring blood pressure with a sphygmomanometer and a stethoscope to hear blood flow. 2020-01-22T15:29:56Z MMO:0000055 NCIT:C69318 PMID:20937442 VSO:0000001 ausculatory sphygmomanometer blood pressure measurement auscultatory blood pressure measurement process auscultatory blood pressure monitoring Although the auscultatory method using mercury sphygmomanometer is regarded as the ‘gold standard’ for office blood pressure measurement, widespread implementation of the ban in use of mercury sphygmomanometers continues to diminish the role of this technique. auscultatory blood pressure measurement Although the auscultatory method using mercury sphygmomanometer is regarded as the ‘gold standard’ for office blood pressure measurement, widespread implementation of the ban in use of mercury sphygmomanometers continues to diminish the role of this technique. PMID:20937442 2020-01-22T20:49:15Z NCIT:C69319 PMID:20937442 VSO:0000026 A blood pressure measurement using a sphygmomanometer and an electronic pressure sensor (transducer) that detects blood flow by the presence of ocillations in the cuff pressure. oscillometric blood pressure measurement A method for monitoring blood pressure without requiring instruments introduced into the body. 2020-01-22T21:01:49Z NCIT:C69319 PMID:20937442 VSO:0000024 non-invasive blood presure measurement noninvasive blood pressure measurement An intra-arterial method of monitoring blood pressure. 2020-01-22T21:18:39Z VSO:0000023 invasive blood pressure measurement Any form of treatment that acts to improve or assist with respiratory function. 2020-01-23T15:55:17Z NCIT:C15322 respiratory therapy Any form of treatment that acts to improve or assist with respiratory function. NCIT:C15322 A set of maneuvers or medical procedures performed to prevent and relieve airway obstruction. This ensures an open pathway for gas exchange between a patient's lungs and the atmosphere. 2020-01-23T15:56:57Z MeSH:D058109 airway management A set of maneuvers or medical procedures performed to prevent and relieve airway obstruction. This ensures an open pathway for gas exchange between a patient's lungs and the atmosphere. PMID:18675024 Removal of an endotracheal tube from the patient. 2020-01-23T16:07:45Z MeSH:D060666 NCIT:C50819 airway extubation tracheal extubation endotracheal extubation Removal of an endotracheal tube from the patient. MeSH:D060666 A procedure involving placement of a tube into the trachea through the mouth or nose in order to provide a patient with oxygen and anesthesia. 2020-01-23T16:16:19Z MeSH:D007442 NCIT:C116648 airway intubation intratracheal intubation tracheal intubation endotracheal intubation A procedure involving placement of a tube into the trachea through the mouth or nose in order to provide a patient with oxygen and anesthesia. MeSH:D007442 Any method of artificial breathing that employs mechanical or non-mechanical means to force the air into and out of the lungs. Artificial respiration or ventilation is used in individuals who have stopped breathing or have respiratory insufficiency to increase their intake of oxygen (O2) and excretion of carbon dioxide (CO2). 2020-01-23T16:34:17Z artificial ventilation mechanical ventilation artificial respiration Surgical formation of an opening into the trachea through the neck, or the opening so created. 2020-01-23T16:48:07Z Tracheostomy and tracheotomy are sometimes used interchangeably, but tracheotomy is simply a surgical incision of the trachea. tracheostomy Surgical formation of an opening into the trachea through the neck, or the opening so created. MeSH:D014139 Tracheostomy and tracheotomy are sometimes used interchangeably, but tracheotomy is simply a surgical incision of the trachea. MeSH:D014140 A manual method for maintaining oxygenation using a mask. 2020-01-23T17:41:09Z bag-mask ventilation mask ventilation Techniques for administering artificial respiration without the need for intratracheal intubation. 2020-01-23T17:52:50Z MeSH:D063087 non-invasive ventilation noninvasive ventilation Techniques for administering artificial respiration without the need for intratracheal intubation. MeSH:D063087 Ventilatory support system using frequencies from 60-900 cycles/min or more. Three types of systems have been distinguished on the basis of rates, volumes, and the system used. 2020-01-23T17:57:32Z MeSH:D006612 high frequency oscillation ventilation high frequency positive pressure ventilation high-frequency ventilation Ventilatory support system using frequencies from 60-900 cycles/min or more. Three types of systems have been distinguished on the basis of rates, volumes, and the system used. MeSH:D006612 A technique of mechanical ventilation in which the lungs are insufflated with an oxygenated perfluorochemical liquid rather than an oxygen-containing gas mixture. 2020-01-23T18:01:24Z MeSH:D021061 liquid-assisted ventilation liquid ventilation A technique of mechanical ventilation in which the lungs are insufflated with an oxygenated perfluorochemical liquid rather than an oxygen-containing gas mixture. PMID:22043370 A method of mechanical ventilation in which pressure is maintained to increase the volume of gas remaining in the lungs at the end of expiration, thus reducing the shunting of blood through the lungs and improving gas exchange. 2020-01-23T18:06:14Z MeSH:D011175 positive end expiratory pressure technique positive-pressure ventilation positive-pressure respiration A method of mechanical ventilation in which pressure is maintained to increase the volume of gas remaining in the lungs at the end of expiration, thus reducing the shunting of blood through the lungs and improving gas exchange. MeSH:D011175 Assisted ventilation by applying intermittent subatmospheric pressure around the thorax, abdomen, or airway and periodically expand the chest wall and inflate the lungs. These devices used include the tank ventilators ("iron lung"), Portalung, Pneumowrap, and chest cuirass ("tortoise shell"). 2020-01-23T18:22:46Z MeSH:D015919 negative-pressure ventilation negative-pressure respiration A form of non-invasive mechanical pressure support ventilation that uses a time-cycled change of the applied positive airway pressure level to support spontaneous breathing activity. 2020-01-23T18:27:45Z MeSH:D007385 NCIT:C124039 BiPAP ventilation IPPV biphasic positive airway pressure ventilation inspiratory positive-pressure ventilation intermittent positive-pressure ventilation bilevel positive airway pressure ventilation A form of non-invasive mechanical pressure support ventilation that uses a time-cycled change of the applied positive airway pressure level to support spontaneous breathing activity. NCIT:C124039 BiPAP ventilation IPPV A form of non-invasive mechanical pressure support ventilation that uses a continuous positive airway pressure level to support spontaneous breathing activity. 2020-01-23T18:31:36Z MeSH:D045422 NCIT:C124040 APRV ventilation CPAP ventilation airway pressure release ventilation bilevel continuous positive airway pressure ventilation biphasic continuous positive airway pressure ventilation nCPAP ventilation nasal continuous positive airway pressure ventilation continuous positive airway pressure ventilation A form of non-invasive mechanical pressure support ventilation that uses a continuous positive airway pressure level to support spontaneous breathing activity. NCIT:C124040 APRV ventilation CPAP ventilation nCPAP ventilation A rehabilitation therapy for removal of copious mucus secretion from the lung of patients with diseases. The patient's head is placed in a downward incline (so the trachea is inferior to the affected area) for 15 to 20 minute sessions. 2020-01-23T19:45:07Z MeSH:D015916 postural respiratory drainage pulmonary postural drainage postural drainage A respiratory support system used to remove mucus and clear airway by oscillating pressure on the chest. 2020-01-23T20:18:02Z MeSH:D035641 external chest wall oscillation high-frequency chest compression high-frequency chest wall oscillation chest wall oscillation A respiratory support system used to remove mucus and clear airway by oscillating pressure on the chest. MeSH:D035641 Application of a life support system that circulates the blood through an oxygenating system, which may consist of a pump, a membrane oxygenator, and a heat exchanger. 2020-01-23T20:23:16Z MeSH:D015199 ECLS treatment ECMO treatment extracorporeal life support extracorporeal membrane oxygenation Application of a life support system that circulates the blood through an oxygenating system, which may consist of a pump, a membrane oxygenator, and a heat exchanger. MeSH:D015199 ECLS treatment ECMO treatment Chest physical therapy (CPT or Chest PT) is an airway clearance technique (ACT) to drain the lungs, and may include percussion (clapping), vibration, deep breathing, and huffing or coughing. 2020-01-23T20:32:18Z CPT Chest PT chest physical therapy chest physiotherapy The insertion of a cannula or tube into a hollow body organ. 2020-01-23T20:44:41Z ERO:0001108 MeSH:D007440 NCIT:C37981 intubation procedure The insertion of a cannula or tube into a hollow body organ. NCIT:C37981 The removal of a previously inserted tube from a hollow organ or passageway, often from the airway. 2020-01-23T20:48:40Z NCIT:C50819 extubation procedure The removal of a previously inserted tube from a hollow organ or passageway, often from the airway. NCIT:C50819 Use of medical ultrasonography in pregnancy where sound waves are used to create a real-time visual image of the developing fetus in the uterus. Imaging can include the mother's ovaries and uterus as well. 2020-01-24T19:29:52Z obstetric sonography prenatal ultrasound procedure obstetric ultrasonography A clinical recommendation to avoid or refrain from certain behaviors in order to maintain health or ameliorate symptoms. 2020-01-29T17:35:05Z behavior avoidance for therapeutic purposes cognitive and behavioral intervention avoidance A type of MRI that takes a series of images of an organ in quick succession and statistically analyzes the differences between the images. 2019-04-26T20:04:29Z NCIT:C17958 Functional MRI fMRI functional magnetic resonance imaging procedure A type of MRI that takes a series of images of an organ in quick succession and statistically analyzes the differences between the images. NCIT:C17958 Functional MRI fMRI Gene therapy involves the use of nucleic acids (DNA or RNA) for the treatment, cure or prevention of human disorders. 2019-05-07T16:28:50Z NCIT:C15238 SCDO:0001344 DNA therapy gene therapies gene transfer procedure genetic therapy gene therapy Gene therapy involves the use of nucleic acids (DNA or RNA) for the treatment, cure or prevention of human disorders. PMID:24106209 The goal of immunotherapy is to induce anti-disease (usually tumor) responses by reprogramming and augmenting immune surveillance, and reducing immune suppression. 2019-05-07T16:32:45Z NCIT:C15262 OGMS:0000114 immune therapy immunologically directed therapy immunotherapy procedure The goal of immunotherapy is to induce anti-disease (usually tumor) responses by reprogramming and augmenting immune surveillance, and reducing immune suppression. PMID:29242097 2019-05-15T16:33:57Z alcohol deterrent drug treatment alcohol deterrent agent therapy 2019-05-15T16:44:49Z smoking cessation drug treatment smoking cessation agent therapy An agent that binds to but does not activate an opioid receptor thereby blocking the actions of endogenous or exogenous opioid receptor agonists. 2019-05-15T16:45:09Z CHEBI:60605 NCIT:C681 opiate antagonist agent therapy opioid antagonist drug treatment opioid antagonist agent therapy An agent that binds to but does not activate an opioid receptor thereby blocking the actions of endogenous or exogenous opioid receptor agonists. CHEBI:60605 The determination of the number of red blood cells, white blood cells, and platelets in a blood sample. 2019-05-16T18:09:14Z NCIT:C28133 CBC complete blood count full blood count blood cell count The determination of the number of red blood cells, white blood cells, and platelets in a blood sample. NCIT:C28133 CBC The determination of the number of erythrocytes in a blood sample. 2019-05-16T18:18:55Z NCIT:C51946 RBC red blood cell count red cell count erythrocyte count The determination of the number of erythrocytes in a blood sample. NCIT:C51946 RBC The determination of the number of platelets in a blood sample, usually expressed as platelets per cubic millimeter (cmm) of whole blood. 2019-05-16T18:20:55Z NCIT:C51951 platelet count The determination of the number of platelets in a blood sample, usually expressed as platelets per cubic millimeter (cmm) of whole blood. NCIT:C51951 2019-05-16T18:24:56Z A test to determine the number of neutrophils in a sample of blood. neutrophil count A test to determine the number of leukocytes in a sample of blood. 2019-05-16T18:25:40Z NCIT:C51948 WBC white blood cell count leukocyte count A test to determine the number of leukocytes in a sample of blood. NCIT:C51948 WBC 2019-06-12T14:22:47Z medical action avoidance Avoid the administration or use of aerobic exercise therapy. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid aerobic exercise therapy avoiding aerobic exercise therapy aerobic exercise therapy avoidance Inoculating an individual with either killed or live agents to prevent contraction of a disease. 2019-06-14T15:47:12Z EFO:0004292 IDOMAL:0001040 NCIT:C15258 VO:0000002 vaccination Inoculating an individual with either killed or live agents to prevent contraction of a disease. NCIT:C15258 Nutrition intake is the process of taking in of nutrients, especially by eating or drinking, considered in relation to the body’s dietary needs. 2019-07-23T18:14:54Z nutrient consumption nutrient intake nutrition consumption nutritional intake take nourishment dietary intake eating food consumption food intake ingesting nutrition intake Nutrition intake is the process of taking in of nutrients, especially by eating or drinking, considered in relation to the body’s dietary needs. http://orcid.org/0000-0001-7941-2961 A vitamin enriched supplement containing higher doses for specific nutrients such as folic acid, intended for women before, during and after pregnancy and also during their lactating phase. 2019-07-23T19:56:32Z NCIT:C92860 antenatal supplements antenatal vitamin supplements antenatal vitamins prenatal supplements prenatal vitamin supplements prenatal vitamin A vitamin enriched supplement containing higher doses for specific nutrients such as folic acid, intended for women before, during and after pregnancy and also during their lactating phase. NCIT:C92860 Substance that produces loss of consciousness. 2019-07-24T15:53:13Z CHEBI:38869 general anaesthetic agents therapy general anaesthetics therapy general anesthesia therapy general anesthetics therapy general anesthetic agent therapy Substance that produces loss of consciousness. CHEBI:38869 A drug used to treat or prevent microbial infections. 2019-07-24T16:13:47Z CHEBI:36043 antimicrobial drug therapy antimicrobial drug treatment antimicrobial treatment antimicrobial agent therapy A drug used to treat or prevent microbial infections. CHEBI:36043 A loosely defined grouping of drugs that have effects on psychological function. 2019-07-24T19:33:44Z CHEBI:35471 psychoactive agent therapy psychoactive drug treatment psychopharmaceutical therapy psychotropic agent drug therapy psychotropic drug treatment treatment with psychotropic drug psychotropic agent therapy A loosely defined grouping of drugs that have effects on psychological function. CHEBI:35471 2019-07-24T19:39:15Z CHEBI:35473 A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour. ataractic agents tranquilisers tranquilising agents tranquilising drug tranquilizers tranquilizing agent tranquilizing drug tranquilizing drugs tranquilizing agent therapy A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour. CHEBI:35473 Any agent that acts on an adrenergic receptor or affects adrenergic signal transduction. 2019-07-25T14:32:48Z CHEBI:37962 NCIT:C29747 adrenergic agent drug treatment adrenergic drug therapy adrenergic agent therapy An agent that selectively binds to and activates beta-adrenergic receptors. 2019-07-25T14:42:00Z CHEBI:35522 b-adrenergic agonist b-adrenergic receptor agonist beta adrenergic receptor agonist beta-adrenergic agonist beta-adrenergic agonist agent beta-adrenergic agonist drugs beta-adrenergic agonists beta-adrenergic receptor agonist drugs beta-adrenergic receptor agonist beta-adrenoceptor agonists beta-adrenergic agonist agent therapy An agent that selectively binds to and activates beta-adrenergic receptors. CHEBI:35522 A medical requirement or recommendation of avoiding cannabis consumption. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid cannabis consumption cessation of cannabis consumption cannabis consumption avoidance A medical requirement or recommendation of avoiding tobacco consumption. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid tobacco consumption cessation of tobacco consumption tobacco consumption avoidance A medical requirement or recommendation of avoiding smoking behavior. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid smoking behavior cessation of smoking behavior smoking behavior avoidance A medical requirement or recommendation of avoiding consumption of an addictive substance. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid consumption of an addictive substance cessation of consumption of an addictive substance consumption of an addictive substance avoidance A medical requirement or recommendation of avoiding agitation behavior. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid agitation behavior agitation avoidance A medical requirement or recommendation of avoiding fear/anxiety related behavior. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid fear/anxiety related behavior fear or anxiety avoidance A medical requirement or recommendation of avoiding sexual activity. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sexual activity sexual activity avoidance A medical requirement or recommendation of avoiding copulation. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid copulation copulation avoidance A medical requirement or recommendation of avoiding stress related behavior. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid stress related behavior stress avoidance A medical requirement or recommendation of avoiding the consumption of gluten. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 avoid gluten intake avoiding gluten intake gluten consumption avoidance Intake may interfere with disease treatment, prolong the recovery phase, or cause complications. gluten intake avoidance A medical requirement or recommendation of avoiding the consumption of liquid. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 avoid liquid intake avoiding liquid intake liquid consumption avoidance liquid intake avoidance A medical requirement or recommendation of avoiding the consumption of protein extract, concentrate or isolate. 2019-11-13T02:36:00Z http://orcid.org/0000-0001-7941-2961 avoid protein extract, concentrate or isolate intake avoiding protein extract, concentrate or isolate intake protein extract, concentrate or isolate consumption avoidance protein intake avoidance A medical requirement or recommendation of avoiding the consumption of fat or oil. 2019-11-13T02:36:00Z http://orcid.org/0000-0001-7941-2961 avoid fat or oil intake avoiding fat or oil intake fat or oil consumption avoidance limited fat dietary intake low fat dietary intake non-fat dietary intake fat or oil intake avoidance Addition of amino-acid betaine to a the diet for complete nutrition support. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 amino-acid betaine supplemental intake dietary supplementation of amino-acid betaine supplementation of amino-acid betaine amino-acid betaine supplementation Addition of folates to a the diet for complete nutrition support. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of folates folates supplemental intake supplementation of folates folates supplementation Addition of carnitine to a the diet for complete nutrition support. 2019-11-13T02:36:00Z http://orcid.org/0000-0001-7941-2961 carnitine supplemental intake dietary supplementation of carnitine supplementation of carnitine carnitine supplementation Addition of methionine to a the diet for complete nutrition support. 2019-11-13T02:36:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of methionine methionine supplemental intake supplementation of methionine methionine supplementation Addition of creatine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 creatine supplemental intake dietary supplementation of creatine supplementation of creatine creatine supplementation Addition of arginine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 arginine supplemental intake dietary supplementation of arginine supplementation of arginine arginine supplementation Addition of biotins to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 biotins supplemental intake dietary supplementation of biotins supplementation of biotins biotins supplementation Addition of chenodeoxycholic acid to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 chenodeoxycholic acid supplemental intake dietary supplementation of chenodeoxycholic acid supplementation of chenodeoxycholic acid chenodeoxycholic acid supplementation Addition of coenzyme Q10 to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 coenzyme Q10 supplemental intake dietary supplementation of coenzyme Q10 supplementation of coenzyme Q10 coenzyme Q10 supplementation Addition of glycine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of glycine glycine supplemental intake supplementation of glycine glycine supplementation Addition of N-acetyl-L-cysteine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 N-acetyl-L-cysteine supplemental intake dietary supplementation of N-acetyl-L-cysteine supplementation of N-acetyl-L-cysteine N-acetyl-L-cysteine supplementation Addition of ornithine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of ornithine ornithine supplemental intake supplementation of ornithine ornithine supplementation Addition of riboflavin to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of riboflavin riboflavin supplemental intake supplementation of riboflavin riboflavin supplementation Addition of vitamin B6 to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of vitamin B6 supplementation of vitamin B6 vitamin B6 supplemental intake vitamin B6 supplementation Addition of citrulline to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 citrulline supplemental intake dietary supplementation of citrulline supplementation of citrulline citrulline supplementation Addition of thiamine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of thiamine supplementation of thiamine thiamine supplemental intake thiamine supplementation Addition of amino acid to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 NCIT:C15509 amino acid supplemental intake dietary supplementation of amino acid supplementation of amino acid A concentrated dietary supplement for injection containing the essential amino acids leucine, isoleucine, lysine, valine, phenylalanine, histidine, threonine, methionine and tryptophan as well as the non-essential amino acids alanine, arginine, glycine, proline, serine and tyrosine, with potential anabolic and anti-catabolic activities. Upon dilution and intravenous infusion of the amino acid nutritional supplement, the amino acids serve as protein building blocks, promote protein synthesis in muscle cells and prevent protein breakdown. NCIT:C15509 amino acid supplementation Addition of L-serine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 L-serine supplemental intake dietary supplementation of L-serine supplementation of L-serine L-serine supplementation Addition of uridine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of uridine supplementation of uridine uridine supplemental intake uridine supplementation Addition of medium-chain fatty acid to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of medium-chain fatty acid medium-chain fatty acid supplemental intake supplementation of medium-chain fatty acid medium-chain fatty acid supplementation Addition of essential fatty acid to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of essential fatty acid essential fatty acid supplemental intake supplementation of essential fatty acid essential fatty acid supplementation Addition of cholesterol to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 cholesterol supplemental intake dietary supplementation of cholesterol supplementation of cholesterol cholesterol supplementation Addition of elemental zinc to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of elemental zinc elemental zinc supplemental intake supplementation of elemental zinc elemental zinc supplementation Addition of hydroxocobalamin to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of hydroxocobalamin hydroxocobalamin supplemental intake supplementation of hydroxocobalamin hydroxocobalamin supplementation Addition of cyanocob(III)alamin to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 cyanocob(III)alamin supplemental intake dietary supplementation of cyanocob(III)alamin supplementation of cyanocob(III)alamin cyanocob(III)alamin supplementation Addition of methylcobalamin to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of methylcobalamin methylcobalamin supplemental intake supplementation of methylcobalamin methylcobalamin supplementation The surgical transfer of a healthy bone marrow to a patient. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of bone marrow bone marrow transplantation The surgical transfer of a healthy bone tissue to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of bone tissue bone grafting The surgical transfer of a healthy heart to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 heart transplantation transplantation of heart cardiac transplantation The surgical transfer of a healthy umbilical cord blood to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 UCBT cord blood transplantation transplantation of umbilical cord blood umbilical cord blood transplantation The surgical transfer of a healthy cornea to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of cornea corneal transplantation The surgical transfer of a healthy dura mater to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 dura mater transplantation transplantation of dura mater dura mater graft The surgical transfer of a healthy intestine to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of intestine intestinal transplantation The surgical transfer of a healthy small intestine to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 small bowel transplantation transplantation of small intestine small intestine transplantation The surgical transfer of a healthy lung to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of lung lung transplantation The surgical transfer of a healthy organ to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of organ organ transplantation The surgical transfer of a healthy ovary to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 ovary transplantation transplantation of ovary ovarian transplantation The surgical transfer of a healthy zone of skin to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 skin transplantation transplantation of zone of skin skin grafting The surgical transfer of a healthy thymus to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of thymus thymic transplantation A medical requirement or recommendation of avoiding the consumption of beverage alcohol. 2019-11-18T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid beverage alcohol intake avoiding beverage alcohol intake beverage alcohol consumption avoidance alcohol intake avoidance A medical requirement or recommendation of avoiding the consumption of broad bean (whole). 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid broad bean (whole) intake avoiding broad bean (whole) intake broad bean (whole) consumption avoidance fava bean avoidance fava bean consumption avoidance) windsor bean intake avoidance fava bean intake avoidance A medical requirement or recommendation of avoiding the consumption of meat food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid meat food product intake avoiding meat food product intake meat food product consumption avoidance meat food product intake avoidance A medical requirement or recommendation of avoiding the consumption of nut food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid nut food product intake avoiding nut food product intake nut food product consumption avoidance nut food product intake avoidance A medical requirement or recommendation of avoiding the consumption of saffron food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid saffron food product intake avoiding saffron food product intake saffron food product consumption avoidance saffron food product intake avoidance A medical requirement or recommendation of avoiding the consumption of seafood product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid seafood product intake avoiding seafood product intake seafood product consumption avoidance seafood product intake avoidance A medical requirement or recommendation of avoiding the consumption of mussel food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid mussel food product intake avoiding mussel food product intake mussel food product consumption avoidance mussel food product intake avoidance A medical requirement or recommendation of avoiding the consumption of clove food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid clove food product intake avoiding clove food product intake clove food product consumption avoidance clove food product intake avoidance A medical requirement or recommendation of avoiding the consumption of dark chocolate. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid dark chocolate intake avoiding dark chocolate intake dark chocolate consumption avoidance dark chocolate intake avoidance A medical requirement or recommendation of avoiding the consumption of pumpkin seed (shell off). 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid pumpkin seed (shell off) intake avoiding pumpkin seed (shell off) intake pumpkin seed (shell off) consumption avoidance pumpkin seed intake avoidance A medical requirement or recommendation of avoiding the consumption of sesame seed. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sesame seed intake avoiding sesame seed intake sesame seed consumption avoidance sesame seed intake avoidance A medical requirement or recommendation of avoiding the consumption of sunflower seed (whole kernel, raw). 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sunflower seed (whole kernel, raw) intake avoiding sunflower seed (whole kernel, raw) intake sunflower seed (whole kernel, raw) consumption avoidance sunflower seed intake avoidance The use of ultrasound to produce images of structures in the abdomen. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 abdomen sonography abdomen ultrasound examination abdomen ultrasound imaging procedure abdomen ultrasound procedure sonography of abdomen ultrasonography of abdomen abdominal ultrasonography The use of ultrasound to produce images of structures in the body of uterus. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 body of uterus sonography body of uterus ultrasound examination body of uterus ultrasound imaging procedure body of uterus ultrasound procedure sonography of body of uterus ultrasonography of body of uterus uterine ultrasonography The use of ultrasound to produce images of structures in the breast. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 breast sonography breast ultrasound examination breast ultrasound imaging procedure breast ultrasound procedure sonography of breast ultrasonography of breast breast ultrasonography The use of ultrasound to produce images of structures in the heart. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 heart sonography heart ultrasound examination heart ultrasound imaging procedure heart ultrasound procedure sonography of heart ultrasonography of heart echocardiography The use of ultrasound to produce images of structures in the liver. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2965 liver sonography liver ultrasound examination liver ultrasound imaging procedure liver ultrasound procedure sonography of liver ultrasonography of liver liver ultrasonography The use of ultrasound to produce images of structures in the lung. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2969 lung sonography lung ultrasound examination lung ultrasound imaging procedure lung ultrasound procedure sonography of lung ultrasonography of lung lung ultrasonography The use of ultrasound to produce images of structures in the lymph node. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2970 lymph node sonography lymph node ultrasound examination lymph node ultrasound imaging procedure lymph node ultrasound procedure sonography of lymph node ultrasonography of lymph node lymph node ultrasonography The use of ultrasound to produce images of structures in the musculoskeletal system. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2975 musculoskeletal system sonography musculoskeletal system ultrasound examination musculoskeletal system ultrasound imaging procedure musculoskeletal system ultrasound procedure sonography of musculoskeletal system ultrasonography of musculoskeletal system musculoskeletal ultrasonography The use of ultrasound to produce images of structures in the neck. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2979 neck sonography neck ultrasound examination neck ultrasound imaging procedure neck ultrasound procedure sonography of neck ultrasonography of neck neck ultrasonography The use of ultrasound to produce images of structures in the pancreas. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2981 pancreas sonography pancreas ultrasound examination pancreas ultrasound imaging procedure pancreas ultrasound procedure sonography of pancreas ultrasonography of pancreas pancreatic ultrasonography The use of ultrasound to produce images of structures in the rectum. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2987 rectum sonography rectum ultrasound examination rectum ultrasound imaging procedure rectum ultrasound procedure sonography of rectum ultrasonography of rectum rectal ultrasonography The use of ultrasound to produce images of structures in the scrotum. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2990 scrotum sonography scrotum ultrasound examination scrotum ultrasound imaging procedure scrotum ultrasound procedure sonography of scrotum ultrasonography of scrotum scrotal ultrasonography The use of ultrasound to produce images of structures in the spleen. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2994 sonography of spleen spleen sonography spleen ultrasound examination spleen ultrasound imaging procedure spleen ultrasound procedure ultrasonography of spleen spleen ultrasonography The use of ultrasound to produce images of structures in the stomach. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2995 sonography of stomach stomach sonography stomach ultrasound examination stomach ultrasound imaging procedure stomach ultrasound procedure ultrasonography of stomach stomach ultrasonography The use of ultrasound to produce images of structures in the thyroid gland. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3000 sonography of thyroid gland thyroid gland sonography thyroid gland ultrasound examination thyroid gland ultrasound imaging procedure thyroid gland ultrasound procedure ultrasonography of thyroid gland thyroid ultrasonography The use of ultrasound to produce images of structures in the urinary bladder. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3008 sonography of urinary bladder ultrasonography of urinary bladder urinary bladder sonography urinary bladder ultrasound examination urinary bladder ultrasound imaging procedure urinary bladder ultrasound procedure bladder ultrasonography The use of ultrasound to produce images of structures in the vagina. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 sonography of vagina ultrasonography of vagina vagina sonography vagina ultrasound examination vagina ultrasound imaging procedure vagina ultrasound procedure vaginal ultrasonography The use of ultrasound to produce images of structures in the kidney. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 kidney sonography kidney ultrasound examination kidney ultrasound imaging procedure kidney ultrasound procedure sonography of kidney ultrasonography of kidney renal ultrasonography The use of ultrasound to produce images of structures in the carotid artery segment. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 carotid artery segment sonography carotid artery segment ultrasound examination carotid artery segment ultrasound imaging procedure carotid artery segment ultrasound procedure carotid ultrasound imaging sonography of carotid artery segment ultrasonography of carotid artery segment carotid ultrasonography The use of ultrasound to produce images of structures in the pelvic region of trunk. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 pelvic region of trunk sonography pelvic region of trunk ultrasound examination pelvic region of trunk ultrasound imaging procedure pelvic region of trunk ultrasound procedure pelvic sonography pelvis sonography sonography of pelvic region of trunk ultrasonography of pelvic region of trunk pelvis ultrasonography The use of ultrasound to produce images of structures in the prostate gland. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 prostate gland sonography prostate gland ultrasound examination prostate gland ultrasound imaging procedure prostate gland ultrasound procedure sonography of prostate gland ultrasonography of prostate gland prostate ultrasonography The use of ultrasound to produce images of structures in the testis. The use of ultrasound to produce images of structures in the venous blood vessel. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 sonography of testis sonography of venous blood vessel testis sonography testis ultrasound examination testis ultrasound imaging procedure testis ultrasound procedure ultrasonography of testis ultrasonography of venous blood vessel venous blood vessel sonography venous blood vessel ultrasound examination venous blood vessel ultrasound imaging procedure venous blood vessel ultrasound procedure venous sonography testicular ultrasonography venous ultrasonography The use of ultrasound to produce images of structures in the brain. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 brain sonography brain ultrasound examination brain ultrasound imaging procedure brain ultrasound procedure sonography of brain ultrasonography of brain neurosonology The ketogenic diet is a high-fat, low-carbohydrate, adequate-protein diet that mimics a fasting state, resulting in the substitution of ketone bodies as a source of energy. The ketogenic diet can be used to reduce recurrent epileptic seizures in individuals with intractable epilepsy. Intractable epilepsy is defined as epilepsy that failed to respond to three or more antiepileptic drugs. keto diet intake classic ketogenic diet intake low glycemic index treatment medium-chain triglyceride(s) (MCT) ketogenic diet intake modified Atkins diet intake ketogenic diet intake The ketogenic diet is a high-fat, low-carbohydrate, adequate-protein diet that mimics a fasting state, resulting in the substitution of ketone bodies as a source of energy. The ketogenic diet can be used to reduce recurrent epileptic seizures in individuals with intractable epilepsy. Intractable epilepsy is defined as epilepsy that failed to respond to three or more antiepileptic drugs. PMID:23419562 PMID:27759811 PMID:28701250 Texture-modified foods and thickened drinks used to reduce the risks of choking and aspiration for individuals with oropharyngeal incoordination or dysphagia. dysphagia diet intake thickness modification of food and fluid for ingestion pureed food intake texture modified food intake thickened liquid intake texture modified diet intake Texture-modified foods and thickened drinks used to reduce the risks of choking and aspiration for individuals with oropharyngeal incoordination or dysphagia. PMID:27913916 PMID:28343526 Dietary approaches avoid excessive phenylalanine consumption, including stringent dietary restriction of natural protein intake, and supplementation of amino acids other than phenylalanine by a chemically manufactured protein substitute. 2019-09-06T19:08:21Z low phenylalanine diet intake phenylalanine free food intake phenylalanine-free diet intake phenylalanine-restricted diet intake phenylalanine restricted diet intake Dietary approaches avoid excessive phenylalanine consumption, including stringent dietary restriction of natural protein intake, and supplementation of amino acids other than phenylalanine by a chemically manufactured protein substitute. PMID:20720592 PMID:20971365 Supplementation of uncooked cornstarch intended to prevent hepatomegaly and hypoglycemia, typically for individuals with irregular hepatic glycogen storage. Supplementation can include both regular cornstarch and extended release cornstarch. 2019-09-05T20:57:49Z administration of uncooked cornstarch uncooked cornstarch therapy uncooked cornstarch supplementation Supplementation of uncooked cornstarch intended to prevent hepatomegaly and hypoglycemia, typically for individuals with irregular hepatic glycogen storage. Supplementation can include both regular cornstarch and extended release cornstarch. PMID:2403059 PMID:25266922 PMID:26303612 "Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences." [wikipedia:Emotions] 2011-04-14T01:03:39Z George Gkoutos affective behaviour mood behavior_ontology emotional behavior Behavior directly related to the production of offspring [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos reproduction reproductive behaviour behavior_ontology GO:0019098 reproductive behavior "Emotional behavior related to fear or anxiety." [NBO:GVG] 2011-04-14T01:03:39Z George Gkoutos fear/anxiety related behaviour behavior_ontology fear/anxiety related behavior "Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG] 2011-04-14T01:03:39Z George Gkoutos behavior_ontology sexual actions sexual activity Male's insertion of sperm-transfer organ into the body of the female [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos copulate behavior_ontology copulation "Emotional behavior related to excitement or restlessness." [NBO:GVG] 2011-03-31T12:22:11Z George Gkoutos behavior_ontology agitation behavior "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 "Behavior related to how the body reacts to a stressor ( a stimulus that causes stress), real or imagined." [wikipedia:Stress_(biological)] 2011-04-08T01:52:36Z George Gkoutos behavior_ontology It refers to the consequence of the failure of an organism to respond adequately to mental, emotional or physical demands, whether actual or imagined. stress related behavior "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 "Behavior related to the intake of substances." [NBOC:GVG] George Gkoutos ingest consumption behavior "Behavior related to the intake of addictive substances." [NBOC:GVG] George Gkoutos consumption of an addictive substance "Any process that modulates the frequency, rate or extent of consumption behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG] George Gkoutos regulation of consumption behavior "Any process that modulates the frequency, rate or extent of consumption of an addictive substance, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG] George Gkoutos regulation of consumption of an addictive substance "Any process that modulates the frequency, rate or extent of sexual activity, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG] George Gkoutos regulation of sexual activity Consumption behavior that involves inhaling a material (such as finely ground tobacco leaves) through the nose. http://orcid.org/0000-0002-2908-3327 2019-09-06T10:51:02Z https://orcid.org/0000-0002-7356-1779 smoking behavior Any habitual use of the tobacco plant leaf and its products. 2020-01-27T20:46:57Z tobacco consumption 2020-01-27T21:03:19Z cannabis consumption Muridae Asteroideae Heliantheae bony vertebrates Euteleostomi Archelosauria Dipnotetrapodomorpha Boreoeutheria Mesangiospermae Pentapetalae jawless vertebrates Cyclostomata Osteoglossocephalai Fabeae Actinopteri Clupeocephala Otophysi Otomorpha NPAAA clade 50 kb inversion clade Hologalegina IRL clade eucaryotes eukaryotes Eukaryota Cyprinoidei Afrotheria Euarchontoglires Rodents and rabbits Glires teleost fishes Teleostei Ostariophysi tetrapods Tetrapoda amniotes Amniota Theria Theria <mammals> diapsids Sauria chlorophyte/embryophyte group green plants Viridiplantae Opisthokonta Bilateria Protostomia deuterostomes Deuterostomia Muroidea angiosperms flowering plants Magnoliopsida cucumber family Cucurbitaceae marrows pumpkins squashes Cucurbita Boston marrow great pumpkin winter squash Cucurbita maxima Canada pumpkin ayote crookneck pumpkin crookneck winter squash cushaw squash lacayote Cucurbita moschata Cucurbita pepo pea family Fabaceae Papilionoideae Vicia broad bean faba bean fava bean Vicia faba Murinae mammals Mammalia Neopterygii daisy family Asteraceae sunflowers Helianthus common sunflower Helianthus annuus vascular plants Tracheophyta seed plants Spermatophyta molluscs mollusks Mollusca bivalves Bivalvia Asteridae asterids rosids Fabales chordates Chordata Vertebrata vertebrates Vertebrata <vertebrates> Petromyzontiformes lampreys Petromyzontidae Gnathostomata jawed vertebrates Gnathostomata <vertebrates> cartilaginous fishes fish fishes Chondrichthyes elasmobranchs Elasmobranchii euphyllophytes Euphyllophyta fish fishes ray-finned fishes Actinopterygii carps and others Cypriniformes Cyprinidae leopard danio zebra danio zebra fish zebrafish Danio rerio anurans frogs frogs and toads Anura Archosauria squamates Squamata birds avian Aves Heliantheae alliance fabids campanulids marsupials Metatheria eutherian mammals placental mammals placentals Eutheria manatees and dugongs (seacows) Sirenia manatees Trichechidae rodent Rodentia A group of organic food substances found in animals and plants in small quantities. They must be supplied in diet or dietary supplement and are essential for normal metabolism. Vitamin organism by taxonomy organism 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. 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 WEB: http://en.wikipedia.org/wiki/Organism organism A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease 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 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 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 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 branchiness quality inhering in a bearer by virtue of the bearer's lacking branches. quality PATO:0000414 unbranched A branchiness quality inhering in a bearer by virtue of the bearer's lacking branches. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. quality aberrant atypia atypical defective PATO:0000460 abnormal A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. PATOC:GVG 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 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 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 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 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 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 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 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 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 quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. george 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 A quality inhering in a bearer by virtue of its constitution. George Gkoutos 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 nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. gkoutos 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 multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010). fruit https://en.wikipedia.org/wiki/Fruit_anatomy A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. portion of plant tissue A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088). seed An anatomical structure that is or was part of a plant, or was derived from a part of a plant. This branch of the ontology needs to be further merged with Plant Ontology 'plant structure' terms. plant structure A portion of plant tissue (PO:0009007) that is the outer layer (wall) of a fruit (PO:0009001), and develops from a plant ovary (PO:0009072) or a carpel (PO:0009030) wall. pericarp A portion of plant tissue (PO:0009007) that is the outer layer of a pericarp (PO:0009084). exocarp A portion of plant tissue (PO:0009007) that is the innermost differentiated layer of a pericarp (PO:0009084). endocarp A portion of plant tissue (PO:0009007) that is the middle layer of a pericarp (PO:0009084). mesocarp 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. multi-tissue plant structure A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) that dehisce along two fruit valves (PO:0000033). legume fruit A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085). berry fruit A berry fruit (PO:0030108) which develops from a superior gynoecium (PO:0009062) and at maturity comprises a thickened exocarp (PO:0009085), thickened mesocarp (PO:0009087), and endocarp (PO:0009086), and has as parts juice sacs (PO:0006013) on a carpel adaxial epidermis (PO:0025618). hesperidium fruit 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 An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. 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 Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] cervical cervix BTO:0001421 BTO:0002249 CALOHA:TS-0134 EFO:0000979 EMAPA:29927 EV:0100114 FMA:17740 GAID:376 MA:0000392 MAT:0000292 MESH:D002584 NCIT:C12311 OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA UMLS:C0007874 VHOG:0001359 galen:CervixUteri canalis cervicis uteri caudal segment of uterus cervical canal of uterus cervix uteri neck of uterus uterine cervix uberon cervical canal cervix of uterus UBERON:0000002 uterine cervix Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] 2012-09-17 VHOG:0001359 VHOG The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] 2012-09-17 VHOG:0001359 VHOG DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004) cervix EFO:0000979 UMLS:C0007874 ncithesaurus:Cervix canalis cervicis uteri FMA:17740 FMA:TA cervical canal of uterus FMA:17740 cervix uteri EMAPA:29927 neck of uterus FMA:17740 uterine cervix FMA:17740 cervical canal FMA:17740 cervix of uterus BTO:0001421 The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. the organ that is specialized for smell and is part of the respiratory system the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359] BTO:0000840 CALOHA:TS-2037 EHDAA2:0001274 EHDAA:1502 EMAPA:16542 EV:0100037 EV:0100370 FMA:46472 GAID:77 MA:0000281 MAT:0000139 MESH:D009666 MIAA:0000139 NCIT:C12756 OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA TAO:0000047 UMLS:C0028429 ZFA:0000047 galen:Nose nasal sac nose peripheral olfactory organ uberon nasus olfactory apparatus proboscis UBERON:0000004 nose FMA ZFA-def ZFA The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. UBERON:cjm Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. ZFA:0000047 a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. the organ that is specialized for smell and is part of the respiratory system MP:0002233 UMLS:C0028429 ncithesaurus:Nose nasal sac ZFA:0000047 nose MA:0000281 peripheral olfactory organ ZFA:0000047 nasus olfactory apparatus UBERON:cjm FBbt:00005157 chemosensory sensory organ uberon UBERON:0000005 chemosensory organ 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 XAO:0000159 pancreatic insula pancreatic islet uberon island of Langerhans island of pancreas islets of Langerhans UBERON:0000006 islet of Langerhans 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) 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) UMLS:C0022131 ncithesaurus:Islet_of_Langerhans island of Langerhans BTO:0000991 island of pancreas BTO:0000991 The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO] An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9] Hp AAO:0010536 BAMS:PIT BAMS:Pit BIRNLEX:1353 BM:Die-Hy-HY BTO:0001073 CALOHA:TS-0798 DHBA:10505 EFO:0000857 EHDAA2:0001471 EHDAA:2183 EHDAA:4477 EMAPA:35998 EV:0100132 FMA:13889 GAID:457 HBA:4634 MA:0000176 MAT:0000077 MESH:D010902 MIAA:0000077 NCIT:C12399 OpenCyc:Mx4rv6NQYJwpEbGdrcN5Y29ycA TAO:0000118 UMLS:C0032005 VHOG:0000143 XAO:0000017 ZFA:0000118 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=399 glandula pituitaria pituitary pituitary body uberon hypophysis hypophysis cerebri UBERON:0000007 pituitary gland BGEE:ANN The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. ZFIN:curator An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO] 2012-06-20 AAO:0010536 AAO AAO:BJB An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO] 2012-08-14 TAO:0000118 TAO ZFIN:curator It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000143 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 Hp BIRNLEX:1353 NIFSTD:NeuroNames_abbrevSource UMLS:C0032005 BIRNLEX:1353 UMLS:C0032005 ncithesaurus:Pituitary_Gland http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=399 BIRNLEX:1353 glandula pituitaria pituitary BTO:0001073 pituitary body BTO:0001073 hypophysis ZFA:0000118 hypophysis cerebri MA:0000176 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 UMLS:C0225344 organ submucosa region of submucosa submucosa of organ submucosa of region of organ uberon submucous layer tela submucosa tunica submucosa UBERON:0000009 submucosa 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]. 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 TAO:0000142 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 XAO:0000178 ZFA:0000142 pars peripherica systema nervosum periphericum uberon UBERON:0000010 peripheral nervous system 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) (...) 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) PNS UMLS:C0206417 BIRNLEX:1111 UMLS:C0206417 ncithesaurus:Peripheral_Nervous_System UMLS:C1305921 BIRNLEX:1111 pars peripherica FMA:9903 FMA:TA systema nervosum periphericum FMA:9903 FMA:TA The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]. Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO] In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG] AAO:0010488 BIRNLEX:2517 BTO:0001833 CALOHA:TS-2094 EFO:0000894 EHDA:10096 EHDAA2:0001402 EHDAA:4655 EMAPA:17270 FMA:9907 GAID:708 MA:0000223 MAT:0000101 MESH:D010275 MIAA:0000101 NCIT:C12764 TAO:0001575 UMLS:C0030510 UMLS:C1305770 VHOG:0000755 ZFA:0001575 PNS - parasympathetic parasympathetic part of autonomic division of nervous system pars parasympathica divisionis autonomici systematis nervosi uberon pars parasympathica divisionis autonomici systematis nervosi UBERON:0000011 parasympathetic nervous system cjm FMA MA WP ZFA-modified-from-isa The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]. GO:0048486 Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO] 2012-06-20 AAO:0010488 AAO AAO:BJB In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000755 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998) UMLS:C0030510 BIRNLEX:2517 UMLS:C0030510 ncithesaurus:Parasympathetic_Nervous_System UMLS:C1305770 BIRNLEX:2517 pars parasympathica divisionis autonomici systematis nervosi FMA:9907 FMA:TA pars parasympathica divisionis autonomici systematis nervosi Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. EFO:0000892 FMA:9904 MA:0002850 MAT:0000099 MIAA:0000099 NLXANAT:100301 PNS - somatic somatic nervous system, somatic division somatic part of peripheral nervous system somatic peripheral nervous system uberon UBERON:0000012 somatic nervous system cjm Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. NLXANAT:100301 somatic nervous system, somatic division NLXANAT:100301 somatic part of peripheral nervous system UBERON:cjm somatic peripheral nervous system NLXANAT:100301 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 TAO:0001576 UMLS:C0039044 UMLS:C1269646 VHOG:0000384 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 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 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 UMLS:C0039044 BIRNLEX:2516 UMLS:C0039044 ncithesaurus:Sympathetic_Nervous_System UMLS:C1269646 BIRNLEX:2516 pars sympathica divisionis autonomici systematis nervosi FMA:9906 FMA:TA pars sympathica divisionis autonomici systematis nervosi 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 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA VHOG:0000860 portion of skin region of skin skin skin region skin zone uberon UBERON:0000014 zone of skin FMA Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. (...) 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) 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 NCIT:C32509 TAO:0001260 VHOG:0000049 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 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 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 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) endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys 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 NCIT:C32546 TAO:0001249 UMLS:C0553695 VHOG:0000048 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 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 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) UMLS:C0553695 ncithesaurus:Exocrine_Pancreas exocrine part of pancreas BTO:0000434 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 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA 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 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) 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 UMLS:C0015392 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 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 An organ that is capable of transducing sensory stimulus to the nervous system. 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 Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here. CALOHA:TS-0051 FMA:71012 skin appendage epidermal appendage uberon epidermal growth UBERON:0000021 cutaneous appendage Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. skin appendage FMA:71012 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. 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 OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA UMLS:C0598782 VSAO:0000075 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 UMLS:C0598782 ncithesaurus:Appendage appendages XAO:0000218 extremitaet BTO:0001492 limbs/digits/tail MP:0000001 Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] BTO:0000784 CALOHA:TS-0579 EFO:0000872 EMAPA:35523 EV:0100050 FMA:5034 GAID:947 MA:0000139 MAT:0000442 MESH:D008198 NCIT:C12745 NCIT:C33027 OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA TAO_RETIRED:0005318 UMLS:C0024204 VHOG:0001273 ZFA_RETIRED:0005318 galen:Lymphnode uberon lymph gland nodus lymphaticus UBERON:0000029 lymph node Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. BTO:0000784 Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] 2012-09-17 VHOG:0001273 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630 UMLS:C0024204 ncithesaurus:Lymph_Node lymph gland VHOG:0001273 nodus lymphaticus 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 UMLS:C1179187 lamina propria mucosa lamina propria mucosae uberon tunica propria UBERON:0000030 lamina propria 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. 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 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 FBbt:00000004 FMA:7154 GAID:61 HAO:0000397 MA:0000023 MAT:0000294 MESH:D006257 MIAA:0000294 NCIT:C12419 OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA SPD:0000016 TAO:0001114 TGMA:0000002 UMLS:C0018670 VHOG:0001644 WBbt:0005739 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 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 UMLS:C0018670 BIRNLEX:1230 UMLS:C0018670 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 TAO:0005425 UMLS:C0036760 ZFA:0005425 tunica serosa wall of serous sac uberon serosa UBERON:0000042 serous membrane 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] 2012-08-14 TAO:0005425 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 UMLS:C0036760 ncithesaurus:Serosa tunica serosa FMA:9581 wall of serous sac FMA:9581 serosa 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 OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA UMLS:C0039508 VHOG:0001286 VSAO:0000073 XAO:0000173 ZFA:0005647 galen:Tendon uberon sinew tendo UBERON:0000043 tendon VSAO OG Dense regular connective tissue that connects muscle to bone[VSAO]. GO_REF:0000034 VSAO:0000073 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) 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 tendo 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 FBbt:00005137 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 XAO:0000209 ZFA:0000190 uberon ganglia neural ganglion UBERON:0000045 ganglion EHDAA2 Bgee:AN A biological tissue mass, most commonly a mass of nerve cell bodies. 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] 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) 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 uberon UBERON:0000047 simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. 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. Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] ureteral ureteric in humans, consists of adventitial, muscular and mucoa layers AAO:0010254 BTO:0001409 CALOHA:TS-1084 EFO:0000930 EHDAA2:0002139 EHDAA:9341 EMAPA:17950 EV:0100097 FMA:9704 GAID:438 MA:0000378 MAT:0000120 MESH:D014513 MIAA:0000120 NCIT:C12416 OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA UMLS:C0041951 VHOG:0000605 XAO:0000144 galen:Ureter uberon metanephric duct UBERON:0000056 ureter GO Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. GO:0090189 Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] 2012-06-20 AAO:0010254 AAO AAO:BJB The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000605 VHOG The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] 2012-09-17 VHOG:0000605 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C0041951 ncithesaurus:Ureter metanephric duct ISBN:0073040584 VHOG:0000605 the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening urethral In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. BTO:0001426 CALOHA:TS-1132 EFO:0000931 EMAPA:30901 EV:0100099 FMA:19667 GAID:390 MA:0000379 MAT:0000121 MESH:D014521 MIAA:0000121 NCIT:C12417 OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA UMLS:C0041967 VHOG:0001264 XAO:0000153 galen:Urethra uberon UBERON:0000057 urethra pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra Wikipedia Wikipedia the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening MGI:anna MP:0000537 UMLS:C0041967 ncithesaurus:Urethra 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 TAO:0005171 UMLS:C0687028 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. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. ZFA:0005171 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:A03.492.411.495 MIAA:0000046 NCIT:C12379 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA UMLS:C0021851 VHOG:0000054 XAO:0000131 galen:LargeIntestine uberon intestinum crassum UBERON:0000059 large intestine 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 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 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 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 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 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 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 uberon anatomical unit body organ element UBERON:0000062 organ 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. GO:0048513 UMLS:C0178784 ncithesaurus:Organ element 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. 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 cardinal organ part uberon regional part of organ UBERON:0000064 organ part A multicellular structure that is a part of an organ. 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 OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA 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 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 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. 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 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. 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. 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. Melissa Haendel 2009-06-18T09:00:04Z BIRNLEX:1157 NCIT:C13040 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 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 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 EHDAA2:0001968 EHDAA:1494 EHDAA:350 EHDAA:4784 EHDAA:4790 EHDAA:4796 EHDAA:7860 EMAPA:16096 FMA:87656 NCIT:C34309 UMLS:C1515087 surface (external) ectoderm surface ectoderm uberon UBERON:0000076 external ectoderm EHDAA2 EHDAA2 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. MGI:anna MP:0012532 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. 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. The organs associated with producing offspring in the gender that produces spermatozoa. 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:0000082 CALOHA:TS-1310 EFO:0000970 EHDAA2:0001054 EHDAA:8136 EMAPA:17968 EV:0100101 FBbt:00004927 FMA:45664 GAID:386 HAO:0000505 MA:0000396 MESH:D005837 NCIT:C12722 OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA TGMA:0000634 UMLS:C0017422 UMLS:C1963704 VHOG:0000725 WBbt:0008423 XAO:0000155 genitalia of male organism male genital system male genitalia male genitals male organism genitalia male organism reproductive system reproductive system of male organism uberon male genital organ male genital tract male reproductive tract systema genitale masculinum UBERON:0000079 male reproductive system The organs associated with producing offspring in the gender that produces spermatozoa. MP:0001145 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:0000725 VHOG ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 UMLS:C0017422 ncithesaurus:Male_Genitalia UMLS:C1963704 ncithesaurus:Male_Reproductive_System genitalia of male organism OBOL:automatic male genital system FMA:45664 male organism genitalia OBOL:automatic male organism reproductive system OBOL:automatic reproductive system of male organism OBOL:automatic male genital organ BTO:0000082 male reproductive tract MA:0000396 systema genitale masculinum BTO:0000082 The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] mesonephric In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified] AAO:0010384 BTO:0001542 CALOHA:TS-0624 EFO:0000928 EHDAA2:0001130 EHDAA:1581 EHDAA:5903 EMAPA:16744 FMA:72171 GAID:1308 MESH:D001755 NCIT:C26467 TAO:0000529 UMLS:C0025492 VHOG:0000038 XAO:0000141 ZFA:0000529 Wolffian body mesonephric kidney mesonephroi uberon amphibian adult kidney corpus Wolffi middle kidney opisthonephros opisto nephros opistonephros UBERON:0000080 mesonephros The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. GO:0001823 A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] 2012-09-17 VHOG:0000038 VHOG Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] 2012-06-20 AAO:0010384 AAO AAO:BJB As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] 2012-09-17 VHOG:0000038 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 UMLS:C0025492 ncithesaurus:Mesonephros Wolffian body BTO:0001542 GOC:yaf MESH:A16.254.500 mesonephric kidney XAO:0000141 mesonephroi amphibian adult kidney XAO:0000141 corpus Wolffi BTO:0001542 middle kidney BTO:0001542 opisthonephros VHOG:0000038 XAO:0000141 opistonephros In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO] TODO check developmental relationships A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] metanephric During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis BTO:0001543 EHDAA2:0001137 EHDAA:3089 EHDAA:5911 EMAPA:17373 EMAPA_RETIRED:17207 FMA:72172 NCIT:C34209 UMLS:C0231049 VHOG:0000039 metanephron uberon definite kidney definitive kidney hind kidney metanephric kidney UBERON:0000081 metanephros definitional GO ISBN:9780878932504 In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO] GO:0001656 A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] 2012-09-17 VHOG:0000039 VHOG The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] 2012-09-17 VHOG:0000039 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C0231049 ncithesaurus:Metanephros metanephron BTO:0001543 definite kidney BTO:0001543 definitive kidney BTO:0001543 hind kidney BTO:0001543 metanephric kidney VHOG:0000039 A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. TODO check Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] AAO:0010389 EHDAA2:0001134 EMAPA:16747 VHOG:0000500 XAO:0000148 uberon renal tubules tubuli mesonephrici UBERON:0000083 mesonephric tubule A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] 2012-09-17 VHOG:0000500 VHOG As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000500 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 renal tubules VHOG:0000500 tubuli mesonephrici An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] BTO:0001646 EHDAA2:0002140 EHDAA:3091 EHDAA:5917 EMAPA:17209 NCIT:C34207 UMLS:C1284058 VHOG:0000541 uberon diverticulum diverticulum metanephricum gemma ureterica metanephric bud metanephric diverticulum ureteric ampulla ureteric diverticulum UBERON:0000084 ureteric bud EHDAA2 EHDAA2 ISBN:9780878932504 An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] MP:0010979 Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] 2012-09-17 VHOG:0000541 VHOG Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. VHOG:0000541 The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] 2012-09-17 VHOG:0000541 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C1284058 ncithesaurus:Metanephric_Diverticulum diverticulum BTO:0001646 diverticulum metanephricum gemma ureterica metanephric bud BTO:0001646 metanephric diverticulum ureteric diverticulum VHOG:0000541 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:A16.254.270.550 NCIT:C34212 UMLS:C0026573 uberon morula (2-16 cells) UBERON:0000085 morula 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 ZFA:0001111 uberon oolemma pellucid zone striated membrane vitelline envelope vitelline membrane zona radiata zona striata UBERON:0000086 zona pellucida 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] 2012-09-17 VHOG:0000720 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159 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 UMLS:C1283994 VHOG:0000742 uberon ICM early embryoblast embryoblast embryoblastus; massa cellularis interna; pluriblastus senior pluriblast UBERON:0000087 inner cell mass 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 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 UMLS:C1283994 ncithesaurus:Inner_Cell_Mass ICM VHOG:0000742 early embryoblast FMA:86557 embryoblastus; massa cellularis interna; pluriblastus senior 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:A11.936 NCIT:C93292 UMLS:C0041178 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 MP-def 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 UMLS:C0041178 ncithesaurus:Trophoblast trophoblast layer MP:0005031 massa cellularis externa trophoblastus 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 bilaminary embryonic disc bilaminary germ disc uberon bilaminar disk UBERON:0000091 bilaminar disc 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 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 stage succeeding embryo, including mature structure 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] cjm 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. cjm 2009-07-30T07:57:38Z TAO:0002173 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] 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. ZFA cardiac neural crest complex complexus cristae neuralis cardiacus 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, commencing with the zygote stage and ending in 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 An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. 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 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. 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 NCIT:C12601 PdumDv:0000100 VHOG:0000745 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. 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 fertilized egg stage BTO:0000854 one-cell stage VHOG:0000745 zygote VHOG:0000745 zygotum 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:A16.254.270 MmusDv:0000004 OGES:000015 OGES:000020 PdumDv:0000200 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 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 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg WBls:0000005 XAO:1000003 ZFS:0000045 uberon UBERON:0000108 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. 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 trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage 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. BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 XAO:1000006 uberon UBERON:0000110 neurula stage 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 uberon segmentation stage UBERON:0000111 organogenesis stage A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. The stage of being a sexually immature adult animal[XAO:1000010]. In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother) BILS:0000112 BTO:0002168 EFO:0001300 EV:0300051 MmusDv:0000043 OGES:000009 XAO:1000010 XtroDO:0000083 ZFS:0000051 immature stage juvenile stage uberon subadult stage UBERON:0000112 sexually immature stage The stage of being a sexually immature adult animal[XAO:1000010]. XAO:1000010 immature stage VHOG:FB juvenile stage XAO:1000010 subadult stage The stage of being a sexually mature adult animal. adult stage BILS:0000113 EV:0300064 EV:0300070 MIAA:0000403 MmusDv:0000110 OGES:000026 OGES:000027 XAO:1000093 ZFS:0000044 uberon UBERON:0000113 post-juvenile adult stage The stage of being a sexually mature adult animal. 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 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 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 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 UMLS:C1514420 UMLS:C1514897 uberon gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum UBERON:0000118 lung bud GO:0060441 EHDAA2 Structure derived from foregut that becomes a lung[GO]. GO:0060431 UMLS:C1514420 ncithesaurus:Primary_Bronchial_Bud UMLS:C1514897 ncithesaurus:Respiratory_Diverticulum gemma pulmonalis gemma respiratoria lung bud primary lung bud GO:0060572 respiratory diverticulum 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 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 nervous system nucleus neuraxis nucleus neuronal nucleus nucleus of CNS uberon nucleus of neuraxis UBERON:0000125 neural nucleus 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 cranial neural nucleus nucleus of cranial nerve uberon nucleus nervi cranialis UBERON:0000126 cranial nerve nucleus 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 the group of motor neurons residing in the pons that innervate the muscles of facial expression FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus. BAMS:7 BAMS:7N BAMS:VII BM:Pons-VII DHBA:12420 EHDAA2:0004638 EMAPA:35338 EV:0100267 FMA:54572 MA:0001014 NCIT:C12898 UMLS:C0228740 VHOG:0001412 facial VII nucleus facial nerve nucleus nucleus of facial nerve uberon facial VII motor nucleus UBERON:0000127 facial nucleus definitional the group of motor neurons residing in the pons that innervate the muscles of facial expression ISBN:0838580343 MP:0000909 FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus. FMA UMLS:C0228740 ncithesaurus:Facial_Nerve_Nucleus facial VII nucleus MA:0001014 nucleus of facial nerve FMA:54572 facial VII motor nucleus MA:0001014 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 NCIT:C12375 UMLS:C0227411 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 Wikipathways:WP2062 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. UMLS:C0227411 ncithesaurus:Anal_Canal canalis analis canalis analis BTO:0001978 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 intestine http://langual.org 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:A03.492.411 MIAA:0000043 NCIT:C12736 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 XAO:0000129 ZFA:0001338 galen:Intestine http://www.langual.org/langual_thesaurus.asp?termid=C0212 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 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 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 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 UMLS:C0008987 VHOG:0001186 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 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 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 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 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 cloaca the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal urogenital sinus EHDAA2:0004060 EHDAA:5029 EHDAA:5919 EMAPA:17379 NCIT:C34322 UMLS:C0231057 VHOG:0000414 UGS fetal UGS sinus urogenitalis uberon UBERON:0000164 primitive urogenital sinus MP-def the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females ISBN:0-683-40008-8 MP:0010116 The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] 2012-09-17 VHOG:0000414 VHOG In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] 2012-09-17 VHOG:0000414 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300 the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal MP urogenital sinus MP:0010116 UMLS:C0231057 ncithesaurus:Urogenital_Sinus UGS MP:0010116 fetal UGS sinus urogenitalis 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 OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 VHOG:0000280 VHOG:0000812 XAO:0003029 ZFA:0000547 ZFA:0000590 galen:Mouth 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 the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts exceptions in some taxa 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] 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) 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 regio oralis BTO:0004698 regio oralis FMA:49184 FMA:TA cavital oralis 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 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. (...) 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) 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 NCIT:C12421 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 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 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 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. segment of colon FMA:222905 1 1 1 1 The pair of anatomical structures comprised of a left lung and right lung. FMA:68877 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA 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. 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 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 portion of excreted substance FMA:9674 waste substance AEO:0000184 excretion BTO:0000491 A fluid that is composed of blood plasma and erythrocytes. Damion Dooley blood This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. http://langual.org 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] 2019-06-12T07:33:21Z 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 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA SUBSET_SIREN:F17130 TAO:0000007 UMLS:C0005767 VHOG:0000224 XAO:0000124 ZFA:0000007 galen:Blood http://www.langual.org/langual_thesaurus.asp?termid=C0185 portion of blood vertebrate blood uberon whole blood UBERON:0000178 subset_siren SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * derives from 'blood' (http://purl.obolibrary.org/obo/UBERON_0000178) blood Bgee:AN A fluid that is composed of blood plasma and erythrocytes. FMA:9670 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) UMLS:C0005767 ncithesaurus:Blood whole blood BTO:0000089 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. cjm 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. Dorsal part (roof region) of the telencephalon[GO]. In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume. In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus cjm 2009-04-18T12:03:09Z UBERON:0007333 BTO:0003399 DMBA:15903 EFO:0003534 TAO:0000505 TAO:0007007 ZFA:0000505 area dorsalis telencephali dorsal part of telencephalon dorsal telencephalic area dorsal telencephalon uberon UBERON:0000203 pallium https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/87 Dorsal part (roof region) of the telencephalon[GO]. GO:0021543 ISBN:0471888893 In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume. NCBITaxon:8782 In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus WP area dorsalis telencephali ZFA:0000505 dorsal part of telencephalon ISBN:0471888893 dorsal telencephalic area ZFA:0000505 dorsal telencephalon ZFA:0000505 Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ. Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]. Portion of connective tissue that connects bone or cartilage.[TAO] Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG] this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament CALOHA:TS-2145 EFO:0001966 EMAPA:35493 FMA:21496 FMA:30319 MA:0000113 MESH:D008022 NCIT:C13046 OpenCyc:Mx4rvVjqpZwpEbGdrcN5Y29ycA TAO:0001682 UMLS:C0023685 VHOG:0001272 XAO:0004031 ZFA:0001675 galen:Ligament ligament organ uberon UBERON:0000211 ligament Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ. GO_REF:0000034 VSAO:0000073 Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]. FMA:21496 Portion of connective tissue that connects bone or cartilage.[TAO] 2012-08-14 TAO:0001682 TAO TAO:wd Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG] 2012-09-17 VHOG:0001272 VHOG PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996) UMLS:C0023685 ncithesaurus:Ligament ligament organ FMA:21496 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 UMLS:C0224856 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 UMLS:C0224856 ncithesaurus:Tendon_Sheath synovial tendon sheath FMA:45087 vagina tendinis 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:A16.254.270.274 OGEM:000006 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg blastula embryo uberon blastosphere UBERON:0000307 blastula 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. blastula embryo BILA:0000059 blastosphere The upper ventral region of the torso of an organism. The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. BTO:0000149 CALOHA:TS-2083 EV:0100124 FMA:9601 GAID:33 MESH:D001940 NCIT:C12971 OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA UMLS:C0006141 galen:Breast mammary part of chest mammary region uberon mamma UBERON:0000310 breast The upper ventral region of the torso of an organism. The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. WP,unvetted UMLS:C0006141 ncithesaurus:Breast mammary part of chest FMA:9601 mammary region FMA:9601 mamma A mucosa that is part of a cecum [Automatically generated definition]. BTO:0000213 FMA:14998 caecum mucosa caecum mucosa of organ caecum mucous membrane caecum organ mucosa cecal mucosa cecum mucosa of organ cecum mucous membrane cecum organ mucosa intestinum crassum caecum mucosa intestinum crassum caecum mucosa of organ intestinum crassum caecum mucous membrane intestinum crassum caecum organ mucosa mucosa of caecum mucosa of cecum mucosa of intestinum crassum caecum mucosa of organ of caecum mucosa of organ of cecum mucosa of organ of intestinum crassum caecum mucous membrane of caecum mucous membrane of cecum mucous membrane of intestinum crassum caecum organ mucosa of caecum organ mucosa of cecum organ mucosa of intestinum crassum caecum uberon UBERON:0000314 cecum mucosa A mucosa that is part of a cecum [Automatically generated definition]. OBOL:automatic caecum mucosa OBOL:automatic caecum mucosa of organ OBOL:automatic caecum mucous membrane OBOL:automatic caecum organ mucosa OBOL:automatic cecal mucosa FMA:14998 cecum mucosa of organ OBOL:automatic cecum mucous membrane OBOL:automatic cecum organ mucosa OBOL:automatic intestinum crassum caecum mucosa OBOL:automatic intestinum crassum caecum mucosa of organ OBOL:automatic intestinum crassum caecum mucous membrane OBOL:automatic intestinum crassum caecum organ mucosa OBOL:automatic mucosa of caecum OBOL:automatic mucosa of cecum OBOL:automatic mucosa of intestinum crassum caecum OBOL:automatic mucosa of organ of caecum OBOL:automatic mucosa of organ of cecum OBOL:automatic mucosa of organ of intestinum crassum caecum OBOL:automatic mucous membrane of caecum OBOL:automatic mucous membrane of cecum OBOL:automatic mucous membrane of intestinum crassum caecum OBOL:automatic organ mucosa of caecum OBOL:automatic organ mucosa of cecum OBOL:automatic organ mucosa of intestinum crassum caecum OBOL:automatic The space between the arachnoid and pia mater. BTO:0000230 EMAPA:32666 FMA:83716 GAID:689 MESH:D013346 uberon cavitas subarachnoidea cavum subarachnoideale spatium leptomeningeum spatium subarachnoideum subarachnoid cavity UBERON:0000315 subarachnoid space ISBN:0471888893 The space between the arachnoid and pia mater. GOC:add cavitas subarachnoidea BTO:0000230 cavum subarachnoideale spatium leptomeningeum BTO:0000230 spatium subarachnoideum spatium subarachnoideum BTO:0000230 subarachnoid cavity BTO:0000230 A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. BTO:0000242 FMA:83689 MESH:D002582 cervix mucus uberon UBERON:0000316 cervical mucus A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. BTO:0000242 cervix mucus OBOL:automatic 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 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. 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 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 An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus. Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]. BTO:0000449 CALOHA:TS-0360 EFO:0001323 FBbt:00005333 FMA:63919 GAID:552 MESH:D005333 NCIT:C13235 OpenCyc:Mx4rvZfC2ZwpEbGdrcN5Y29ycA UMLS:C0015965 fetus uberon embryo late growth stage embryo late stage UBERON:0000323 late embryo An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. BGEE:ANiknejad Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]. FMA:63919 UMLS:C0015965 ncithesaurus:Fetus fetus BTO:0000449 embryo late growth stage BTO:0000449 embryo late stage BTO:0000449 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). wall of gut FMA:45653 bone marrow in which the fat cells predominate in the meshes of the reticular network. BTO:0000635 FMA:74596 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. 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 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]. 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 OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA UMLS:C0026724 galen:Mucosa mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa uberon region of mucosa tunica mucosa UBERON:0000344 mucosa 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] 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 tunica mucosa BTO:0000886 The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead. Sensory medial ramus of the trigeminal nerve.[AAO] The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG] AAO:0010648 BTO:0000926 EHDAA2:0002088 EHDAA:3744 EMAPA:17800 FMA:52621 GAID:837 MA:0001104 MESH:D009882 NCIT:C33215 OpenCyc:Mx4rwEs_K5wpEbGdrcN5Y29ycA UMLS:C0029082 VHOG:0001349 cranial nerve V, branch V1 first branch of fifth cranial nerve first division of fifth cranial nerve first division of trigeminal nerve nervus ophthalmicus (V1) nervus ophthalmicus (Va) nervus ophthalmicus [v1] nervus ophthalmicus [va] ophthalmic division [V1] ophthalmic division [Va] ophthalmic division of fifth cranial nerve ophthalmic division of trigeminal nerve (V1) ophthalmic division of trigeminal nerve (Va) ophthalmic nerve [V1] ophthalmic nerve [Va] opthalmic nerve ramus opthalmicus profundus (ramus V1) rostral branch of trigeminal nerve trigeminal V nerve ophthalmic division uberon ciliary nerve ethmoidal nerve ophthalmic division profundal nerve profundus profundus nerve trigeminal nerve ophthalmic division UBERON:0000348 Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html] ophthalmic nerve may be a distinct nerve in teleosts multiple The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead. MP:0009798 Sensory medial ramus of the trigeminal nerve.[AAO] 2012-06-20 AAO:0010648 AAO AAO:EJS The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG] 2012-09-17 VHOG:0001349 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177 UMLS:C0029082 ncithesaurus:Ophthalmic_Nerve cranial nerve V, branch V1 first branch of fifth cranial nerve first division of fifth cranial nerve FMA:52621 first division of trigeminal nerve FMA:52621 nervus ophthalmicus (V1) FMA:52621 nervus ophthalmicus (Va) FMA:52621 nervus ophthalmicus [v1] FMA:52621 FMA:TA nervus ophthalmicus [va] FMA:52621 FMA:TA ophthalmic division [V1] FMA:52621 ophthalmic division [Va] FMA:52621 ophthalmic division of fifth cranial nerve FMA:52621 ophthalmic division of trigeminal nerve (V1) FMA:52621 ophthalmic division of trigeminal nerve (Va) FMA:52621 ophthalmic nerve [V1] FMA:52621 ophthalmic nerve [Va] FMA:52621 opthalmic nerve ramus opthalmicus profundus (ramus V1) AAO:0010648 rostral branch of trigeminal nerve trigeminal V nerve ophthalmic division MA:0001104 ciliary nerve ethmoidal nerve ophthalmic division ophthalmic division BTO:0000926 profundal nerve profundus profundus nerve trigeminal nerve ophthalmic division EMAPA:17800 A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity. BTO:0000928 CALOHA:TS-1307 FMA:242000 GAID:615 MESH:A08.186.211.577 NCIT:C94541 OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA UMLS:C0023715 uberon visceral brain UBERON:0000349 includes the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia] limbic system A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. BIRNLEX:Limbic_system UMLS:C0023715 ncithesaurus:Limbic_System visceral brain ISBN:0123813611 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 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 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. 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 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 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 mucous membrane of pharynx 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:A16.254.085 NCIT:C13739 UMLS:C1281743 uberon blastocystis blastula UBERON:0000358 blastocyst The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. GO:0001824 UMLS:C1281743 ncithesaurus:Blastocyst blastocystis blastula FMA:83041 the inner portion of the kidney consisting of the renal pyramids The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water BTO:0001167 CALOHA:TS-1157 EMAPA:19279 GAID:425 MA:0000373 MESH:D007679 NCIT:C12740 UMLS:C0022664 galen:MedullaOfKidney kidney medulla medulla of kidney medulla renalis pyramides renales renal medullae renal medullae set renal pyramids renal pyramids set uberon medullary pyramids renal marrow UBERON:0000362 renal medulla the inner portion of the kidney consisting of the renal pyramids ISBN:0-683-40008-8 MGI:smb MP:0003014 UMLS:C0022664 ncithesaurus:Renal_Medulla kidney medulla OBOL:automatic medulla of kidney OBOL:automatic medulla renalis FMA:74268 FMA:TA pyramides renales FMA:74268 FMA:TA renal medullae FMA:86327 renal medullae set FMA:86327 renal pyramids FMA:74268 renal pyramids set FMA:74268 medullary pyramids FMA:74268 renal marrow BTO:0001167 The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini. AAO:0010688 AAO:0010703 BTO:0001375 EHDAA2:0002086 EMAPA:17798 FMA:52996 GAID:834 MA:0001101 MESH:D008340 NCIT:C32779 OpenCyc:Mx4rvcQKSpwpEbGdrcN5Y29ycA UMLS:C0024695 VHOG:0001345 inferior maxillary nerve mandibular division [V3] mandibular division [Vc] mandibular division of fifth cranial nerve mandibular division of trigeminal nerve [Vc; V3] mandibular nerve [V3] mandibular nerve [Vc] nervus mandibularis [Vc; V3] nervus mandibularis [v3] nervus mandibularis [vc] ramus mandibularis (ramus V3) third division of fifth cranial nerve third division of trigeminal nerve trigeminal V nerve mandibular division uberon n. mandibularis nervus mandibularis trigeminal nerve mandibular division UBERON:0000375 mandibular nerve The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini. MP:0009800 UMLS:C0024695 ncithesaurus:Inferior_Maxillary_Nerve inferior maxillary nerve FMA:52996 mandibular division [V3] FMA:52996 mandibular division [Vc] FMA:52996 mandibular division of fifth cranial nerve FMA:52996 mandibular division of trigeminal nerve [Vc; V3] FMA:52996 mandibular nerve [V3] FMA:52996 mandibular nerve [Vc] FMA:52996 nervus mandibularis [Vc; V3] FMA:52996 nervus mandibularis [v3] FMA:52996 FMA:TA nervus mandibularis [vc] FMA:52996 FMA:TA ramus mandibularis (ramus V3) AAO:0010688 third division of fifth cranial nerve FMA:52996 third division of trigeminal nerve FMA:52996 trigeminal V nerve mandibular division MA:0001101 n. mandibularis nervus mandibularis BTO:0001375 trigeminal nerve mandibular division EMAPA:17798 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 OpenCyc:Mx4rvWNU9JwpEbGdrcN5Y29ycA VHOG:0001346 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 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 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 nervus maxillaris BTO:0001378 trigeminal nerve maxillary division EMAPA:17799 The muscular portion of the tongue. The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] BTO:0001386 EHDAA2:0002065 EHDAA:9146 EMAPA:17883 FMA:46689 MA:0001596 NCIT:C49301 NCIT:C52707 UMLS:C0448325 UMLS:C1710437 VHOG:0001390 muscle of tongue muscle organ of tongue skeletal muscle tissue of tongue tongue skeletal muscle tongue skeletal muscle tissue uberon musculi linguae UBERON:0000378 tongue muscle FEED:rd ISBN:1607950324 The muscular portion of the tongue. MP:0004136 The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0001390 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) UMLS:C0448325 ncithesaurus:Tongue_Muscle UMLS:C1710437 ncithesaurus:Tongue_Skeletal_Muscle_Tissue muscle of tongue FMA:46689 muscle organ of tongue OBOL:accepted skeletal muscle tissue of tongue OBOL:automatic tongue skeletal muscle OBOL:automatic tongue skeletal muscle tissue OBOL:automatic musculi linguae A mucosa that is part of a respiratory airway. BTO:0001390 FMA:7471 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 mucous membrane of trachea 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 FBbt:00005069 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:A09.371.509.225 cortex of lens uberon UBERON:0000389 lens cortex Tissue that surrounds the lens nucleus cortex of lens FMA:58970 The core of the crystalline lens, surrounded by the cortex. BTO:0001633 FMA:58971 MESH:A09.371.509.670 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 pia mater or arachnoid mater. check relationship to secondary meninx in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular BTO:0001634 CALOHA:TS-0546 FMA:231515 NCIT:C32979 NLXANAT:090207 UMLS:C0228126 leptomeninges uberon arachnoid mater and pia mater arachnoidea mater et pia mater pia-arachnoid pia-arachnoid of neuraxis UBERON:0000391 leptomeninx pia mater or arachnoid mater. in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular FMA UMLS:C0228126 ncithesaurus:Leptomeninges leptomeninges NLXANAT:090207 arachnoid mater and pia mater FMA:231515 arachnoidea mater et pia mater BTO:0001634 pia-arachnoid BTO:0001634 pia-arachnoid of neuraxis FMA:231515 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 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 colon epithelium 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 The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]. BTO:0001761 CALOHA:TS-0660 FMA:59644 vestibular part of nasal cavity uberon vestibulum nasale vestibulum nasi UBERON:0000402 nasal vestibule The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]. vestibular part of nasal cavity FMA:59644 vestibulum nasale BTO:0001761 vestibulum nasi vestibulum nasi BTO:0001761 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 uberon UBERON:0000409 serous gland A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. MP:0008052 EMAPA:37950 MA:th A mucosa that is part of a bronchus [Automatically generated definition]. BTO:0001846 FMA:62652 bronchi mucosa bronchi mucosa of organ bronchi mucous membrane bronchi organ mucosa bronchial trunk mucosa bronchial trunk mucosa of organ bronchial trunk mucous membrane bronchial trunk organ mucosa bronchus mucosa bronchus mucosa of organ bronchus mucous membrane bronchus organ mucosa mucosa of bronchi mucosa of bronchial trunk mucosa of bronchus mucosa of organ of bronchi mucosa of organ of bronchial trunk mucosa of organ of bronchus mucous membrane of bronchi mucous membrane of bronchial trunk mucous membrane of bronchus organ mucosa of bronchi organ mucosa of bronchial trunk organ mucosa of bronchus tunica mucosa bronchi uberon UBERON:0000410 bronchial mucosa A mucosa that is part of a bronchus [Automatically generated definition]. OBOL:automatic bronchi mucosa OBOL:automatic bronchi mucosa of organ OBOL:automatic bronchi mucous membrane OBOL:automatic bronchi organ mucosa OBOL:automatic bronchial trunk mucosa OBOL:automatic bronchial trunk mucosa of organ OBOL:automatic bronchial trunk mucous membrane OBOL:automatic bronchial trunk organ mucosa OBOL:automatic bronchus mucosa OBOL:automatic bronchus mucosa of organ OBOL:automatic bronchus mucous membrane OBOL:automatic bronchus organ mucosa OBOL:automatic mucosa of bronchi OBOL:automatic mucosa of bronchial trunk OBOL:automatic mucosa of bronchus OBOL:automatic mucosa of organ of bronchi OBOL:automatic mucosa of organ of bronchial trunk OBOL:automatic mucosa of organ of bronchus OBOL:automatic mucous membrane of bronchi OBOL:automatic mucous membrane of bronchial trunk OBOL:automatic mucous membrane of bronchus FMA:62652 mucous membrane of bronchus OBOL:automatic organ mucosa of bronchi OBOL:automatic organ mucosa of bronchial trunk OBOL:automatic organ mucosa of bronchus OBOL:automatic tunica mucosa bronchi FMA:62652 FMA:TA 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 glandula mucosa uberon muciparous gland mucous secreting gland mucus gland mucus-secreting gland UBERON:0000414 mucous gland 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] NCBITaxon:8292 ISBN:0073040584 EMAPA:37913 MA:th glandula mucosa 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 The prostate epithelium. TODO - check 2 FMA IDs UBERON:0002452 BTO:0002397 CALOHA:TS-2065 EMAPA:35711 FMA:66812 FMA:79643 MA:0001737 NCIT:C13103 UMLS:C1179826 epithelial tissue of prostate epithelial tissue of prostate gland epithelium of prostate epithelium of prostate gland epithelium of prostatic gland prostate epithelial tissue prostate gland epithelial tissue prostate gland epithelium prostatic epithelium prostatic gland epithelium uberon UBERON:0000428 prostate epithelium The prostate epithelium. MP:0001168 UMLS:C1179826 ncithesaurus:Prostatic_Epithelium epithelial tissue of prostate OBOL:automatic epithelial tissue of prostate gland OBOL:automatic epithelium of prostate OBOL:automatic epithelium of prostate gland OBOL:automatic epithelium of prostatic gland FMA:79643 prostate epithelial tissue OBOL:automatic prostate gland epithelial tissue OBOL:automatic prostatic epithelium FMA:66812 A vein that drains the left pampiniform plexus and empties into the left renal vein. BTO:0002679 EMAPA:37383 FMA:14341 MA:0002220 NCIT:C52697 right spermatic vein vena testicularis (adrenalis) dextra uberon vena testicularis dextra vena testicularis sinistra UBERON:0000442 right testicular vein A vein that drains the left pampiniform plexus and empties into the left renal vein. Dorlands_Medical_Dictionary:MerckSource EMAPA:37383 MA:th right spermatic vein MA:0002220 vena testicularis (adrenalis) dextra FMA:14341 vena testicularis dextra BTO:0002679 vena testicularis sinistra BTO:0002680 A vein that drains the right pampiniform plexus and empties into the inferior vena cava. BTO:0002680 EMAPA:37167 FMA:14345 MA:0002219 NCIT:C52696 left spermatic vein uberon vena testicularis dextra vena testicularis sinistra UBERON:0000443 left testicular vein A vein that drains the right pampiniform plexus and empties into the inferior vena cava. Dorlands_Medical_Dictionary:MerckSource EMAPA:37167 MA:th left spermatic vein MA:0002219 vena testicularis dextra BTO:0002679 vena testicularis sinistra BTO:0002680 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. 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 Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses. BTO:0002996 FMA:70527 cavernous branch of cavernous part of internal carotid artery ramus sinus cavernosi (pars cavernosa) (arteria carotis interna) uberon UBERON:0000457 cavernous artery Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses. BTO:0002996 cavernous branch of cavernous part of internal carotid artery FMA:70527 ramus sinus cavernosi (pars cavernosa) (arteria carotis interna) FMA:70527 FMA:TA The region of the opening of the uterine cervix into the uterine cavity. BTO:0003002 FMA:86485 NCIT:C12309 UMLS:C0227837 uberon UBERON:0000458 endocervix The region of the opening of the uterine cervix into the uterine cavity. BTO:0003002 UMLS:C0227837 ncithesaurus:Endocervix An anatomical wall that is part of a uterus [Automatically generated definition]. BTO:0003083 FMA:17560 anatomical wall of uterus uterus anatomical wall uterus wall wall of uterus uberon UBERON:0000459 uterine wall An anatomical wall that is part of a uterus [Automatically generated definition]. OBOL:automatic anatomical wall of uterus OBOL:automatic uterus anatomical wall OBOL:automatic uterus wall OBOL:automatic wall of uterus OBOL:automatic 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. 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. Damion Dooley 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 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. 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. 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. 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. 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 MA:0000003 NCIT:C12919 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 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 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 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism animal 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 organism FBbt:00000001 VHOG:0000671 WBbt:0007833 multi-cellular organism CARO:0000012 animal BTO:0000042 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 compound organ components ZFA:0001489 A gonad of a male animal. A gonad produces and releases sperm. Male 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] testicular The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally UBERON:0002117 AAO:0000606 BILA:0000124 BSA:0000085 BTO:0001363 CALOHA:TS-1030 EFO:0000984 EHDAA2:0002007 EHDAA:8146 EMAPA:17972 EV:0100102 FBbt:00004928 FMA:7210 GAID:396 HAO:0001007 MA:0000411 MAT:0000132 MESH:D013737 MIAA:0000132 NCIT:C12412 OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA TAO:0000598 UMLS:C0039597 VHOG:0000252 WBbt:0006794 XAO:0000157 ZFA:0000598 galen:Testis gonad of male genitalia gonad of male reproductive system male gonad testicle uberon orchis testes testiculus UBERON:0000473 testis A gonad of a male animal. A gonad produces and releases sperm. Male reproductive organ.[TAO] 2012-08-14 TAO:0000598 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:0000252 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) The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally ISBN:0123971756 NCBITaxon:40674 UMLS:C0039597 ncithesaurus:Testis gonad of male genitalia OBOL:automatic gonad of male reproductive system OBOL:automatic male gonad OBOL:automatic testicle FMA:7210 orchis BTO:0001363 testes testiculus BTO:0001363 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 OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA TGMA:0000635 UMLS:C0700038 VHOG:0000726 WBbt:0006748 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 The organs and associated structures associated with bearing offspring in a female animal. MP:0001119 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 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 OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 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 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. acellular anatomical structures ZFA:0000382 Anatomical group that has its parts adjacent to one another. Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3] AAO:0010009 AEO:0000041 BILA:0000041 CARO:0000041 EHDAA2:0003041 FBbt:00007277 FMA:49443 HAO:0000041 TADS:0000605 TAO:0001478 TGMA:0001842 VHOG:0001737 XAO:0003160 ZFA:0001478 uberon UBERON:0000477 anatomical cluster Anatomical group that has its parts adjacent to one another. 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 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 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 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 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 TAO:0001486 UMLS:C0014609 VHOG:0000387 XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium uberon UBERON:0000483 epithelium 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] 2012-09-17 VHOG:0000387 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 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 XAO:0004009 ZFA:0001497 epithelium simplex cuboideum uberon simple cuboidal epithelia UBERON:0000484 simple cuboidal epithelium Unilaminar epithelium that consists of a single layer of cuboidal cells. 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 TAO:0001496 UMLS:C0836135 XAO:0004008 ZFA:0001496 epithelium simplex columnare simple columnar epithelium uberon simple columnar epithelia UBERON:0000485 simple columnar epithelium Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] FMA:FMA columnar epithelium EHDAA2:0003068 columnar epithlium AEO:0000068 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 TAO:0001494 UMLS:C0682575 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 Epithelium that consists of more than one layer of epithelial cells.[CARO] 2012-06-20 CARO:0000069 CARO FMA:45562 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 XAO:0004010 ZFA:0001498 epithelium simplex squamosum uberon simple squamous epithelia UBERON:0000487 simple squamous epithelium Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] FMA:45565 Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] 2012-06-20 CARO:0000070 CARO FMA:45565 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. 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. 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 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 Epithelium that consists of a single layer of epithelial cells.[CARO] 2012-06-20 CARO:0000073 CARO FMA:45561 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 OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA UMLS:C0026727 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. UMLS:C0026727 ncithesaurus:Mucus Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. ENVO:02000042 FMA:9673 NCIT:C120839 intercellular fluid tissue fluid uberon UBERON:0000913 interstitial fluid Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. intercellular fluid ENVO:02000042 tissue fluid ENVO:02000042 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 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. 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:A01.047 MIAA:0000298 OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA 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. 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 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA UMLS:C0013935 VHOG:0001766 XAO:0000113 ZFA:0000103 embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo 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 Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo ZFA 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:A16.254.425 NCIT:C12950 NCIT:C54105 TAO:0001122 UMLS:C0920502 UMLS:C1708239 VHOG:0001223 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. 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 embryonic tissue FMA:69069 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:A16.254.425.273 MIAA:0000173 NCIT:C12703 TAO:0000016 UMLS:C0013574 VHOG:0000153 XAO:0000001 ZFA:0000016 embryonic ectoderm uberon UBERON:0000924 ectoderm Bgee:AN 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] 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 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:A16.254.425.407 MIAA:0000175 NCIT:C12706 TAO:0000017 UMLS:C0014144 VHOG:0000154 XAO:0000090 ZFA:0000017 uberon entoderm UBERON:0000925 endoderm Bgee:AN 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] 2012-09-17 VHOG:0000154 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 UMLS:C0014144 ncithesaurus:Endoderm entoderm 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:A16.254.425.660 MIAA:0000174 NCIT:C12750 TAO:0000041 UMLS:C0025485 VHOG:0000152 XAO:0000050 ZFA:0000041 uberon embryonic mesoderm entire mesoderm mesodermal mantle UBERON:0000926 mesoderm sometimes not considered primary Bgee:AN 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] 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 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 UMLS:C0025485 ncithesaurus:Mesoderm embryonic mesoderm VHOG:0000152 entire mesoderm 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 XAO:0000269 ZFA:0001290 mouth primordium primitive oral cavity stomatodeum stomodaeum uberon mouth pit oral ectoderm oral pit UBERON:0000930 stomodeum 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. 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 UMLS:C1514977 ncithesaurus:Stomodeum mouth primordium XAO:0000269 primitive oral cavity stomatodeum 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 XAO:0001019 ZFA:0000066 embryonic proctodaeum proctodaeum amnioproctodeal invagination uberon anal pit anus porus UBERON:0000931 proctodeum EHDAA2 EHDAA2 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. ZFA:0000066 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 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. stomach http://langual.org 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:A03.492.766 MIAA:0000051 NCIT:C12391 OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA TAO:0002121 UMLS:C0038351 VHOG:0000408 XAO:0000128 galen:Stomach http://www.langual.org/langual_thesaurus.asp?termid=C0211 stomach chamber uberon anterior intestine gaster mesenteron ventriculus maw (mammal) UBERON:0000945 stomach cjm cjm 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 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) 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 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 OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA UMLS:C0003483 VHOG:0001523 XAO:0003010 galen:Aorta trunk of aortic tree trunk of systemic arterial tree dorsal aorta uberon arteria maxima UBERON:0000947 aorta 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 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 UMLS:C0003483 ncithesaurus:Aorta dorsal aorta ZFA:0000014 arteria maxima A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. heart (animal) http://langual.org 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 OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA TAO:0000114 UMLS:C0018787 VHOG:0000276 XAO:0000064 ZFA:0000114 galen:Heart http://www.langual.org/langual_thesaurus.asp?termid=C0201 chambered heart vertebrate heart branchial heart uberon Herz@de 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 MA 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] 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 UMLS:C0018787 ncithesaurus:Heart chambered heart branchial heart Herz@de BTO:0000562 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 TAO:0001158 UMLS:C0014136 VHOG:0000098 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 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) 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 brain http://langual.org 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 OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA PBA:3999 TAO:0000008 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 XAO:0000010 ZFA:0000008 galen:Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 http://www.langual.org/langual_thesaurus.asp?termid=C0199 uberon encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain UBERON:0000955 brain 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]. 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) (...) 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 UMLS:C0006104 BIRNLEX:796 UMLS:C0006104 ncithesaurus:Brain UMLS:C1269537 BIRNLEX:796 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 BIRNLEX:796 encephalon BTO:0000142 suprasegmental levels of nervous system NeuroNames:21 suprasegmental structures NeuroNames:21 the brain NeuroNames:21 The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus). The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743] BAMS:C BAMS:CTX BAMS:Cerebral_cortex BAMS:Cx BIRNLEX:1494 BM:Tel-Cx BTO:0000233 CALOHA:TS-0091 DHBA:10159 EFO:0000328 EHDAA2:0000234 EHDAA:5464 EMAPA:17544 EV:0100166 FMA:61830 GAID:629 HBA:4008 MA:0000185 MAT:0000108 MBA:688 MESH:A08.186.211.730.885.213 MIAA:0000108 NCIT:C12443 PBA:128011354 UMLS:C0007776 VHOG:0000722 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=39 cortex of cerebral hemisphere uberon brain cortex cortex cerebralis cortex cerebri cortical plate (CTXpl) cortical plate (areas) pallium of the brain UBERON:0000956 cerebral cortex FMA GO ISBN:0471888893 FMA MA The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. BIRNLEX:1494 The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] 2012-09-17 VHOG:0000722 VHOG DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969) UMLS:C0007776 BIRNLEX:1494 UMLS:C0007776 ncithesaurus:Cortex http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=39 BIRNLEX:1494 cortex of cerebral hemisphere BTO:0000233 FMA:61830 brain cortex BTO:0000233 cortex cerebralis NeuroNames:39 cortex cerebri cortical plate (CTXpl) NeuroNames:39 cortical plate (areas) NeuroNames:39 pallium of the brain BTO:0000233 Middle part of an organ, surrounded by the cortex. this class is used in a very general sense medullary FMA:61108 galen:Medulla medulla uberon UBERON:0000958 medulla of organ Middle part of an organ, surrounded by the cortex. medulla FMA:61108 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 UMLS:C0228815 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 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]. UMLS:C0228815 ncithesaurus:Cervical_Nerve cervical nerve FMA:5859 nervus cervicalis FMA:5859 FMA:TA 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 OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA TAO:0000640 UMLS:C0010031 VHOG:0000164 XAO:0000180 ZFA:0000640 cornea of camera-type eye uberon corneas tunica cornea UBERON:0000964 cornea XAO 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 Transparent part of camera-type eye that helps to refract 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:A09.371.509 MIAA:0000141 NCIT:C12743 OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000975 TAO:0000035 UMLS:C0023317 VHOG:0000169 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 lens of camera-type eye Transparent part of camera-type eye that helps to refract 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] 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) UMLS:C0023317 ncithesaurus:Crystalline_Lens camera-type eye lens GO:0002088 eye lens lens lens crystallina crystalline lens BTO:0000723 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 OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA TAO:0000152 UMLS:C0035298 UMLS:C1278894 VHOG:0000229 XAO:0000009 ZFA:0000152 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 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. 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) UMLS:C0035298 BIRNLEX:1153 UMLS:C0035298 ncithesaurus:Retina UMLS:C1278894 BIRNLEX:1153 retina of camera-type eye GO:0060041 Netzhaut BTO:0001175 retinas ZFA:0000152 An organ that detects light. eye 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) http://langual.org 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 OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA http://www.langual.org/langual_thesaurus.asp?termid=C0256 uberon light-detecting organ visual apparatus UBERON:0000970 eye An organ that detects light. visual apparatus EV:0100336 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 OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA UMLS:C0027530 galen:Neck uberon collum neck (volume) UBERON:0000974 neck An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. ISBN:9780674021839 UMLS:C0027530 ncithesaurus:Neck collum 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 OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA UMLS:C0032225 VHOG:0000394 wall of pleural sac uberon pleura pleural tissue UBERON:0000977 pleura 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 BGEE:AN ISBN:978-0030223693 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 UMLS:C0032225 ncithesaurus:Pleural_Tissue pleural tissue BTO:0001791 NCIT:C12469 Anatomical cluster 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 OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0003182 TAO:0000367 UMLS:C0022417 VHOG:0001276 VSAO:0000101 XAO:0000171 ZFA:0001596 galen:Joint uberon articular joint joints UBERON:0000982 skeletal joint Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. GO_REF:0000034 VSAO:0000101 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 UMLS:C0032639 UMLS:C1280999 VHOG:0001176 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 pons Varolii pons of Varolius uberon pons cerebri UBERON:0000988 pons 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 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 UMLS:C0032639 BIRNLEX:733 UMLS:C0032639 ncithesaurus:Pons_Varolii UMLS:C1280999 BIRNLEX:733 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 BIRNLEX:733 pons Varolii ncithesaurus:Pons_Varolii pons cerebri NeuroNames:547 A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination penile phallic Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca BTO:0000405 CALOHA:TS-0758 EFO:0000987 EHDAA2:0001433 EHDAA:9380 EMAPA:18682 EMAPA_RETIRED:18996 EV:0100107 FMA:9707 GAID:389 MA:0000408 MAT:0000186 MESH:D010413 MIAA:0000186 NCIT:C12409 OpenCyc:Mx4rvVjkCZwpEbGdrcN5Y29ycA UMLS:C0030851 VHOG:0000727 galen:Penis uberon penes phallus UBERON:0000989 penis Wikipedia Wikipedia EHDAA2 A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination ISBN:0-683-40008-8 MP:0005187 Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca WP UMLS:C0030851 ncithesaurus:Penis penes 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] 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 MIAA:0000305 NCIT:C12841 OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA TAO:0000632 UMLS:C1261210 VHOG:0000182 WBbt:0005747 XAO:0000142 ZFA:0000632 uberon Geschlechtsorgan animal reproductive system genital system genital tract genitalia organa genitalia reproductive tissue reproductive tract systemata genitalia UBERON:0000990 reproductive system Anatomical system that has as its parts the organs concerned with reproduction. 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) UMLS:C1261210 ncithesaurus:Reproductive_System Geschlechtsorgan BTO:0000081 animal reproductive system BTO:0000081 genitalia organa genitalia BTO:0000081 reproductive tissue BTO:0000081 systemata genitalia 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 OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA TAO:0000413 UMLS:C0018067 VHOG:0000397 WBbt:0005175 XAO:0003146 ZFA:0000413 gonada uberon gonads UBERON:0000991 gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). ISBN:0140512888 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) FMA xref is a 'general anatomical term' FMA 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 OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA TAO:0000403 UMLS:C0029939 VHOG:0000251 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 the gonad of a female organism which contains germ cells ISBN:0-683-40008-8 MP:0001126 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) 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 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 A tube or collection of tubes in an animal from the ovaries to the outside of the body. sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP] in birds divided into infundibulum, magnum, isthmus, uterus, and vagina AAO:0010533 BSA:0000083 BTO:0000980 EFO:0000974 EMAPA:18984 GAID:366 MAT:0000126 MESH:D010057 MIAA:0000126 NCIT:C77957 TAO:0000560 UMLS:C0029954 VHOG:0001136 XAO:0003052 ZFA:0000560 ovarian duct ovarian tube uterine tube uberon female reproductive tracts oviducts tuba uterina tuba uterinae tubular parts of female reproductive system UBERON:0000993 oviduct A tube or collection of tubes in an animal from the ovaries to the outside of the body. A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] 2012-09-17 VHOG:0001136 VHOG In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] 2012-09-17 VHOG:0001136 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688 UMLS:C0029954 ncithesaurus:Oviduct ovarian duct ovarian tube female reproductive tracts oviducts ZFA:0000560 tuba uterina BTO:0000980 tuba uterinae BTO:0000980 tubular parts of female reproductive system the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] uterine Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus] BTO:0001424 CALOHA:TS-1102 EFO:0000975 EMAPA:29915 EV:0100113 FMA:17558 GAID:172 MA:0000389 MAT:0000127 MESH:D014599 MIAA:0000127 NCIT:C12405 OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA UMLS:C0042149 VHOG:0001137 galen:Uterus uberon UBERON:0000995 uterus cjm the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth MGI:csmith MP:0001120 The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] 2012-09-17 VHOG:0001137 VHOG An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] 2012-09-17 VHOG:0001137 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678 UMLS:C0042149 ncithesaurus:Uterus A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] vaginal 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688 BTO:0000243 CALOHA:TS-1103 EFO:0000976 EMAPA:18986 EV:0100117 FMA:19949 GAID:381 MA:0000394 MAT:0000128 MESH:D014621 MIAA:0000128 NCIT:C12407 OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA UMLS:C0042232 VHOG:0001138 galen:Vagina uberon distal oviductal region distal portion of oviduct vaginae UBERON:0000996 vagina cjm FMA Wikipedia A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] 2012-11-29 FMA:19949 FMA The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001138 VHOG The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] 2012-09-17 VHOG:0001138 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 UMLS:C0042232 ncithesaurus:Vagina vaginae external genital organs of the female mammal[WP]. The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG] vulval BTO:0003101 CALOHA:TS-1168 EFO:0000978 EMAPA:36631 EV:0100118 FMA:20462 GAID:383 MA:0000395 MAT:0000169 MESH:D014844 MIAA:0000169 NCIT:C12408 OpenCyc:Mx4rvgAWeJwpEbGdrcN5Y29ycA UMLS:C0042993 VHOG:0001458 galen:Vulva female pudendum mammalian vulva puboperineal region pudendum femininum skin of female pudendum skin of vulva vulva uberon pudendum pudendum femininum pudendum muliebre UBERON:0000997 mammalian vulva external genital organs of the female mammal[WP]. The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG] 2012-09-17 VHOG:0001458 VHOG UMLS:C0042993 ncithesaurus:Vulva female pudendum BTO:0003101 female pudendum FMA:20462 puboperineal region FMA:20462 pudendum femininum FMA:20462 FMA:TA vulva MA:0000395 pudendum BTO:0003101 pudendum femininum pudendum muliebre BTO:0003101 Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG] (In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG] The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid. seminal gland AAO:0010788 BTO:0001234 CALOHA:TS-0919 EFO:0000986 EMAPA:19180 EV:0100106 FMA:19386 GAID:394 MA:0000410 MAT:0000171 MESH:D012669 MIAA:0000171 NCIT:C12787 OpenCyc:Mx4rwTtRpJwpEbGdrcN5Y29ycA UMLS:C0036628 VHOG:0001379 uberon glandula seminalis glandula vesiculosa gonecyst vas efferens vesicula seminalis vesiculae seminales vesicular gland vesicular glands vesicular seminalis vesiculæ seminales UBERON:0000998 seminal vesicle Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. BTO:0001234 Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG] 2012-09-17 VHOG:0001379 VHOG (In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG] 2012-09-17 VHOG:0001379 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556 UMLS:C0036628 ncithesaurus:Seminal_Vesicle glandula seminalis BTO:0001234 glandula vesiculosa BTO:0001234 vesicula seminalis vesicula seminalis BTO:0001234 vesiculae seminales vesiculae seminales vesicular gland vesicular glands vesicular seminalis vesiculæ seminales The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted]. BTO:0001580 CALOHA:TS-0211 EFO:0000985 EMAPA:19088 FMA:19325 GAID:388 MA:0003247 MAT:0000170 MESH:D004543 MIAA:0000170 NCIT:C32493 OpenCyc:Mx4rwOt7MJwpEbGdrcN5Y29ycA UMLS:C0013747 ductus ejaculatorii ductus ejaculatorius uberon ductus ejaculatorii UBERON:0000999 ejaculatory duct The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted]. UMLS:C0013747 ncithesaurus:Ejaculatory_Duct ductus ejaculatorii BTO:0001580 ductus ejaculatorius BTO:0001580 ductus ejaculatorii A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG] Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall. BTO:0001427 CALOHA:TS-1105 EFO:0000981 EMAPA:18681 EV:0100105 FMA:19234 GAID:404 MA:0000413 MESH:D014649 MIAA:0000129 NCIT:C12813 OpenCyc:Mx4rvjv7bpwpEbGdrcN5Y29ycA UMLS:C0042360 VHOG:0001135 galen:VasDeferens deferent duct ductus deferens vas deferen uberon sperm duct vasa deferentia UBERON:0001000 vas deferens FMA A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct ISBN:0-683-40008-8 MGI:pvb MP:0002769 The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG] 2012-09-17 VHOG:0001135 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670 Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall. WP UMLS:C0042360 ncithesaurus:Vas_Deferens ductus deferens 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 TAO:0000105 UMLS:C0014520 VHOG:0000077 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 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 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 OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA TAO:0000272 UMLS:C0035237 VHOG:0000202 XAO:0000117 ZFA:0000272 apparatus respiratorius respiratory system uberon Atmungssystem apparatus respiratorius systema respiratorium UBERON:0001004 respiratory system 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] 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 UMLS:C0035237 ncithesaurus:Respiratory_System Atmungssystem BTO:0000203 apparatus respiratorius BTO:0000203 systema respiratorium 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 uberon UBERON:0001005 respiratory airway An airway through which respiratory air passes in organisms. airway airways 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 TADS:0000170 TAO:0000339 WBbt:0005748 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 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 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.. 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 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 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 TADS:0000162 TAO:0000163 UMLS:C1508753 VHOG:0000723 WBbt:0005736 XAO:0000143 ZFA:0000163 galen:UrinaryTract excretory system renal system systema urinaria systema urinarium urinary system urinary tract uberon renal or urinary system renal/urinary system UBERON:0001008 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.. GO:0072001 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 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 UMLS:C1508753 ncithesaurus:Urinary_System renal system GO:0001977 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 FBbt:00005057 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA VHOG:0001248 uberon systema cardiovasculare UBERON:0001009 circulatory system 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]. 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 systema cardiovasculare 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 OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA TAO:0002134 UMLS:C0001527 VHOG:0001284 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 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) 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 OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA TAO:0000548 UMLS:C0026845 VSAO:0005038 WBbt:0005737 ZFA:0000548 muscle group muscles set musculature musculi set of muscles set of skeletal muscles uberon muscle system muscles musculature system UBERON:0001015 musculature 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. 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 OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA TAO:0000396 UMLS:C0027763 VHOG:0000402 WBbt:0005735 XAO:0000177 ZFA:0000396 neurological system nerve net uberon systema nervosum UBERON:0001016 nervous system 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 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 UMLS:C0027763 ncithesaurus:Nervous_System neurological system GO:0050877 nerve net systema nervosum 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 OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA TAO:0000012 UMLS:C0927232 VHOG:0000293 XAO:0000215 ZFA:0000012 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 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) UMLS:C0927232 BIRNLEX:1099 UMLS:C0927232 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 OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA TAO:0007009 UMLS:C0027740 UMLS:C0031119 VHOG:0000901 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 A portion of tissue which is a fasiculated group of axons.[TAO] 2012-08-14 TAO:0007009 TAO ZFIN:curator UMLS:C0027740 ncithesaurus:Nerve UMLS:C0031119 ncithesaurus:Peripheral_Nerve nerves TAO:0007009 peripheral nerve 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 OpenCyc:Mx4rv0GdXpwpEbGdrcN5Y29ycA nervus sensorius uberon afferent nerve UBERON:0001027 sensory nerve A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. UBERON:cjm nervus sensorius 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 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 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] 2012-09-17 VHOG:0001674 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) organa sensuum FMA:75259 FMA:TA sense organs FMA:75259 sense organs set FMA:75259 sensory systems TAO:0000282 organa sensuum set of sense organs FMA:75259 The sensory system for the sense of taste. The sensory system for the sense of taste[NLXANAT:090803]. The sensory system used for the sense of taste.[AAO] gustatory in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes AAO:0010577 BILA:0000143 EFO:0000830 FMA:7194 MA:0002446 MAT:0000275 MIAA:0000275 NLXANAT:090803 TAO:0001101 XAO:0003197 ZFA:0001101 gustatory organ system taste system uberon UBERON:0001033 gustatory system The sensory system for the sense of taste. NLXANAT:090803 The sensory system for the sense of taste[NLXANAT:090803]. NLXANAT:090803 The sensory system used for the sense of taste.[AAO] 2012-06-20 AAO:0010577 AAO AAO:EJS in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes ZFA A filament, mostly protein, that grows from follicles found in the dermis[WP]. TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales) this class defines an individual hair BTO:0001501 CALOHA:TS-0430 EFO:0000958 EMAPA:18769 EV:0100157 FMA:53667 GAID:71 MA:0000155 MAT:0000160 MESH:D006197 MIAA:0000160 NCIT:C32705 OpenCyc:Mx4rvVjOX5wpEbGdrcN5Y29ycA-Mp88EdaAAACgycbRww UMLS:C0018494 VHOG:0001191 hair uberon coat hair coat/ hair fur microchaeta quill setulae vibrissa whisker UBERON:0001037 strand of hair FMA FMA FMA A filament, mostly protein, that grows from follicles found in the dermis[WP]. UMLS:C0018494 ncithesaurus:Hair quill vibrissa whisker 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:A16.254.403.981 NCIT:C14128 UMLS:C0043425 VHOG:0000830 uberon saccus vitellinus vesicula umbilicalis UBERON:0001040 yolk sac 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]. One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] 2012-09-17 VHOG:0000830 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 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 UMLS:C0043425 ncithesaurus:Yolk_Sac saccus vitellinus vesicula umbilicalis 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 TGMA:0001014 UMLS:C0231051 VHOG:0000285 XAO:0000232 uberon praeenteron proenteron UBERON:0001041 foregut Anterior subdivision of a digestive tract. 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 UMLS:C0231051 ncithesaurus:Foregut praeenteron proenteron 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:A03.867 NCIT:C12425 OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA TAO:0000056 UMLS:C0031354 VHOG:0000462 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]. 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 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 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:A03.365 MIAA:0000048 NCIT:C12389 OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA TAO:0000204 UMLS:C0014876 VHOG:0000450 XAO:0000127 ZFA:0000204 galen:Esophagus gullet oesophagus uberon UBERON:0001043 esophagus 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] 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) 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 saliva-secreting exocrine glands of the oral cavity[GO] currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals. A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG] The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands BTO:0001203 CALOHA:TS-0892 EFO:0000859 EHDAA2:0001775 EHDAA:7987 EMAPA:17751 EV:0100059 FBbt:00005382 FMA:9597 GAID:937 MA:0000346 MAT:0000079 MESH:D012469 MIAA:0000079 NCIT:C12426 OpenCyc:Mx4rvVjl5ZwpEbGdrcN5Y29ycA UMLS:C0036098 VHOG:0000376 galen:SalivaryGland salivary gland uberon glandulae salivariae UBERON:0001044 saliva-secreting gland saliva-secreting exocrine glands of the oral cavity[GO] GO:0007431 currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals. 3 A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000376 VHOG In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG] 2012-09-17 VHOG:0000376 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211 UMLS:C0036098 ncithesaurus:Salivary_Gland salivary gland MA:0000346 glandulae salivariae 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 TGMA:0001036 UMLS:C0231052 VHOG:0000290 XAO:0000103 uberon mesenteron UBERON:0001045 midgut 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 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 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 UMLS:C0231052 ncithesaurus:Midgut mesenteron 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 TGMA:0001020 UMLS:C0231053 VHOG:0000459 XAO:0000104 uberon metenteron UBERON:0001046 hindgut Wikipedia The caudalmost subdivision of a digestive tract. 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 in FMA this class has no children. In MA it has a single child hindgut epithelium FMA UMLS:C0231053 ncithesaurus:Hindgut metenteron 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 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 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 MIAA:0000069 NCIT:C34226 TAO:0001135 UMLS:C0231024 VHOG:0000307 XAO:0003204 ZFA:0001135 uberon neural primordium presumptive central nervous system tubus neuralis UBERON:0001049 neural tube 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]. 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 (...) 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 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 UMLS:C0231024 ncithesaurus:Neural_Tube tubus neuralis Bottom part of the pharynx that connects to the esophagus. The inferior portion of the pharynx, between the epiglottis and the larynx. [TFD][VHOG] hypopharyngeal BTO:0001740 CALOHA:TS-2020 EFO:0001388 EHDAA2:0004574 EV:0100068 FMA:54880 GAID:338 MA:0001796 MESH:A03.867.490 NCIT:C12246 OpenCyc:Mx4rvq5O0JwpEbGdrcN5Y29ycA UMLS:C0020629 VHOG:0000445 laryngeal pharynx laryngopharynx uberon pars laryngea pharyngis UBERON:0001051 hypopharynx Bottom part of the pharynx that connects to the esophagus. The inferior portion of the pharynx, between the epiglottis and the larynx. [TFD][VHOG] 2012-09-17 VHOG:0000445 VHOG UMLS:C0020629 ncithesaurus:Hypopharynx laryngeal pharynx FMA:54877 laryngopharynx FMA:54877 pars laryngea pharyngis pars laryngea pharyngis BTO:0001740 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:A03.492.411.495.767 MIAA:0000050 NCIT:C12390 OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA UMLS:C0034896 VHOG:0001751 XAO:0000238 galen:Rectum terminal portion of intestine uberon intestinum rectum rectal sac terminal portion of large intestine UBERON:0001052 rectum 4 cjm MA EHDAA2 ISBN:0073040584 the terminal portion of the intestinal tube, terminating with the anus ISBN:0-683-40008-8 MP:0000492 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 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 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon 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. FMA:62955 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. in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue 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 UMLS:C0030288 VHOG:0000256 chief pancreatic duct duct of Wirsung main pancreatic duct uberon canal of Wirsung ductus pancreatis ventralis hepaticopancreatic duct UBERON:0001064 ventral pancreatic duct 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. 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) 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 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]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region EMAPA:36392 FMA:10462 FMA:22985 MA:0000498 back skin back zone of skin skin, dorsal region zone of skin of back uberon UBERON:0001068 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 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 OpenCyc:Mx4rwVJkPZwpEbGdrcN5Y29ycA UMLS:C0007275 VHOG:0000265 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 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 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 UMLS:C0226271 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. EMAPA:37117 MA:th UMLS:C0226271 ncithesaurus:Superficial_Cervical_Artery superficial branch 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 UMLS:C0042458 VHOG:0001194 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 lexical 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]. 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 UMLS:C0042458 ncithesaurus:Inferior_Vena_Cava inferior caval vein inferior vena cava posterior vena cava caudal vena cava VHOG:0001194 vena cava inferior vena cava inferior BTO:0002682 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 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 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 TAO:0002220 UMLS:C0225972 VHOG:0000556 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. 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 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 cavitas pericardiaca Endocardium that is part of the cardiac ventricle. EMAPA:32747 FMA:12148 MA:0000079 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 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 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 TAO:0005061 VHOG:0000604 ZFA:0005061 ventricle myocardium ventricular myocardium uberon ventricle cardiac muscle UBERON:0001083 myocardium of ventricle 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 ventricle cardiac muscle VHOG:0000604 A zone of skin that is part of a head [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region FMA:12166 FMA:24756 MA:0000582 NCIT:C52757 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 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]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region EMAPA:37278 FMA:12167 FMA:23093 MA:0000517 NCIT:C12295 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 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 ncithesaurus:Pleural_Fluid uberon UBERON:0001087 pleural fluid Transudate contained in the pleural cavity. FMA:12273 Excretion that is the output of a kidney kidney excreta from some taxa (e.g. in aves) may not be liquid BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 NCIT:C13283 OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA UMLS:C0042036 galen:Urine uberon UBERON:0001088 urine Excretion that is the output of a kidney UMLS:C0042036 ncithesaurus:Urine 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 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. 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 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 OpenCyc:Mx4rv9IEzZwpEbGdrcN5Y29ycA TAO:0000326 UMLS:C0223616 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). 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 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 OpenCyc:Mx4rvVivz5wpEbGdrcN5Y29ycA UMLS:C0011980 VHOG:0000713 diaphragm muscle diaphragm of thorax thoracic diaphragm uberon midriff phren UBERON:0001103 diaphragm definitional A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control MP:0002279 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 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 UMLS:C0447541 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. 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 TAO:0005173 UMLS:C0227481 VHOG:0001424 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 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] 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 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 TAO:0005172 UMLS:C0227486 VHOG:0001423 ZFA:0005172 left liver lobe liver left lobe lobus hepaticus sinister uberon left hepatic lobe lobus hepatis sinister UBERON:0001115 left lobe of liver 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] 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 A lobe of tissue that is part of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] EHDAA2:0002032 EMAPA:18196 FMA:13367 MA:0000131 NCIT:C33784 UMLS:C0447647 VHOG:0000732 lobus (glandula thyroidea) lobus glandulae thyroideae thyroid gland lobe thyroid lobe uberon lobuli glandulae thyroideae UBERON:0001118 The lobes of the thyroid gland are conical in shape, the apex of each being directed upward and lateralward as far as the junction of the middle with the lower third of the thyroid cartilage; the base looks downward, and is on a level with the fifth or sixth tracheal ring. Each lobe is about 5 cm. long; its greatest width is about 3 cm. , and its thickness about 2 cm. The lateral or superficial surface is convex, and covered by the skin, the superficial and deep fasciæ, the Sternocleidomastoideus, the superior belly of the Omohyoideus, the Sternohyoideus and Sternothyreoideus, and beneath the last muscle by the pretracheal layer of the deep fascia, which forms a capsule for the gland. The deep or medial surface is moulded over the underlying structures, viz. , the thyroid and cricoid cartilages, the trachea, the Constrictor pharyngis inferior and posterior part of the Cricothyreoideus, the esophagus (particularly on the left side of the neck), the superior and inferior thyroid arteries, and the recurrent nerves. The anterior border is thin, and inclines obliquely from above downward toward the middle line of the neck, while the posterior border is thick and overlaps the common carotid artery, and, as a rule, the parathyroids lobe of thyroid gland FMA-abduced-lr A lobe of tissue that is part of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000732 VHOG UMLS:C0447647 ncithesaurus:Thyroid_Gland_Lobe lobus glandulae thyroideae FMA:13367 FMA:TA lobuli glandulae thyroideae A lobe of thyroid gland that is in the right side of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001759 EMAPA:18198 FMA:13368 MA:0000729 NCIT:C33491 UMLS:C0229581 VHOG:0000733 lobus dexter (glandula thyroidea) right thyroid lobe thyroid gland right lobe uberon UBERON:0001119 right lobe of thyroid gland A lobe of thyroid gland that is in the right side of a thyroid gland. OBOL:automatic Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000733 VHOG UMLS:C0229581 ncithesaurus:Right_Thyroid_Gland_Lobe A lobe of thyroid gland that is in the left side of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000965 EMAPA:18197 FMA:13369 MA:0000728 NCIT:C32973 UMLS:C0229582 VHOG:0000734 left thyroid lobe lobus sinister (glandula thyroidea) thyroid gland left lobe uberon UBERON:0001120 left lobe of thyroid gland A lobe of thyroid gland that is in the left side of a thyroid gland. OBOL:automatic Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000734 VHOG UMLS:C0229582 ncithesaurus:Left_Thyroid_Gland_Lobe 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 OpenCyc:Mx4rv2j-CpwpEbGdrcN5Y29ycA OpenCyc:Mx4rv6GF55wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkFEpwpEbGdrcN5Y29ycA TAO:0001559 UMLS:C0037949 UMLS:C1519455 VHOG:0001142 VSAO:0000185 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 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 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 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 OpenCyc:Mx4rv_EvQZwpEbGdrcN5Y29ycA vertebra neural canal uberon foramen vertebrale UBERON:0001131 vertebral foramen 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] 2012-06-20 AAO:0000729 AAO AAO:LAP EMAPA:37803 MA:th foramen vertebrale 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 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 ZFA 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 UMLS:C0242692 uberon skeletal muscle system somatic muscle UBERON:0001134 skeletal muscle tissue Muscle tissue that consists primarily of skeletal muscle fibers. 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) 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 FBbt:00003525 FMA:14070 GAID:167 MA:0000166 MAT:0000303 MESH:D009130 MIAA:0000303 NCIT:C12437 OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA TAO:0005274 UMLS:C1267092 VHOG:0001246 WBbt:0005781 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 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 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) UMLS:C1267092 ncithesaurus:Smooth_Muscle_Tissue textus muscularis nonstriatus FMA:14070 FMA:TA visceral muscle visceral muscle tissue textus muscularis levis; textus muscularis nonstriatus 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 UMLS:C0086610 uberon UBERON:0001136 mesothelium 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 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:A01.176 NCIT:C13062 OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA UMLS:C0004600 galen:Back back back of body proper dorsal part of organism uberon UBERON:0001137 dorsum 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 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 OpenCyc:Mx4rwFjmM5wpEbGdrcN5Y29ycA UMLS:C0226742 VHOG:0000552 uberon upper mesenteric vein vena mesenterica superior UBERON:0001138 superior mesenteric 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]. UMLS:C0226742 ncithesaurus:Superior_Mesenteric_Vein upper mesenteric vein BTO:0002783 vena mesenterica superior Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. in EHDAA2, the renal vein is part of the kidney BTO:0002681 EHDAA2:0001602 EHDAA:8722 EMAPA:28376 FMA:14334 GAID:544 MA:0002210 MESH:D012082 NCIT:C33462 OpenCyc:Mx4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0035092 galen:RenalVein kidney vein renal venous tree vein of kidney uberon venae renales UBERON:0001140 renal vein Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. ISBN:0-683-40008-8 MGI:csmith MP:0011323 The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. in EHDAA2, the renal vein is part of the kidney EHDAA2 UMLS:C0035092 ncithesaurus:Renal_Vein kidney vein OBOL:automatic vein of kidney OBOL:automatic venae renales A renal vein that drains the right kidney A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]. EMAPA:37381 FMA:14335 MA:0002212 NCIT:C52695 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0508000 uberon UBERON:0001141 right renal vein A renal vein that drains the right kidney A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]. ncithesaurus:Right_Renal_Vein EMAPA:37381 MA:th UMLS:C0508000 ncithesaurus:Right_Renal_Vein A renal vein that drains the left kidney A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]. EMAPA:37166 FMA:14336 MA:0002211 NCIT:C52693 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0508001 uberon UBERON:0001142 left renal vein A renal vein that drains the left kidney A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]. ncithesaurus:Left_Renal_Vein EMAPA:37166 MA:th UMLS:C0508001 ncithesaurus:Left_Renal_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 OpenCyc:Mx4rv5GivJwpEbGdrcN5Y29ycA TAO:0000670 UMLS:C0019155 XAO:0000387 ZFA:0000670 galen:HepaticVein liver vein vein of liver vena hepatica uberon hepatic veins venae hepaticae UBERON:0001143 hepatic vein FMA-abduced-lr Vein that carries blood away from the liver[ZFA]. ZFA:0000670 UMLS:C0019155 ncithesaurus:Hepatic_Vein liver vein OBOL:automatic vein of liver OBOL:automatic vena hepatica hepatic veins venae hepaticae A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis. TODO - check testicular vs spermatic vein (MA:0002218) In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel BTO:0002678 EMAPA:18647 FMA:14344 MA:0002218 MA:0002234 NCIT:C53050 OpenCyc:Mx4rv1WIHpwpEbGdrcN5Y29ycA UMLS:C0226718 male gonadal vein spermatic vein testicle vein testicular venous tree vein of testicle uberon vena tesicularis vena testicularis dextra vena testicularis sinistra venae spermaticae UBERON:0001144 testicular vein A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis. UMLS:C0226718 ncithesaurus:Spermatic_Vein male gonadal vein spermatic vein testicle vein OBOL:automatic testicular venous tree vein of testicle OBOL:automatic vena tesicularis BTO:0002678 vena testicularis dextra vena testicularis sinistra venae spermaticae 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 OpenCyc:Mx4rvrST5ZwpEbGdrcN5Y29ycA UMLS:C0226720 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 A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. 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 vena ovarica sinistra A vein that drains the adrenal gland. EHDAA2:0001966 EHDAA:8731 FMA:14348 MA:0002081 MA:0002229 NCIT:C53129 UMLS:C0226717 uberon adrenal vein UBERON:0001146 suprarenal vein A vein that drains the adrenal gland. UMLS:C0226717 ncithesaurus:Suprarenal_Vein adrenal vein MA:0002081 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:A03.159.183.419 NCIT:C32421 OpenCyc:Mx4rveBeC5wpEbGdrcN5Y29ycA TAO:0005166 UMLS:C0010672 VHOG:0000213 ZFA:0005166 galen:CysticDuct uberon ductus cysticus UBERON:0001152 cystic duct 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 UMLS:C0010672 ncithesaurus:Cystic_Duct ductus cysticus A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. caecal A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. BTO:0000166 CALOHA:TS-0122 EFO:0000850 EHDAA2:0000206 EHDAA:3913 EMAPA:35197 EV:0100397 FMA:14541 GAID:307 MA:0000334 MESH:A03.492.411.495.209 MIAA:0000288 NCIT:C12381 OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA UMLS:C0007531 VHOG:0001559 galen:Cecum caecum cecum intestinum crassum caecum caeca ceca uberon blind intestine blindgut intestinum caecum intestinum crassum cecum UBERON:0001153 Kardong: in some herbivorous lizards, a cecum is present between small and large intestines caecum EHDAA2 Wikipedia Wikipedia A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. WP UMLS:C0007531 ncithesaurus:Cecum caecum VHOG:0001559 cecum FMA:14541 caeca NCBITaxon:8782 ceca NCBITaxon:8782 blind intestine BTO:0000166 blindgut BTO:0000166 intestinum caecum BTO:0000166 intestinum crassum cecum BTO:0000166 A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]. A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG] appendiceal vermix BTO:0000084 CALOHA:TS-1267 EFO:0000849 EHDAA2:0000588 EMAPA:35140 EV:0100076 EV:0100080 FMA:14542 GAID:308 MA:0001540 MAT:0000287 MESH:A03.492.411.495.209.290 MIAA:0000287 NCIT:C12380 OpenCyc:Mx4rvVjGgJwpEbGdrcN5Y29ycA UMLS:C0003617 VHOG:0001306 galen:AppendixVermiformis appendix appendix vermiformis caecal appendix cecal appendix uberon apex of caecum apex of cecum appendix vermiformis UBERON:0001154 vermiform appendix MA Wikipedia A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]. FMA:14542 A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG] 2012-09-17 VHOG:0001306 VHOG DOI:10.1111/j.1420-9101.2009.01809.x Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009) UMLS:C0003617 ncithesaurus:Vermiform_Appendix appendix vermiformis FMA:14542 FMA:TA apex of caecum EMAPA:35140 apex of cecum VHOG:0001306 appendix vermiformis Last portion of the large intestine before it becomes the rectum. 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:A03.492.411.495.356 NCIT:C12382 OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA TAO:0000706 UMLS:C0009368 VHOG:0000648 XAO:0000243 ZFA:0000706 galen:Colon large bowel posterior intestine uberon hindgut UBERON:0001155 colon 3 cjm FMA Last portion of the large intestine before it becomes the rectum. ZFIN:curator 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 UMLS:C0009368 ncithesaurus:Colon Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified] in MA, this is a subclass of colon BTO:0000270 CALOHA:TS-0057 EFO:0000843 EMAPA:35151 FMA:14545 MA:0001541 MAT:0000311 MIAA:0000311 NCIT:C12265 OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA UMLS:C0227375 galen:AscendingColon colon ascendens uberon spiral colon UBERON:0001156 ascending colon FMA Wikipedia Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified] FMA:14545 in MA, this is a subclass of colon MA UMLS:C0227375 ncithesaurus:Ascending_Colon colon ascendens spiral colon The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. BTO:0000272 CALOHA:TS-2052 EFO:0000844 EMAPA:35880 FMA:14546 MA:0001543 MAT:0000312 MIAA:0000312 NCIT:C12385 OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA UMLS:C0227386 galen:TransverseColon colon transversum uberon UBERON:0001157 transverse colon FMA Wikipedia The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. BTO:0000272 UMLS:C0227386 ncithesaurus:Transverse_Colon colon transversum The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. BTO:0000641 CALOHA:TS-2010 EFO:0000845 EMAPA:35285 FMA:14547 MA:0001542 MAT:0000313 MIAA:0000313 NCIT:C12268 OpenCyc:Mx4rwHsNhpwpEbGdrcN5Y29ycA UMLS:C0227389 galen:DescendingColon colon descendens uberon UBERON:0001158 descending colon FMA Wikipedia The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. BTO:0000641 UMLS:C0227389 ncithesaurus:Descending_Colon colon descendens 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:A03.492.411.495.356.668 MIAA:0000314 NCIT:C12384 NCIT:C33550 OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA UMLS:C0227391 UMLS:C0682612 galen:SigmoidColon uberon colon sigmoideum pelvic colon sigmoid colon sigmoid flexure UBERON:0001159 sigmoid colon 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. UMLS:C0227391 ncithesaurus:Sigmoid_Colon UMLS:C0682612 ncithesaurus:Sigmoid_Flexure colon sigmoideum 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 UMLS:C0227230 galen:GastricCorpus corpus gastricum (ventriculare) gastric body stomach body uberon corpus gastricum corpus ventriculare corpus ventriculi gastric corpus UBERON:0001161 body of stomach 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 UMLS:C0227230 ncithesaurus:Body_of_Stomach corpus gastricum corpus gastricum BTO:0000505 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:A03.492.766.716 NCIT:C12259 UMLS:C0034193 galen:PyloricAntrum antrum of stomach stomach pyloric antrum uberon antrum of Willis antrum pylori antrum pyloricum gastric antrum stomach antrum UBERON:0001165 pyloric antrum 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 antrum pyloricum BTO:0001732 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:A03.492.766.799 NCIT:C12260 UMLS:C0034196 VHOG:0000420 galen:Pylorus pars pylorica pars pylorica gastricae pyloric part of stomach pyloric region stomach pyloric region uberon valvula pylori UBERON:0001166 pylorus 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 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 UMLS:C0034196 ncithesaurus:Pylorus pars pylorica pars pylorica gastricae FMA:14581 FMA:TA stomach pyloric region EHDAA2:0001580 valvula pylori 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 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 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]. EMAPA:37745 MA:th mesentery (proper) 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 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. 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 UMLS:C0005423 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. Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] 2012-06-20 AAO:0011020 AAO UBERON:0001173 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 TAO:0005165 UMLS:C0009437 VHOG:0000214 ZFA:0005165 galen:CommonBileDuct ductus choledochus (biliaris) uberon ductus choledochus UBERON:0001174 common bile duct 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 UMLS:C0009437 ncithesaurus:Common_Bile_Duct ductus choledochus 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 UMLS:C0019149 VHOG:0000220 uberon ductus hepaticus communis hepatic duct UBERON:0001175 common hepatic duct 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]. 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 UMLS:C0019149 ncithesaurus:Common_Hepatic_Duct ductus hepaticus communis 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 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. 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 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 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. 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 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 TAO:0005132 VHOG:0001528 ZFA:0005132 visceral serous membrane of peritoneum uberon UBERON:0001178 visceral peritoneum The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. 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:A01.047.025.600.678 NCIT:C12769 UMLS:C1704247 VHOG:0000852 uberon cavitas peritonealis saccus serosus peritonei UBERON:0001179 peritoneal cavity Wikipedia 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] 2012-09-17 VHOG:0000852 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] 2012-09-17 VHOG:0000852 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 UMLS:C1704247 ncithesaurus:Peritoneal_Cavity cavitas peritonealis cavitas peritonealis BTO:0001782 saccus serosus peritonei Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted]. IMA BTO:0002302 EHDAA2:0000817 EHDAA:4345 EMAPA:18618 FMA:14750 GAID:501 MA:0002004 MESH:D017537 NCIT:C32780 OpenCyc:Mx4rv-t-S5wpEbGdrcN5Y29ycA UMLS:C0162860 VHOG:0001116 galen:InferiorMesentericArtery inferior mesenteric arterial tree uberon arteria mesenterica inferior UBERON:0001183 inferior mesenteric artery Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted]. IMA UMLS:C0162860 ncithesaurus:Inferior_Mesenteric_Artery arteria mesenterica inferior arteria mesenterica inferior BTO:0002302 One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability. Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] AAO:0010223 BTO:0001165 EFO:0002552 EHDAA2:0004100 EHDAA:5321 EHDAA:8594 EMAPA:28373 FMA:14751 GAID:507 MA:0002035 MESH:D012077 NCIT:C12778 OpenCyc:Mx4rveOFHpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001600 TAO:0000420 UMLS:C0035065 ZFA:0000420 galen:RenalArtery renal arterial tree uberon arteria renalis renal arteries UBERON:0001184 renal artery One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. ISBN:0073040584 Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] 2012-06-20 AAO:0010223 AAO AAO:BJB The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] Wikipedia UMLS:C0035065 ncithesaurus:Renal_Artery arteria renalis renal arteries Renal artery that supplies the right kidney EMAPA:37380 FMA:14752 MA:0002037 NCIT:C52740 OpenCyc:Mx4rtW8I0KgEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rveOFHpwpEbGdrcN5Y29ycA UMLS:C0226332 right renal arterial tree uberon UBERON:0001185 The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP] right renal artery Renal artery that supplies the right kidney EMAPA:37380 MA:th UMLS:C0226332 ncithesaurus:Right_Renal_Artery Renal artery that supplies the left kidney EMAPA:37098 FMA:14753 MA:0002036 NCIT:C52741 OpenCyc:Mx4rtW8I0agEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rveOFHpwpEbGdrcN5Y29ycA UMLS:C0226333 left renal arterial tree uberon UBERON:0001186 The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP] left renal artery Renal artery that supplies the left kidney EMAPA:37098 MA:th UMLS:C0226333 ncithesaurus:Left_Renal_Artery One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad. EMAPA:18621 FMA:14758 MA:0002063 testicular arterial tree uberon arteria testicularis internal spermatic internal spermatic arteries internal spermatic artery internal spermatic vessels spermatic arteries spermatic artery spermatic vessels testicular arteries UBERON:0001187 testicular artery One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad. arteria testicularis internal spermatic internal spermatic arteries internal spermatic artery internal spermatic vessels spermatic arteries spermatic artery spermatic vessels testicular arteries A testicular artery that supplies a right testicle. EMAPA:37382 FMA:14759 MA:0002042 NCIT:C52738 UMLS:C0734076 right spermatic artery trunk of right testicular arterial tree uberon UBERON:0001188 right testicular artery A testicular artery that supplies a right testicle. OBOL:automatic EMAPA:37382 MA:th UMLS:C0734076 ncithesaurus:Right_Spermatic_Artery A testicular artery that supplies a left testicle. EMAPA:37099 FMA:14760 MA:0002041 NCIT:C52739 UMLS:C0734077 left spermatic artery trunk of left testicular arterial tree uberon UBERON:0001189 left testicular artery A testicular artery that supplies a left testicle. OBOL:automatic EMAPA:37099 MA:th UMLS:C0734077 ncithesaurus:Left_Spermatic_Artery 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 OpenCyc:Mx4rwOa9PZwpEbGdrcN5Y29ycA UMLS:C0226411 ovarian arterial tree uberon arteria ovarica UBERON:0001190 ovarian artery 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]. UMLS:C0226411 ncithesaurus:Ovarian_Artery arteria ovarica 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 OpenCyc:Mx4rvzKtFpwpEbGdrcN5Y29ycA TAO:0005161 UMLS:C0019145 ZFA:0005161 galen:HepaticArtery arteria hepatica propria uberon arteria hepatica UBERON:0001193 hepatic artery An artery that supplies the liver. 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 OpenCyc:Mx4rv0cb2ZwpEbGdrcN5Y29ycA UMLS:C0037996 galen:SplenicArtery arteria splenica lienal artery uberon arteria lienalis UBERON:0001194 splenic artery An artery that supplies the spleen. UMLS:C0037996 ncithesaurus:Splenic_Artery arteria splenica lienal artery MA:0001991 arteria lienalis 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:A03.492.766.440 NCIT:C32656 OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA UMLS:C0017136 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 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]. 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 tunica mucosa gastris BTO:0001308 the fibrous connective tissue layer beneath the stomach mucosa BTO:0002110 EMAPA:35825 FMA:14908 MA:0002685 NCIT:C32663 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 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 OpenCyc:Mx4rvly2ZZwpEbGdrcN5Y29ycA 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]. (...) 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 UMLS:C0227238 ncithesaurus:Pyloric_Sphincter pyloric valve 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 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 UMLS:C0227268 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. 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 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:A03.492.411.620.270.322 NCIT:C13010 UMLS:C0006323 Brunner's gland gland of Brunner submucosal gland of duodenum uberon glandula duodenales glandula duodenales Brunneri UBERON:0001212 duodenal gland compound tubular FMA, modified 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]. 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 TAO:0005125 UMLS:C1519988 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 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 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 OpenCyc:Mx4rvcV53ZwpEbGdrcN5Y29ycA UMLS:C0226754 VHOG:0001118 uberon lower mesenteric vein vena mesenterica inferior UBERON:0001215 inferior mesenteric vein 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]. UMLS:C0226754 ncithesaurus:Inferior_Mesenteric_Vein lower mesenteric vein BTO:0002782 vena mesenterica inferior The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted]. EMAPA:37174 FMA:15406 MA:0002181 OpenCyc:Mx4rvywYIpwpEbGdrcN5Y29ycA vena colica media (intermedia) uberon vena colica media UBERON:0001218 middle colic vein The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted]. EMAPA:37174 MA:th vena colica media An ureter that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37373 FMA:15571 MA:0001685 NCIT:C49327 UMLS:C0227682 uberon UBERON:0001222 right ureter An ureter that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37373 MA:th UMLS:C0227682 ncithesaurus:Right_Ureter An ureter that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37372 FMA:15572 MA:0001684 NCIT:C49324 UMLS:C0227683 uberon UBERON:0001223 left ureter An ureter that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37372 MA:th UMLS:C0227683 ncithesaurus:Left_Ureter A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. CALOHA:TS-2230 EMAPA:17948 FMA:15575 GAID:426 MA:0000374 MESH:D007682 NCIT:C12887 UMLS:C0227666 galen:RenalPelvis kidney pelvis pelvis of ureter uberon p. renallis pyelum UBERON:0001224 In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter renal pelvis MA FMA A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. MP:0004194 UMLS:C0227666 ncithesaurus:Renal_Pelvis p. renallis pyelum MP:0004194 Outer cortical portion of the kidney, between the renal capsule and the renal medulla. In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP] BTO:0001166 CALOHA:TS-0503 EMAPA:17952 FMA:15581 GAID:424 MA:0000372 MESH:D007672 NCIT:C12739 UMLS:C0022655 galen:CortexOfKidney cortex renalis kidney cortex renal cortex uberon UBERON:0001225 cortex of kidney FMA Outer cortical portion of the kidney, between the renal capsule and the renal medulla. UMLS:C0022655 ncithesaurus:Renal_Cortex cortex renalis FMA:15581 FMA:TA An epithelial tube that is part of the nephron, the functional part of the kidney. note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA UBERON:0004210 renal tubule BTO:0000343 CALOHA:TS-1262 EFO:0003666 EMAPA:27782 EV:0100387 FMA:15627 GAID:433 MA:0000377 MESH:D007684 NCIT:C49274 TAO:0001287 UMLS:C0022674 ZFA:0001287 kidney tubule tubulus renalis uberon uriniferous tubule UBERON:0001231 nephron tubule GO MA ZFA GO checkme An epithelial tube that is part of the nephron, the functional part of the kidney. GO:0072078 note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA MA UMLS:C0022674 ncithesaurus:Renal_Tubule kidney tubule GAID:433 uriniferous tubule MA:0000377 The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient Renal duct that collects the output from renal tubules.[TAO] in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron BTO:0000761 CALOHA:TS-0860 EMAPA:28407 EV:0100391 FMA:15628 GAID:434 MA:0000371 MESH:D007685 TAO:0005294 ZFA:0005294 collecting duct kidney collecting duct renal collecting tubule tubulus renalis arcuatus tubulus renalis colligens uberon arcuate renal tubule collecting duct system collecting tubule junctional tube kidney collecting tubule ureteric tree UBERON:0001232 collecting duct of renal tubule checkme GO The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient GO:0072044 Renal duct that collects the output from renal tubules.[TAO] 2012-08-14 TAO:0005294 TAO ZFIN:curator in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron FMA collecting duct GO:0072044 renal collecting tubule FMA:15628 tubulus renalis arcuatus arcuate renal tubule collecting duct system BTO:0000761 junctional tube ureteric tree EMAPA:28407 An adrenal gland that is in the right side of the abdomen https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, the right adrenal gland is triangular shaped EMAPA:37357 FMA:15629 MA:0000719 NCIT:C49325 UMLS:C0229559 glandula suprarenalis dexter right suprarenal gland uberon UBERON:0001233 right adrenal gland An adrenal gland that is in the right side of the abdomen OBOL:automatic In humans, the right adrenal gland is triangular shaped WP EMAPA:37357 MA:th UMLS:C0229559 ncithesaurus:Right_Adrenal_Gland glandula suprarenalis dexter An adrenal gland that is in the left side of the abdomen https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, the left adrenal gland is semilunar shaped EMAPA:37356 FMA:15630 MA:0000718 NCIT:C49322 UMLS:C0229560 glandula suprarenalis sinister left suprarenal gland uberon UBERON:0001234 left adrenal gland An adrenal gland that is in the left side of the abdomen OBOL:automatic In humans, the left adrenal gland is semilunar shaped WP EMAPA:37356 MA:th UMLS:C0229560 ncithesaurus:Left_Adrenal_Gland glandula suprarenalis sinister the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO AAO:0011009 BTO:0000045 CALOHA:TS-0015 EFO:0000237 EMAPA:18427 EV:0100136 FMA:15632 GAID:447 MA:0000118 MAT:0000494 MESH:D000302 NCIT:C12396 UMLS:C0001613 VHOG:0001481 XAO:0000165 adrenal gland cortex cortex (glandula suprarenalis) cortex of adrenal gland cortex of suprarenal gland suprarenal cortex uberon cortex glandulae suprarenalis suprarenal UBERON:0001235 adrenal cortex the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone ISBN:0-683-40008-8 MGI:llw2 MP:0008288 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001481 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 UMLS:C0001613 ncithesaurus:Adrenal_Cortex cortex glandulae suprarenalis cortex glandulae suprarenalis BTO:0000045 the inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] AAO:0011010 BTO:0000049 CALOHA:TS-0018 EFO:0000852 EMAPA:18428 EV:0100137 FMA:15633 GAID:451 MA:0000119 MAT:0000495 MESH:D019439 NCIT:C12397 UMLS:C0001629 VHOG:0001378 XAO:0000166 adrenal gland medulla medulla (glandula suprarenalis) medulla glandulae suprarenalis medulla of adrenal gland medulla of suprarenal gland suprarenal medulla uberon adrenal central medulla chromaffin cells medulla of glandula suprarenalis UBERON:0001236 adrenal medulla Wikipedia the inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine MESH:A06.407.071.265 MGI:llw2 MP:0008289 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001378 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 UMLS:C0001629 ncithesaurus:Adrenal_Medulla medulla glandulae suprarenalis FMA:15633 FMA:TA medulla of adrenal gland OBOL:automatic medulla of glandula suprarenalis BTO:0000049 Lamina propria that is part_of the small intestine. EMAPA:35779 FMA:15651 MA:0001554 NCIT:C49297 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:A03.492.411.369 NCIT:C49241 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:00003148 FMA:15711 GAID:312 MA:0000331 MESH:A03.492.411.495.767.288 NCIT:C43362 OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA TADS:0000066 TGMA:0001279 UMLS:C0003461 WBbt:0005364 galen:Anus anal opening anal orifice opening of terminal part of digestive tract uberon proctodeum UBERON:0001245 anus 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. ZFIN:curator 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 UMLS:C0227515 interlobular ductule uberon UBERON:0001246 interlobular bile duct MA-part-of FMA 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 adventitia that is part of a ureter. EMAPA:28114 FMA:15892 MA:0002652 external adventitia of ureter tunica adventitia (ureter) tunica adventitia ureteris ureter adventitia ureteral adventitia uberon UBERON:0001252 adventitia of ureter An adventitia that is part of a ureter. OBOL:automatic tunica adventitia (ureter) FMA:15892 FMA:TA tunica adventitia ureteris FMA:15892 FMA:TA A lamina propria that is part of a ureter [Automatically generated definition]. EMAPA:28841 FMA:15896 MA:0002653 lamina propria mucosa of ureter lamina propria mucosae of ureter ureter lamina propria ureter lamina propria mucosa ureter lamina propria mucosae uberon UBERON:0001253 lamina propria of ureter true A lamina propria that is part of a ureter [Automatically generated definition]. OBOL:automatic lamina propria mucosa of ureter OBOL:automatic lamina propria mucosae of ureter OBOL:automatic ureter lamina propria mucosa OBOL:automatic ureter lamina propria mucosae OBOL:automatic distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] vesical The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] bladder AAO:0000623 BTO:0001418 CALOHA:TS-1090 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 MA:0000380 MAT:0000122 MESH:A05.810.161 MIAA:0000122 NCIT:C12414 OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA UMLS:C0005682 VHOG:0000740 XAO:0000154 galen:UrinaryBladder vesica urinaria uberon urocyst vesica UBERON:0001255 urinary bladder BTO FMA upper part of UG sinus distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. MGI:anna A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000740 VHOG Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] 2012-06-20 AAO:0000623 AAO AAO:BJB In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] 2012-09-17 VHOG:0000740 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78 bladder EHDAA2:0000174 UMLS:C0005682 ncithesaurus:Bladder vesica urinaria urocyst vesica BTO:0001418 An anatomical wall that lines the insider of a urinary bladder. BTO:0001462 EMAPA:35175 FMA:15902 MA:0002493 NCIT:C48941 UMLS:C0458421 anatomical wall of bladder anatomical wall of urinary bladder bladder anatomical wall bladder wall urinary bladder anatomical wall urinary bladder wall wall of bladder uberon UBERON:0001256 wall of urinary bladder An anatomical wall that lines the insider of a urinary bladder. UMLS:C0458421 ncithesaurus:Bladder_Wall anatomical wall of bladder OBOL:automatic anatomical wall of urinary bladder OBOL:automatic bladder anatomical wall OBOL:automatic bladder wall OBOL:automatic urinary bladder anatomical wall OBOL:automatic wall of bladder OBOL:automatic The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]. EMAPA:36078 FMA:15912 MA:0002491 NCIT:C12336 UMLS:C0227716 galen:UrinaryBladderNeck bladder neck cervix vesicae collum vesicae neck of bladder urinary bladder neck vesical neck uberon cervix vesicae urinariae UBERON:0001258 neck of urinary bladder The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]. MP:anna UMLS:C0227716 ncithesaurus:Bladder_Neck cervix vesicae FMA:15912 FMA:TA collum vesicae FMA:15912 FMA:TA cervix vesicae urinariae the mucous membrane lining the urinary bladder EFO:0000293 EMAPA:35897 FMA:15928 MA:0001692 NCIT:C32205 UMLS:C0227691 galen:MucousMembraneOfUrinaryBladder bladder mucosa bladder mucous membrane bladder organ mucosa mucosa of bladder mucous membrane of bladder mucous membrane of urinary bladder tunica mucosa (vesica urinaria) tunica mucosa vesicae tunica mucosa vesicae urinariae urinary bladder mucosa urinary bladder mucous membrane uberon UBERON:0001259 mucosa of urinary bladder the mucous membrane lining the urinary bladder MGI:anna MP:0011766 UMLS:C0227691 ncithesaurus:Bladder_Mucosa bladder mucous membrane OBOL:automatic bladder organ mucosa OBOL:automatic mucosa of bladder OBOL:automatic tunica mucosa (vesica urinaria) FMA:15928 FMA:TA tunica mucosa vesicae FMA:15928 FMA:TA tunica mucosa vesicae urinariae MP:MP urinary bladder mucous membrane OBOL:automatic A serous membrane that is part of a urinary bladder [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:28661 FMA:15932 MA:0001696 bladder serosa bladder serous membrane serosa of bladder serous coat of bladder serous coat of urinary bladder serous membrane of bladder serous membrane of urinary bladder tunica serosa (vesica urinaria) tunica serosa vesicae urinary bladder serosa urinary bladder serous membrane visceral peritoneum of urinary bladder uberon UBERON:0001260 serosa of urinary bladder tunica serosa vesicae FMA:15932 FMA:TA urinary bladder serous membrane OBOL:automatic A serous membrane that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic bladder serous membrane OBOL:automatic serous membrane of bladder OBOL:automatic serous membrane of urinary bladder OBOL:automatic tunica serosa (vesica urinaria) FMA:15932 FMA:TA A lamina propria that is part of a urinary bladder [Automatically generated definition]. Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue EMAPA:30088 FMA:15935 MA:0001695 NCIT:C48940 UMLS:C1706967 bladder lamina propria bladder lamina propria mucosa bladder lamina propria mucosae lamina propria mucosa of bladder lamina propria mucosa of urinary bladder lamina propria mucosae of bladder lamina propria mucosae of urinary bladder lamina propria of bladder urinary bladder lamina propria urinary bladder lamina propria mucosa urinary bladder lamina propria mucosae uberon UBERON:0001261 lamina propria of urinary bladder A lamina propria that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic UMLS:C1706967 ncithesaurus:Bladder_Lamina_Propria bladder lamina propria OBOL:automatic bladder lamina propria mucosa OBOL:automatic bladder lamina propria mucosae OBOL:automatic lamina propria mucosa of bladder OBOL:automatic lamina propria mucosa of urinary bladder OBOL:automatic lamina propria mucosae of bladder OBOL:automatic lamina propria mucosae of urinary bladder OBOL:automatic lamina propria of bladder OBOL:automatic urinary bladder lamina propria mucosa OBOL:automatic urinary bladder lamina propria mucosae OBOL:automatic 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. EMAPA:35651 FMA:16011 MA:0002417 NCIT:C49268 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 UMLS:C0227578 ncithesaurus:Pancreatic_Acinus acinus pancreaticus FMA:16011 pancreatic acinar TEMP:MP pancreatic acini An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. pancreas http://langual.org 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 OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA TAO:0000140 UMLS:C0030274 VHOG:0000050 XAO:0000136 ZFA:0000140 galen:Pancreas http://www.langual.org/langual_thesaurus.asp?termid=C0204 uberon UBERON:0001264 pancreas Wikipedia Wikipedia An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[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) 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 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 UMLS:C0030274 ncithesaurus:Pancreas Transudate contained in the peritoneal cavity. BTO:0001031 EMAPA:35683 FMA:16515 MA:0002531 ncithesaurus:Peritoneal_Fluid uberon UBERON:0001268 peritoneal fluid FMA Transudate contained in the peritoneal cavity. FMA:16515 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 pectoral 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 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 pectoral girdle regions. FMA:16581 FMA:23217 UBERONREF:0000003 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 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 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 TAO:0005124 UMLS:C0226890 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 UMLS:C0227514 trias hepatica uberon trias hepatica UBERON:0001279 portal triad 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 UMLS:C0227514 ncithesaurus:Portal_Triad trias hepatica 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 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) 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 TAO:0005091 UMLS:C0227523 VHOG:0000708 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 Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers. 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) 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 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 UMLS:C0227517 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 duct of Herring intrahepatic bile ductule The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP] kidney terms require review for cross-vertebrate compatibility and developmental relationships. Functional unit of the kidney that filters waste.[TAO] In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) BTO:0000924 CALOHA:TS-1312 EMAPA:28491 EMAPA:35592 EV:0100384 FMA:17640 GAID:428 MA:0000375 MESH:D009399 NCIT:C13048 TAO:0002153 UMLS:C0027713 ZFA:0005282 mature nephron uberon nephroneum tubulus renalis UBERON:0001285 nephron FMA Bgee:AN The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP] Functional unit of the kidney that filters waste.[TAO] 2012-08-14 TAO:0002153 TAO ZFIN:curator In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) GO UMLS:C0027713 ncithesaurus:Nephron mature nephron EMAPA:28491 nephroneum tubulus renalis the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy The mucous membrane lining the uterus. [TFD][VHOG] The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] endometrial Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead in FMA this is subdivided into basal and outer BTO:0001422 CALOHA:TS-0276 EFO:0000980 EMAPA:29917 EV:0100115 FMA:17742 GAID:377 MA:0000390 MAT:0000319 MESH:D004717 MIAA:0000319 NCIT:C12313 UMLS:C0014180 VHOG:0001285 tunica mucosa (endometrium) tunica mucosa uteri uterine endometrium uberon uterine mucosa uterine mucous membrane UBERON:0001295 endometrium FMA the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy MESH:A05.360.319.679.490 MGI:smb MP:0004896 The mucous membrane lining the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001285 VHOG The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] 2012-09-17 VHOG:0001285 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144 in FMA this is subdivided into basal and outer FMA UMLS:C0014180 ncithesaurus:Endometrium tunica mucosa (endometrium) FMA:17742 tunica mucosa uteri uterine endometrium BTO:0001422 uterine mucous membrane BTO:0001422 Outer serosa layer of the uterus. TODO - check for parallel structure with peritoneum EMAPA:37792 FMA:17744 MA:0001729 NCIT:C33298 UMLS:C0227824 perimetrium serous coat of uterus serous membrane of uterus tunica serosa (perimetrium) tunica serosa uteri uterine serosa uterus serosa uterus serous membrane visceral peritoneum of uterus uberon UBERON:0001297 serosa of uterus Outer serosa layer of the uterus. EMAPA:37792 MA:th UMLS:C0227824 ncithesaurus:Perimetrium perimetrium serous coat of uterus serous membrane of uterus OBOL:automatic tunica serosa uteri FMA:17744 FMA:TA uterus serous membrane OBOL:automatic the conic expansion of the corpus spongiosum that forms the head of the penis glans BTO:0003118 EMAPA:18988 EV:0100108 FMA:18247 GAID:0000012 MA:0002726 NCIT:C12324 OpenCyc:Mx4rvdCpE5wpEbGdrcN5Y29ycA UMLS:C0227948 VHOG:0001475 uberon balanus coronal sulcus UBERON:0001299 glans penis Bgee:AN the conic expansion of the corpus spongiosum that forms the head of the penis MGI:anna MP:0009102 glans EV:0100108 UMLS:C0227948 ncithesaurus:Glans_Penis balanus BTO:0003118 coronal sulcus the external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus. scrotal In elephants the testes remain in the abdomen In hedgehogs the testes remain in the inguinal canal In humans and some other mammals, the base of the scrotum becomes covered with pubic hair at puberty In marsupials, the scrotum is not homologous to the eutherian scrotum, and development is under the control of X-linked genes, not androgens In marsupials, the scrotum is positioned in the caudal area of the abdomen, in the same position as the pouch in females. It has been suggested that the pouch and marsupial scrotum are sexual homologs, but it is more likely they arise from different primordia in the same morphogenetic field The scrotum of marsupials is not homologous with the scrotum of mammals[ISBN:113945742X] BTO:0003098 CALOHA:TS-2341 EMAPA:19296 FMA:18252 GAID:393 MA:0000409 MESH:D012611 NCIT:C12785 OpenCyc:Mx4rwUC_upwpEbGdrcN5Y29ycA UMLS:C0036471 galen:Scrotum uberon UBERON:0001300 scrotum Wikipedia the external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus. ISBN:0-683-40008-8 MP:0002669 In elephants the testes remain in the abdomen PMC1570914 NCBITaxon:9780 In hedgehogs the testes remain in the inguinal canal PMC1570914 NCBITaxon:9363 In humans and some other mammals, the base of the scrotum becomes covered with pubic hair at puberty NCBITaxon:9606 In marsupials, the scrotum is not homologous to the eutherian scrotum, and development is under the control of X-linked genes, not androgens NCBITaxon:9263 In marsupials, the scrotum is positioned in the caudal area of the abdomen, in the same position as the pouch in females. It has been suggested that the pouch and marsupial scrotum are sexual homologs, but it is more likely they arise from different primordia in the same morphogenetic field ISBN:113945742X NCBITaxon:9263 UMLS:C0036471 ncithesaurus:Scrotum the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens Kardong has epididymis in elasmobranch epididymal A similar, but probably non-homologous, structure is found in cartilaginous fishes Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells. BTO:0000408 CALOHA:TS-0285 EFO:0000982 EMAPA:19290 EV:0100103 FMA:18255 GAID:397 MA:0000397 MAT:0000130 MESH:A05.360.444.849.286 MIAA:0000130 NCIT:C12328 UMLS:C0014533 VHOG:0001265 galen:Epididymis uberon Nebenhoden@de UBERON:0001301 epididymis FMA Wikipedia the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens MGI:pvb MP:0002631 A similar, but probably non-homologous, structure is found in cartilaginous fishes WP UMLS:C0014533 ncithesaurus:Epididymis Nebenhoden@de BTO:0000408 A fallopian tube that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern non-functional in monotremes[ISBN:978-0226870137] EMAPA:37369 FMA:18483 MA:0001717 NCIT:C33475 UMLS:C0227900 right fallopian tube right oviduct uberon UBERON:0001302 right uterine tube A fallopian tube that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37369 MA:th UMLS:C0227900 ncithesaurus:Right_Fallopian_Tube A fallopian tube that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37368 FMA:18484 MA:0001716 NCIT:C32959 UMLS:C0227902 left fallopian tube left oviduct uberon UBERON:0001303 left uterine tube A fallopian tube that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37368 MA:th UMLS:C0227902 ncithesaurus:Left_Fallopian_Tube layer of simple cuboidal cells covering surface of ovary[WP]. BTO:0004483 EHDAA:8126 EMAPA:17963 FMA:18629 MA:0001711 NCIT:C61518 RETIRED_EHDAA2:0001361 UMLS:C0227875 VHOG:0000630 epithelium superficiale (ovarium) germinal epithelium (female) ovarian surface epithelium ovary germinal epithelium surface epithelium of ovary uberon female coelomic epithelium ovary surface epithelium UBERON:0001304 Controversial - see article. Requires expert input. Also check BTO placement germinal epithelium of ovary layer of simple cuboidal cells covering surface of ovary[WP]. UMLS:C0227875 ncithesaurus:Ovarian_Surface_Epithelium germinal epithelium (female) ovarian surface epithelium BTO:0004483 female coelomic epithelium EMAPA:17384 ovary surface epithelium EMAPA:17963 A capsule that surrounds a female gonad. EMAPA:35626 FMA:18662 MA:0001706 NCIT:C49265 UMLS:C0227877 ovarian capsule ovary capsule uberon UBERON:0001307 capsule of ovary A capsule that surrounds a female gonad. OBOL:automatic UMLS:C0227877 ncithesaurus:Ovarian_Capsule The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted]. todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships BTO:0000841 CALOHA:TS-1077 EHDAA:1026 EHDAA:410 EMAPA:16331 EMAPA:16372 FMA:18820 GAID:516 MA:0002072 MESH:D014469 NCIT:C33827 OpenCyc:Mx4rCWdhMGWbEd2AAABQjYGu0g RETIRED_EHDAA2:0002106 UMLS:C0041632 uberon a. umbilicalis UBERON:0001310 umbilical artery The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted]. UMLS:C0041632 ncithesaurus:Umbilical_Artery a. umbilicalis An artery that supplies blood to the upper urinary bladder. The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP] EMAPA:37123 FMA:18839 MA:0002080 NCIT:C52686 UMLS:C0226376 arteria vesicali superior arteria vesicalis superior uberon arteriae vesicales superiores UBERON:0001312 superior vesical artery An artery that supplies blood to the upper urinary bladder. EMAPA:37123 MA:th UMLS:C0226376 ncithesaurus:Superior_Vesical_Artery arteria vesicali superior arteria vesicalis superior arteriae vesicales superiores A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]. EHDAA2:0000874 EMAPA:37148 FMA:18884 MA:0002139 MA:0002145 NCIT:C32847 UMLS:C0226764 VHOG:0000749 galen:InternalIliacVein uberon hypogastric vein v. hypogastrica v. iliaca interna UBERON:0001317 internal iliac vein MA A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]. EMAPA:37148 MA:th UMLS:C0226764 ncithesaurus:Internal_Iliac_Vein hypogastric vein MA:0002139 v. hypogastrica v. iliaca interna One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]. EMAPA:37796 FMA:18899 MA:0002251 vagina vein vein of vagina uberon UBERON:0001319 vaginal vein FMA/obol One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]. EMAPA:37796 MA:th vagina vein OBOL:automatic vein of vagina OBOL:automatic 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 A portion of a prostate that forms a lobe. Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue BTO:0000548 EMAPA:35712 FMA:19570 MA:0001738 NCIT:C52726 UMLS:C0227970 lobe of prostate gland prostate gland lobe prostatic lobe uberon UBERON:0001328 lobe of prostate A portion of a prostate that forms a lobe. Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue UMLS:C0227970 ncithesaurus:Prostate_Gland_Lobe The pampiniform plexus is a network of many small veins found in the male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted]. EMAPA:37385 FMA:19607 MA:0001866 pampiniform venous plexus plexus of veins of fascia of prostate plexus venosus pampiniformis venous plexus of fascia of prostate venous plexus of fascia of prostate gland uberon UBERON:0001330 pampiniform plexus The pampiniform plexus is a network of many small veins found in the male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted]. EMAPA:37385 MA:th plexus venosus pampiniformis FMA:19607 FMA:TA A zone of skin that is part of a penis [Automatically generated definition]. EMAPA:35675 FMA:19638 MA:0002727 penile skin penis skin penis zone of skin zone of skin of penis uberon UBERON:0001331 skin of penis A zone of skin that is part of a penis [Automatically generated definition]. OBOL:automatic penile skin FMA:19638 penis zone of skin OBOL:automatic zone of skin of penis OBOL:automatic A urethra that is part of a male reproductive system. BTO:0004089 EMAPA:18692 FMA:19668 MA:0002640 NCIT:C33050 UMLS:C0458452 uberon UBERON:0001333 male urethra A urethra that is part of a male reproductive system. UMLS:C0458452 ncithesaurus:Male_Urethra A urethra that is part of a female reproductive system. BTO:0004088 EMAPA:28747 FMA:19669 MA:0002637 NCIT:C32591 UMLS:C0458485 uberon urethra feminina urethra muliebris UBERON:0001334 female urethra A urethra that is part of a female reproductive system. UMLS:C0458485 ncithesaurus:Female_Urethra urethra feminina BTO:0004088 urethra muliebris BTO:0004088 Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine NCIT:C12339 paraurethral gland belongs here EMAPA:37784 FMA:19683 MA:0001688 gland of urethra urethra gland urethra gland (male or female) urethral mucuous gland uberon UBERON:0001338 urethral gland MP Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine MP:anna NCIT:C12339 paraurethral gland belongs here NCIT EMAPA:37784 MA:th gland of urethra OBOL:automatic The tubules in the testes where spermatogenesis occurs. Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO] One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG] Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG] AAO:0010399 BTO:0001235 CALOHA:TS-1239 EFO:0001404 EMAPA:18685 EMAPA:31476 EV:0100380 FMA:19825 GAID:400 MA:0000412 MAT:0000503 MESH:D012671 NCIT:C13047 NCIT:C34293 UMLS:C0036630 UMLS:C1519236 VHOG:0001363 XAO:0003088 seminiferous cord seminiferous tubule testis - seminiferous tubule tubuli seminiferi uberon tubuli seminiferi UBERON:0001343 seminiferous tubule of testis Wikipedia The tubules in the testes where spermatogenesis occurs. ISBN:0-683-40008-8 MGI:csmith MP:0002216 Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO] 2012-06-20 AAO:0010399 AAO AAO:BJB One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG] 2012-09-17 VHOG:0001363 VHOG Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG] 2012-09-17 VHOG:0001363 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28 UMLS:C0036630 ncithesaurus:Seminiferous_Tubule UMLS:C1519236 ncithesaurus:Seminiferous_Cord seminiferous cord EMAPA:18685 tubuli seminiferi The epithelial layer of the vagina. FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous) BTO:0000422 CALOHA:TS-1325 EMAPA:30991 FMA:19978 MA:0001730 NCIT:C49313 UMLS:C0920840 epithelial tissue of vagina vagina epithelial tissue vagina epithelium vaginal epithelium uberon epithelium, vaginal UBERON:0001344 epithelium of vagina The epithelial layer of the vagina. MP:0001140 FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous) FMA UMLS:C0920840 ncithesaurus:Vaginal_Epithelium epithelial tissue of vagina OBOL:automatic vagina epithelial tissue OBOL:automatic epithelium, vaginal BTO:0000422 The upper dilated end of the nasolacrimal duct that is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla; it connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity; like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue. FMA:20289 MA:0001298 NCIT:C32909 UMLS:C0229289 lachrymal sac lacrymal sac saccus lacrimalis uberon UBERON:0001351 lacrimal sac The upper dilated end of the nasolacrimal duct that is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla; it connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity; like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue. MGI:anna UMLS:C0229289 ncithesaurus:Lacrimal_Sac saccus lacrimalis 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 UMLS:C0230120 VHOG:0000395 WBbt:0006919 uberon posterior posterior end of organism UBERON:0001353 anal region cjm 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] 2012-09-17 VHOG:0000395 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0230120 ncithesaurus:Anal_Region A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6] Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] EHDAA2 models this as developing from CP, which is wrong the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. BIRNLEX:1798 BTO:0000237 CALOHA:TS-0130 EFO:0000329 EHDAA2:0004441 ENVO:02000029 EV:0100311 FMA:20935 GAID:1181 MA:0002503 MAT:0000499 MESH:A12.207.268 NCIT:C12692 TAO:0002184 UMLS:C0007806 VHOG:0001278 ZFA:0001626 CSF cerebral spinal fluid uberon liquor cerebrospinalis spinal fluid UBERON:0001359 cerebrospinal fluid Wikipedia EHDAA2 see notes EHDAA2 A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] 2012-08-14 TAO:0002184 TAO ZFIN:curator In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] 2012-09-17 VHOG:0001278 VHOG DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005) EHDAA2 models this as developing from CP, which is wrong EHDAA2 the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. FMA UMLS:C0007806 BIRNLEX:1798 UMLS:C0007806 ncithesaurus:Cerebrospinal_Fluid cerebral spinal fluid ZFA:0001626 liquor cerebrospinalis spinal fluid BTO:0000237 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 TAO:0005131 VHOG:0001527 ZFA:0005131 parietal serous membrane of peritoneum uberon peritoneal cavity lining UBERON:0001366 parietal peritoneum The outer layer of peritoneum that is attached to the abdominal and pelvic walls. 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 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 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 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 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 A zone of skin that is part of a limb [Automatically generated definition]. EMAPA:32726 FMA:23100 MA:0000694 NCIT:C53276 UMLS:C1282135 limb skin limb zone of skin zone of skin of limb uberon UBERON:0001419 skin of limb A zone of skin that is part of a limb [Automatically generated definition]. OBOL:automatic UMLS:C1282135 ncithesaurus:Skin_of_the_Extremity limb zone of skin OBOL:automatic zone of skin of limb 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 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 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 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 A lymphatic vessel that is part of a face [Automatically generated definition]. FMA:233946 TAO:0005108 ZFA:0005108 buccal lymphatic vessel face lymph vessel face lymphatic vessel lymph vessel of face lymphatic vessel of face uberon FL UBERON:0001422 facial lymphatic vessel A lymphatic vessel that is part of a face [Automatically generated definition]. OBOL:automatic face lymph vessel OBOL:automatic face lymphatic vessel OBOL:automatic lymph vessel of face OBOL:automatic lymphatic vessel of face OBOL:automatic FMA:234865 TAO:0005107 ZFA:0005107 uberon PL UBERON:0001425 pectoral lymphatic vessel PL 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 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA 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 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) 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 The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle TODO - find a home for: FMA:24139 ! skeleton of upper limb Skeletal structure of the paired, anterior appendages.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 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] AAO:0000202 EHDAA2:0002222 EMAPA:32623 FMA:24142 VHOG:0001256 VSAO:0000151 XAO:0003061 bones of upper limb fore limb skeleton forelimb skeleton free upper limb skeleton ossa membri superioris pectoral limb skeleton set of bones of upper limb skeleton of forelimb skeleton of free upper limb skeleton of pectoral limb skeleton of upper limb upper limb skeleton wing skeleton uberon UBERON:0001440 forelimb skeleton FMA The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle Skeletal structure of the paired, anterior appendages.[AAO] 2012-06-20 AAO:0000202 AAO AAO:LAP relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0000202 AAO 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:0001256 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 forelimb skeleton VHOG:0001256 free upper limb skeleton FMA:24142 ossa membri superioris FMA:24139 FMA:TA skeleton of free upper limb FMA:24142 skeleton of upper limb FMA:24139 upper limb skeleton EHDAA2:0002222 wing skeleton NCBITaxon:8782 OBOL:automatic Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. Skeletal structure of the paired, posterior appendages.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 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] AAO:0000217 EHDAA2:0002226 EMAPA:32633 FMA:24144 OpenCyc:Mx4rvZcKkZwpEbGdrcN5Y29ycA VHOG:0001255 VSAO:0000152 XAO:0003062 bones of lower limb free lower limb skeleton hind limb skeleton hind-limb skeleton hindlimb skeleton lower limb skeleton ossa membri inferioris set of bones of lower limb skeleton of free lower limb skeleton of lower limb uberon UBERON:0001441 TOOD - find a home for: FMA:24140 hindlimb skeleton FMA Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. Skeletal structure of the paired, posterior appendages.[AAO] 2012-06-20 AAO:0000217 AAO AAO:LAP relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0000217 AAO 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:0001255 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 free lower limb skeleton FMA:24144 hind limb skeleton XAO:0003062 hind-limb skeleton VSAO:0000152 hindlimb skeleton VHOG:0001255 ossa membri inferioris FMA:24140 FMA:TA skeleton of free lower limb FMA:24144 skeleton of lower limb FMA:24140 Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax 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; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]. FMA:24216 present in FMA1, but gone in subsequent versions pectoral thoracic BTO:0001368 CALOHA:TS-1039 EFO:0000965 EMAPA:37232 EV:0100010 FMA:9576 GAID:91 MA:0000031 MAT:0000295 MESH:A01.911 MIAA:0000295 NCIT:C12799 NCIT:C25389 OpenCyc:Mx4rvVikFZwpEbGdrcN5Y29ycA UMLS:C0817096 UMLS:C1527391 galen:Chest galen:Thorax anterolateral part of thorax front of thorax pectus ventral part of thoracic region uberon thoracic body wall thorax UBERON:0001443 chest FMA-modified FMA MA Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax 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; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]. FMA:9576 EMAPA:37232 MA:th UMLS:C0817096 ncithesaurus:Thorax UMLS:C1527391 ncithesaurus:Chest pectus FMA:24816 FMA:TA thoracic body wall MA:0000031 thorax thorax FMA:9576 FMA:24218 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 OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA UMLS:C0015450 galen:Face uberon facia/facies visage UBERON:0001456 face 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. FMA:24728 The area that extends from the median ocellus to the oral foramen[HAO]. HAO:0000316 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 visage BTO:0003369 A zone of skin that is part of a lip [Automatically generated definition]. EMAPA:37643 FMA:24764 MA:0001579 NCIT:C12291 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 The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted]. EMAPA:37801 FMA:29713 MA:0002257 venous vaginal plexus uberon plexus venosus vaginalis UBERON:0001472 vaginal venous plexus The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted]. EMAPA:37801 MA:th plexus venosus vaginalis A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]. A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] A vessel that contains or conveys lymph.[AAO] Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] AAO:0011005 BTO:0000752 CALOHA:TS-2102 EFO:0000873 EMAPA:35532 FMA:30315 MA:0000138 MAT:0000443 NCIT:C33038 OpenCyc:Mx4rwA1fYZwpEbGdrcN5Y29ycA TAO:0005105 UMLS:C0229889 VHOG:0001249 XAO:0000375 lymph vessel uberon vas lymphaticum UBERON:0001473 lymphatic vessel A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]. BTO:0000752 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] 2012-08-14 TAO:0005105 TAO ZFIN:curator A vessel that contains or conveys lymph.[AAO] 2012-06-20 AAO:0011005 AAO AAO:EJS Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] 2012-09-17 VHOG:0001249 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627 UMLS:C0229889 ncithesaurus:Lymphatic_Vessel vas lymphaticum 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 OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 XAO:0000169 ZFA:0001514 galen:Bone 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 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) 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 UMLS:C0206207 galen:JointCapsule capsula articularis fibrous capsule of joint joint capsule joint fibrous capsule uberon capsulae articulares UBERON:0001484 articular capsule An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita ncit EMAPA:37621 MA:th UMLS:C0206207 ncithesaurus:Joint_Capsule capsula articularis FMA:34836 FMA:TA capsulae articulares 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 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 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 OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA UMLS:C0011666 pars descendens aortae uberon aorta descendens pars descendens aortae UBERON:0001514 descending aorta 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 UMLS:C0011666 ncithesaurus:Descending_Aorta pars descendens aortae FMA:3784 aorta descendens aorta descendens pars descendens aortae 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 OpenCyc:Mx4rveb9TpwpEbGdrcN5Y29ycA UMLS:C1522460 galen:ThoracicAorta aorta thoracica thoracic part of aorta uberon aorta thoracalis pars thoracica aortae UBERON:0001515 thoracic aorta 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 UMLS:C1522460 ncithesaurus:Thoracic_Aorta aorta thoracica FMA:3786 FMA:TA aorta thoracalis pars thoracica aortae 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 OpenCyc:Mx4rvYhWCZwpEbGdrcN5Y29ycA UMLS:C0003484 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 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 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 aorta abdominalis BTO:0002976 pars abdominalis aortae pars abdominalis aortae BTO:0002976 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 UMLS:C0162859 VHOG:0000272 carotid artery system common carotid artery trunk of common carotid tree uberon a. carotis communis UBERON:0001530 common carotid artery plus branches 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]. 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 The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk. placement of the MA class here is not strictly correct, as the MA class does not include the branches EMAPA:35749 FMA:3941 MA:0001928 NCIT:C33473 OpenCyc:Mx4rtW9-AqgEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvg7rcJwpEbGdrcN5Y29ycA UMLS:C0226086 right common carotid artery trunk of right common carotid tree uberon right common carotid artery UBERON:0001531 right common carotid artery plus branches FMA The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk. UBERON:cjm UMLS:C0226086 ncithesaurus:Right_Common_Carotid_Artery right common carotid artery MA:0001928 trunk of right common carotid tree FMA:3941 right common carotid artery FMA:3941 A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP] Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG] One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO] AAO:0010219 AAO:0011054 BTO:0004697 EFO:0001952 EHDAA2:0000873 EHDAA:408 EHDAA:6389 EMAPA:16328 FMA:3947 GAID:481 MA:0001930 MESH:D002343 NCIT:C32836 OpenCyc:Mx4rvYx8KZwpEbGdrcN5Y29ycA TAO:0005081 UMLS:C0007276 VHOG:0000267 XAO:0000366 ZFA:0005081 cranial carotid artery internal carotid uberon ICA arteria carotis interna UBERON:0001532 internal carotid artery MA cjm FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP] MGI:anna Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG] 2012-09-17 VHOG:0000267 VHOG One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO] 2012-06-20 AAO:0011054 AAO UMLS:C0007276 ncithesaurus:Internal_Carotid_Artery cranial carotid artery ZFA:0005081 internal carotid AAO:0010219 ICA arteria carotis interna 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 OpenCyc:Mx4rvp8u1JwpEbGdrcN5Y29ycA TAO:0005086 UMLS:C0038530 XAO:0000365 ZFA:0005086 arteria subclavia arterial tree of upper limb pectoral artery subclavian arterial tree uberon PA arteria subclavia UBERON:0001533 subclavian artery EHDAA2 EHDAA2 One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta ISBN:0073040584 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] 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 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 OpenCyc:Mx4rtW7hwqgEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvp8u1JwpEbGdrcN5Y29ycA UMLS:C0226261 arteria subclavia dextra uberon UBERON:0001534 right subclavian artery The subclavian artery that supplies the right pectoral appendage EMAPA:37384 MA:th UMLS:C0226261 ncithesaurus:Right_Subclavian_Artery arteria subclavia dextra FMA:3953 FMA:TA The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax. placement of the MA class here is not strictly correct, as the MA class does not include the branches EMAPA:35491 FMA:4058 MA:0001927 NCIT:C32956 OpenCyc:Mx4rdz4xcLVIEduAAAAOpmP6tw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvg7rcJwpEbGdrcN5Y29ycA UMLS:C0226087 left common carotid artery trunk of left common carotid tree uberon left common carotid artery UBERON:0001536 left common carotid artery plus branches FMA The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax. UBERON:cjm UMLS:C0226087 ncithesaurus:Left_Common_Carotid_Artery left common carotid artery MA:0001927 trunk of left common carotid tree FMA:4058 left common carotid artery FMA:4058 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 NCIT:C34082 OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA 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. 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 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 UMLS:C0017189 ncithesaurus:Gastrointestinal_Tract enteric tract ZFA:0000112 digestive canal BTO:0000058 Subdivision of urinary system which consists of the urinary bladder and the urethra. FMA:45659 MA:0002636 galen:LowerUrinaryTract uberon UBERON:0001556 lower urinary tract Subdivision of urinary system which consists of the urinary bladder and the urethra. FMA:45659 The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] EHDAA2:0002136 EMAPA:17669 FMA:45661 MA:0000442 OpenCyc:Mx4rtT2HwgJMEdyAAADggVbxzQ VHOG:0000406 uberon UBERON:0001557 upper respiratory tract The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] FMA 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 OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g VHOG:0000382 lower respiratory system uberon UBERON:0001558 lower respiratory tract The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] FMA:45733 organ neck uberon UBERON:0001560 neck of organ FMA The muscles associated with the larynx. BTO:0001626 EMAPA:35473 FMA:46562 GAID:144 MA:0001768 MESH:D007821 NCIT:C32934 UMLS:C0023054 laryngeal muscle larynx muscle larynx muscle organ muscle organ of larynx musculi laryngeales uberon UBERON:0001568 muscle of larynx prolog The muscles associated with the larynx. MP:0002263 UMLS:C0023054 ncithesaurus:Laryngeal_Muscle larynx muscle organ OBOL:automatic muscle organ of larynx OBOL:automatic Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG] Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO] see Intrinsic Tongue.[FEED] relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians. AAO:0010660 EHDAA2:0000704 EHDAA:9150 EMAPA:18276 FMA:46690 MA:0002307 NCIT:C52928 UMLS:C0224194 VHOG:0000847 genioglossus m. genioglossus musculus genioglossus uberon UBERON:0001571 genioglossus muscle FMA EHDAA2 Wikipedia Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. VHOG:0000847 Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG] 2012-09-17 VHOG:0000847 VHOG Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO] 2012-06-20 AAO:0010660 AAO AAO:BMZ see Intrinsic Tongue.[FEED] 2012-07-02 FEED http://www.feedexp.org relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] 2012-06-20 AAO:0010660 AAO The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000847 VHOG DOI:10.1002/dvdy.20587, DOI:10.1186/1471-213X-8-24 Table 7 Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians. AAO:0010660 UMLS:C0224194 ncithesaurus:Genioglossus A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII Makes up part of the tongue in frogs and salamanders.[AAO] The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED] relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] AAO:0010663 EMAPA:18277 FMA:46691 MA:0002317 MFMO_0000064 NCIT:C53161 UMLS:C0224196 hyoglossus m. hyoglossus uberon UBERON:0001572 hyoglossus muscle FMA lingual process in horse dbpedia A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII FEED:rd Makes up part of the tongue in frogs and salamanders.[AAO] 2012-06-20 AAO:0010663 AAO AAO:BMZ The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED] 2012-07-02 FEED http://www.feedexp.org relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] 2012-06-20 AAO:0010663 AAO UMLS:C0224196 ncithesaurus:Hyoglossus_Muscle hyoglossus A muscle organ that attaches the tongue to some other structure. The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus. EHDAA2:0002063 EHDAA:9148 EMAPA:18275 FMA:46699 MA:0002296 VHOG:0000825 extrinsic lingual muscle extrinsic tongue muscle uberon UBERON:0001575 extrinsic muscle of tongue true check palatoglossus Wikipedia A muscle organ that attaches the tongue to some other structure. The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000825 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement WP All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus. WP The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII. The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED] The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone EHDAA2:0002064 EHDAA:9152 EMAPA:18280 FMA:46701 MA:0002327 VHOG:0000748 intrinsic lingual muscle intrinsic tongue muscle uberon UBERON:0001576 intrinsic muscle of tongue true FEED Wikipedia EHDAA2 The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII. The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED] 2012-07-02 FEED http://www.feedexp.org The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000748 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone WP A muscle innervated by a facial nerve. FMA:46751 GAID:143 MA:0003160 MESH:D005152 MFMO:0000005 NCIT:C13073 UMLS:C0015460 XAO:0001013 face muscle face muscle organ facial muscle facial muscle proper facial nerve innervated muscle facial nerve muscle muscle of face muscle organ of face uberon cranial-facial muscle cranio-facial muscle craniofacial muscle mimetic muscles muscle of facil expression muscles of facial expression musculi faciei UBERON:0001577 facial muscle FEED Wikipedia A muscle innervated by a facial nerve. FEED:rd UMLS:C0015460 ncithesaurus:Facial_Muscle face muscle FMA:46751 face muscle organ OBOL:automatic facial muscle FMA:46751 facial muscle XAO:0001013 facial nerve innervated muscle muscle of face FMA:46751 muscle organ of face OBOL:automatic cranial-facial muscle EMAPA:25133 cranio-facial muscle EMAPA:25133 craniofacial muscle EMAPA:25133 mimetic muscles muscle of facil expression muscles of facial expression musculi faciei 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 OpenCyc:Mx4rtW7hw6gEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvp8u1JwpEbGdrcN5Y29ycA UMLS:C0226262 arteria subclavia (sinistra) uberon UBERON:0001584 left subclavian artery The subclavian artery that supplies the left pectoral appendage 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 UMLS:C0042459 VHOG:0001195 galen:SuperiorVenaCava superior caval vein superior vena cava uberon cranial vena cava precava vena cava superior vena maxima UBERON:0001585 anterior vena cava lexical 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] 2012-09-17 VHOG:0001195 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 UMLS:C0042459 ncithesaurus:Superior_Vena_Cava superior caval vein superior vena cava FMA:4720 cranial vena cava VHOG:0001195 vena cava superior vena cava superior BTO:0002683 vena maxima 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 OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000878 UMLS:C0226550 XAO:0000382 galen:InternalJugularVein internal jugular internal jugular venous tree uberon vena jugularis interna UBERON:0001586 internal jugular vein 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] 2012-06-20 AAO:0010236 AAO AAO:BJB UMLS:C0226550 ncithesaurus:Internal_Jugular_Vein internal jugular EHDAA2:0000877 vena jugularis interna A vein that drains blood from the thymus. EMAPA:36325 FMA:4747 MA:0002246 NCIT:C53143 UMLS:C0226698 thymic tributary of brachiocephalic vein vena thymica uberon venae thymicae UBERON:0001591 thymic vein A vein that drains blood from the thymus. UMLS:C0226698 ncithesaurus:Thymic_Vein vena thymica venae thymicae The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]. EMAPA:36284 FMA:4749 MA:0002088 NCIT:C53031 UMLS:C0226650 bronchial venous tree uberon UBERON:0001592 bronchial vein The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]. UMLS:C0226650 ncithesaurus:Bronchial_Vein A congregation of multiple veins. EMAPA:36327 FMA:4767 MA:0000069 venous network uberon plexus venosus rete venosum UBERON:0001593 venous plexus A congregation of multiple veins. plexus venosus rete venosum 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 UMLS:C0559230 musculus ciliarus uberon Bowman`s muscles ciliaris musculus ciliaris UBERON:0001605 ciliary muscle 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]. UMLS:C0559230 ncithesaurus:Ciliary_Muscle musculus ciliarus BTO:0000654 Bowman`s muscles BTO:0000654 ciliaris musculus ciliaris . 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 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 UMLS:C0229189 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 BTO ISBN:0781772214 encircles iris dbpedia encircles iris dbpedia dbpedia A sphincter muscle that is part of the iris. UMLS:C0229189 ncithesaurus:Sphincter_Pupillae_Muscle iris sphincter muscle BTO:0000656 musculus sphincter pupillae BTO:0000656 sphincter muscle of pupil BTO:0000656 circular fibers constrictor pupillae iris constrictor muscle iris sphincter m. sphincter pupillae pupillary constrictor muscle pupillary sphincter pupillary sphincter muscle sphincter pupillae sphincter pupillae muscle spincter pupillae 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 UMLS:C0229190 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 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]. UMLS:C0229190 ncithesaurus:Dilator_Pupillae_Muscle dilator pupillae muscle iris dilator muscle BTO:0001371 musculus dilatator pupillae FMA:49158 FMA:TA pupillary dilator muscle radial muscle of iris dilator pupillae muscle BTO:0001371 iris dilator musculus dilatator pupillae musculus dilator pupillae BTO:0001371 pupil dilator pupil dilator muscle pupillary dilator pupillary muscle radial muscle radiating fibers The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP]. Part of the external carotid which supplies blood to the tongue.[AAO] relationship loss: part_of external carotid (AAO:0010218)[AAO] AAO:0010492 EMAPA:36324 FMA:49526 MA:0001992 NCIT:C52961 OpenCyc:Mx4rvfqDCZwpEbGdrcN5Y29ycA UMLS:C0226104 lingual branch of external carotid artery uberon arteria lingualis UBERON:0001610 lingual artery FMA-abduced-lr The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP]. Part of the external carotid which supplies blood to the tongue.[AAO] 2012-06-20 AAO:0010492 AAO AAO:BJB relationship loss: part_of external carotid (AAO:0010218)[AAO] 2012-06-20 AAO:0010492 AAO UMLS:C0226104 ncithesaurus:Lingual_Artery arteria lingualis A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. EMAPA:19213 FMA:49549 MA:0001950 NCIT:C32578 OpenCyc:Mx4rwCt95ZwpEbGdrcN5Y29ycA UMLS:C0226109 uberon arteria maxillaris externa external maxillary artery UBERON:0001612 facial artery A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. UMLS:C0226109 ncithesaurus:Facial_Artery arteria maxillaris externa 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 OpenCyc:Mx4rwDDJ45wpEbGdrcN5Y29ycA UMLS:C0024949 uberon arteria maxillaris internal maxillary artery UBERON:0001616 maxillary 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 UMLS:C0024949 ncithesaurus:Maxillary_Artery arteria maxillaris The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]. Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO] relationship loss: part_of internal carotid (AAO:0010219)[AAO] AAO:0010497 EHDAA2:0001300 EHDAA:7363 EMAPA:17007 FMA:49868 GAID:503 MA:0002011 MESH:D009880 NCIT:C33216 OpenCyc:Mx4rvcCxpJwpEbGdrcN5Y29ycA UMLS:C0029078 XAO:0000368 uberon arteria ophthalmica opthalmic artery UBERON:0001619 ophthalmic artery The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]. Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO] 2012-06-20 AAO:0010497 AAO AAO:BJB relationship loss: part_of internal carotid (AAO:0010219)[AAO] 2012-06-20 AAO:0010497 AAO UMLS:C0029078 ncithesaurus:Opthalmic_Artery arteria ophthalmica opthalmic artery The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]. EMAPA:37094 FMA:49927 MA:0001988 NCIT:C52948 UMLS:C0226171 uberon a. lacrimalis UBERON:0001622 lacrimal artery FMA The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]. EMAPA:37094 MA:th UMLS:C0226171 ncithesaurus:Lacrimal_Artery a. lacrimalis One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery. An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO] todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery EHDAA2:0004518 EHDAA:3352 EMAPA:18600 FMA:50084 MA:0002023 NCIT:C33357 OpenCyc:Mx4rwDDlqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001487 TAO:0005001 UMLS:C0149559 ZFA:0005001 caudal communicating segment posterior communicating segment of the basilar artery uberon PCA PCS arteria cerebri communicans posterior UBERON:0001628 posterior communicating artery FMA-abduced-lr FMA ZFA One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery. An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005001 TAO ZFIN:curator UMLS:C0149559 ncithesaurus:Posterior_Communicating_Artery caudal communicating segment ZFA:0005001 posterior communicating segment of the basilar artery ZFA:0005001 arteria cerebri communicans posterior 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 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA 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 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 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 OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA TAO:0000005 UMLS:C0003842 VHOG:0001251 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) 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 OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA TAO:0000082 UMLS:C0042449 VHOG:0001743 XAO:0000115 ZFA:0000082 galen:Vein venous tree organ part uberon vascular element vena venae UBERON:0001638 vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. 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) UMLS:C0042449 ncithesaurus:Vein vascular element EMAPA:th vena venae VHOG:0001743 The first major branch of the abdominal aorta. EHDAA2:0004519 EMAPA:35202 FMA:50737 GAID:483 MA:0001931 MESH:D002445 NCIT:C52846 UMLS:C0007569 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 ISBN:0073040584 ISBN:0073040584 ISBN:0073040584 ISBN:0073040584 The first major branch of the abdominal aorta. UMLS:C0007569 ncithesaurus:Coeliac_Artery coeliac artery arteria coeliaca arteria cœliaca celiac trunk coeliac axis coeliac trunck coeliac trunk truncus coeliacus truncus coeliacus truncus cœliacus 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 OpenCyc:Mx4rwMF8CJwpEbGdrcN5Y29ycA TAO:0000697 UMLS:C0040996 VHOG:0000704 XAO:0003092 ZFA:0000697 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 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 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 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 UMLS:C0040996 ncithesaurus:Trigeminal_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=549 BIRNLEX:869 nervus trigeminus nervus trigeminus [v] FMA:50866 FMA:TA trigeminal V EHDAA2:0002084 nerve V NeuroNames:549 nervus trigeminus BTO:0001072 trigeminus BTO:0001072 Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches). Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[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] 7n AAO:0010472 BAMS:7n BAMS:VIIn BAMS:Viin BAMS:nVII BIRNLEX:827 BM:Pons-VIIN EHDAA2:0000489 EHDAA:3729 EMAPA:17796 FMA:50868 GAID:719 HBA:9328 MA:0001091 MBA:798 MESH:D005154 NCIT:C12714 OpenCyc:Mx4rvthgEpwpEbGdrcN5Y29ycA TAO:0000664 UMLS:C0015462 VHOG:0000706 XAO:0003094 ZFA:0000664 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=551 branchiomeric cranial nerve face nerve facial VII facial VII nerve facial nerve [VII] facial nerve tree nerve of face nervus facialis nervus facialis [vii] seventh cranial nerve uberon CN-VII cranial nerve VII facial nerve or its root facial nerve/root nerve VII nervus facialis UBERON:0001647 facial nerve ZFA Wikipedia Wikipedia Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches). ISBN:0471209627 Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO] 2012-06-20 AAO:0010472 AAO AAO:DSM 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:0000706 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 7n BIRNLEX:827 NIFSTD:NeuroNames_abbrevSource UMLS:C0015462 BIRNLEX:827 UMLS:C0015462 ncithesaurus:Facial_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=551 BIRNLEX:827 face nerve OBOL:automatic facial VII EHDAA2:0000489 nerve of face OBOL:automatic nervus facialis ZFA:0000664 nervus facialis [vii] FMA:50868 FMA:TA facial nerve or its root BAMS:7n facial nerve/root BAMS:7n nerve VII NeuroNames:551 nervus facialis Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[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] 9n AAO:0010474 BAMS:9n BAMS:IXn BIRNLEX:899 BTO:0004979 EHDAA2:0000709 EHDAA:3733 EMAPA:17268 FMA:50870 GAID:827 HBA:9334 MA:0001093 MBA:808 MESH:D005930 NCIT:C12723 OpenCyc:Mx4rwIr5X5wpEbGdrcN5Y29ycA TAO:0000668 UMLS:C0017679 UMLS:C1305752 VHOG:0000701 XAO:0003096 ZFA:0000668 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=701 glossopharyngeal IX glossopharyngeal IX nerve glossopharyngeal nerve [IX] glossopharyngeal nerve tree nervus glossopharyngeus nervus glossopharyngeus [ix] ninth cranial nerve uberon CN-IX cranial nerve IX nerve IX nervus glossopharyngeus UBERON:0001649 glossopharyngeal nerve motor Wikipedia Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). ISBN:0471209627 Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] 2012-06-20 AAO:0010474 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:0000701 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 9n BIRNLEX:899 NIFSTD:NeuroNames_abbrevSource UMLS:C0017679 BIRNLEX:899 UMLS:C0017679 ncithesaurus:Glossopharyngeal_Nerve UMLS:C1305752 BIRNLEX:899 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=701 BIRNLEX:899 glossopharyngeal IX EHDAA2:0000709 nervus glossopharyngeus ZFA:0000668 nervus glossopharyngeus [ix] FMA:50870 FMA:TA CN-IX nerve IX NeuroNames:701 nervus glossopharyngeus Cranial nerve that innervates the muscles of the tongue. Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO] Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves 12n AAO:0010477 BAMS:12n BAMS:XIIn BAMS:nXII BIRNLEX:820 BTO:0003386 EHDAA2:0000798 EHDAA:2859 EMAPA:17269 FMA:50871 GAID:828 HBA:9343 MA:0001094 MBA:813 MESH:D007002 NCIT:C12732 OpenCyc:Mx4rv9eWA5wpEbGdrcN5Y29ycA UMLS:C0020614 VHOG:0000693 XAO:0004215 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=704 cranial nerve XII hypoglossal XII hypoglossal XII nerve hypoglossal nerve [XII] hypoglossal nerve tree nervus hypoglossus [xii] twelfth cranial nerve uberon CN-XII hypoglossal nerve/ root nerve XII nervi hypoglossalis nervus hypoglossus UBERON:0001650 hypoglossal nerve Cranial nerve that innervates the muscles of the tongue. ISBN:080184780X VHOG:0000693 Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000693 VHOG In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis ISBN:080184780X Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO] 2012-06-20 AAO:0010477 AAO AAO:EJS Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] 2012-09-17 VHOG:0000693 VHOG 12n BIRNLEX:820 NIFSTD:NeuroNames_abbrevSource UMLS:C0020614 BIRNLEX:820 UMLS:C0020614 ncithesaurus:Hypoglossal_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=704 BIRNLEX:820 cranial nerve XII BIRNLEX:820 hypoglossal XII EHDAA2:0000798 nervus hypoglossus [xii] FMA:50871 FMA:TA CN-XII VHOG:0000693 hypoglossal nerve/ root BAMS:12n nerve XII NeuroNames:704 nervi hypoglossalis NeuroNames:704 nervus hypoglossus The pulmonary artery that supplies the right lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37378 FMA:50872 MA:0002500 NCIT:C33489 UMLS:C0923924 galen:RightPulmonaryArtery right main pulmonary artery right pulmonary arterial tree uberon arteria pulmonalis dextra UBERON:0001651 right pulmonary artery The pulmonary artery that supplies the right lung. UBERON:cjm EMAPA:37378 MA:th UMLS:C0923924 ncithesaurus:Right_Pulmonary_Artery arteria pulmonalis dextra The pulmonary artery that supplies the left lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37097 FMA:50873 MA:0002032 NCIT:C32971 UMLS:C0923925 galen:LeftPulmonaryArtery left main pulmonary artery left pulmonary arterial tree uberon arteria pulmonalis sinistra UBERON:0001652 left pulmonary artery The pulmonary artery that supplies the left lung. UBERON:cjm EMAPA:37097 MA:th UMLS:C0923925 ncithesaurus:Left_Pulmonary_Artery arteria pulmonalis sinistra 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 OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA UMLS:C0226532 face vein vein of face uberon anterior facial vein vena facialis anterior UBERON:0001653 facial vein 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]. 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 vena facialis anterior The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]. EMAPA:37140 FMA:50981 GAID:530 MA:0002096 MESH:D002550 NCIT:C53037 UMLS:C0007797 XAO:0004160 uberon venae cerebri venae encephali UBERON:0001663 cerebral vein The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]. EMAPA:37140 MA:th UMLS:C0007797 ncithesaurus:Cerebral_Vein venae cerebri venae encephali A vein that drains the cerebellum. EMAPA:37139 FMA:51227 MA:0002093 NCIT:C53032 UMLS:C0226601 cerebellum vein epencephalon-1 vein vein of cerebellum vein of epencephalon-1 uberon UBERON:0001668 cerebellar vein A vein that drains the cerebellum. EMAPA:37139 MA:th UMLS:C0226601 ncithesaurus:Cerebellar_Vein cerebellum vein OBOL:automatic epencephalon-1 vein OBOL:automatic vein of cerebellum OBOL:automatic vein of epencephalon-1 OBOL:automatic 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 TAO:0000295 UMLS:C0040995 VHOG:0000694 XAO:0000427 XAO:0000428 ZFA:0000295 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 ncithesaurus Bgee:AN The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. 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. XAO:0004093 UMLS:C0040995 ncithesaurus:Trigeminal_Ganglion 5th ganglion ZFA:0000295 Gasserian ganglion fifth ganglion ZFA:0000295 ganglion of trigeminal complex semilunar ganglion ISBN:0471888893 trigeminal V ganglion MA:0001080 fused trigeminal ganglion NCBITaxon:32524 Gasser's ganglion BTO:0001231 Gasserian ganglia ganglion of trigeminal nerve BTO:0001231 ganglion semilunare ganglion trigeminale ganglion trigeminale BTO:0001231 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 OpenCyc:Mx4rwQtsiZwpEbGdrcN5Y29ycA UMLS:C0028784 uberon occipital complex occipital squama os occipitale UBERON:0001676 occipital bone FMA FMA basi paired exo and supra occipital bones MA-modified interparietal (postparietal) 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 fusion of basi-, exo- and supra-occipitals (and maybe tabular) Kardong UMLS:C0028784 ncithesaurus:Occipital_Bone occipital complex os occipitale the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA EHDAA:6035 EMAPA:17682 FMA:52737 GAID:232 MA:0001476 MESH:D013701 NCIT:C12797 OpenCyc:Mx4rvbkAk5wpEbGdrcN5Y29ycA UMLS:C0039484 VHOG:0000800 uberon os temporale UBERON:0001678 temporal bone FMA petrosal squamosal plus angular temporal series styloid process the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous ISBN:0-683-40008-8 MP:0005272 fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) chond. The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. [WP] Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA FMA UMLS:C0039484 ncithesaurus:Temporal_Bone os temporale A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified]. Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO] relationship loss: part_of hyoid plate (AAO:0000664)[AAO] The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia. AAO:0000684 EMAPA:18650 FMA:52749 GAID:197 MA:0001484 MESH:D006928 NCIT:C32752 UMLS:C0020417 VHOG:0001325 uberon hyoid hyoid bone hyoideum lingual bone os hyoideum UBERON:0001685 hyoid bone FMA Wikipedia Wikipedia A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified]. Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO] 2012-06-20 AAO:0000684 AAO AAO:LAP relationship loss: part_of hyoid plate (AAO:0000664)[AAO] 2012-06-20 AAO:0000684 AAO The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia. https://github.com/obophenotype/uberon/issues/548 WP UMLS:C0020417 ncithesaurus:Hyoid_Bone hyoid hyoid bone hyoideum lingual bone os hyoideum os hyoideum Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. http://langual.org The organ of hearing and of equilibrium. [TFD][VHOG] Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] auricular AAO:0011014 BIRNLEX:1062 BTO:0000368 CALOHA:TS-1165 EFO:0000826 EHDAA2:0000423 EHDAA:502 EMAPA:16193 EV:0100353 FMA:52780 GAID:62 MA:0000236 MAT:0000138 MESH:D004423 MIAA:0000138 NCIT:C12394 OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA UMLS:C0013443 UMLS:C0521421 VHOG:0000330 XAO:0000189 galen:Ear http://www.langual.org/langual_thesaurus.asp?termid=C0311 uberon auditory apparatus auris UBERON:0001690 ear Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. GO:0042471 The organ of hearing and of equilibrium. [TFD][VHOG] 2012-09-17 VHOG:0000330 VHOG Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] 2012-09-17 VHOG:0000330 VHOG DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005) UMLS:C0013443 BIRNLEX:1062 UMLS:C0013443 ncithesaurus:Ear UMLS:C0521421 BIRNLEX:1062 auris BTO:0000368 The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]. The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG] derivative of prootic and opisthotic petrosal EHDAA2:0001452 EMAPA:17683 FMA:52871 GAID:234 MA:0001477 MESH:D010579 NCIT:C32316 UMLS:C1261761 VHOG:0001553 pars petrosa (os temporale) pars petrosa ossis temporalis petromastoid part of temporal bone temporal bone petrous part uberon petrosal bone petrous bone UBERON:0001694 petrous part of temporal bone FMA The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]. The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG] 2012-09-17 VHOG:0001553 VHOG petrosal VHOG:0001553 UMLS:C1261761 ncithesaurus:Ciliary_Process pars petrosa (os temporale) FMA:52871 petromastoid part of temporal bone FMA:52871 petrosal bone FMA:52871 petrous bone FMA:52871 the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve) resolve facial VII vs geniculate (see EHDAA2) 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] geniculate BAMS:GgVII EFO:0003669 EHDAA2:0000491 EHDAA2:0004623 EHDAA:5567 EHDAA:6644 EMAPA:17569 FMA:53414 GAID:718 MA:0001076 MESH:D005830 NCIT:C12721 TAO:0001291 UMLS:C0017406 VHOG:0000707 ZFA:0001291 facial VII ganglion gVII ganglion genicularum genicular ganglion uberon facial ganglion ganglion geniculi ganglion geniculi nervi facialis geniculate ganglion internal genu UBERON:0001700 geniculate ganglion ncithesaurus EHDAA2:0004623 ZFA EHDAA2:0004623 EHDAA2:0000491 the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve) ISBN:0-683-40008-8 MP:0001082 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:0000707 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) geniculate UMLS:C0017406 ncithesaurus:Geniculate_Ganglion facial VII ganglion MA:0001076 gVII ZFA:0001291 ganglion genicularum FMA:53414 genicular ganglion genicular ganglion FMA:53414 facial ganglion ZFA:0001291 ganglion geniculi ganglion geniculi nervi facialis geniculate ganglion MA:0001076 internal genu The group of neuron cell bodies associated with the ninth cranial nerve. 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] EHDAA2:0000710 EHDAA:2838 EMAPA:16795 FMA:53471 MA:0001077 TAO:0001301 VHOG:0000702 ZFA:0001301 ganglion of glossopharyngeal nerve ganglion of glosspharyngeal nerve glossopharyngeal IX ganglion petrosal ganglion uberon gIX UBERON:0001701 glossopharyngeal ganglion ZFA dorsal EHDAA2 ISBN:0471888893 ZFA ventrolateral EHDAA2 ISBN:0471888893 ZFA The group of neuron cell bodies associated with the ninth cranial nerve. MP:0001096 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:0000702 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) ganglion of glosspharyngeal nerve FMA:53471 glossopharyngeal IX ganglion MA:0001077 petrosal ganglion ZFA:0001301 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 TAO:0001580 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. TAO:MAH 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 braincase ZFA:0001580 An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong. Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO] a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG] in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures AAO:0000314 BTO:0002096 EHDAA2:0001226 EHDAA:6801 EMAPA:17604 FMA:54378 GAID:350 MA:0000284 MESH:D009296 NCIT:C12424 TAO:0000130 UMLS:C0027423 VHOG:0000271 ZFA:0000130 cavity of nose cavity of olfactory apparatus nasal canal nasal conduit space nasal fossa olfactory chamber cavity uberon cavitas nasalis cavitas nasi cavum nasi nasal pit olfactory cavity olfactory chamber olfactory pit UBERON:0001707 nasal cavity cjm An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO] 2012-06-20 AAO:0000314 AAO AAO:LAP a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG] 2012-09-17 VHOG:0000271 VHOG DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006) in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures HP UMLS:C0027423 ncithesaurus:Nasal_Cavity cavity of olfactory apparatus nasal canal ZFA:0000130 nasal conduit space nasal fossa olfactory chamber cavity cavitas nasalis BTO:0002096 cavitas nasi cavitas nasi BTO:0002096 cavum nasi olfactory chamber olfactory pit ZFA:0000130 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 OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA TAO:0001227 UMLS:C0022359 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. 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 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 VHOG:0000453 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 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] 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) 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 TAO:0000013 VHOG:0000076 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 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 A muscular organ in the floor of the mouth. in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence. tongue http://langual.org A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG] Muscular organ in the floor of the mouth.[FEED] The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] glossal lingual Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions AAO:0010360 BTO:0001385 CALOHA:TS-1050 EFO:0000833 EHDAA2:0002062 EHDAA:9144 EMAPA:17185 EV:0100058 FMA:54640 GAID:816 MA:0000347 MAT:0000040 MESH:D014059 MIAA:0000040 NCIT:C12422 OpenCyc:Mx4rvVjmJ5wpEbGdrcN5Y29ycA_53KXLq9EdqAAAACs6hnmQ TAO:0005333 UMLS:C0040408 VHOG:0000419 XAO:0000446 ZFA:0005333 http://www.langual.org/langual_thesaurus.asp?termid=C0189 uberon glossus UBERON:0001723 tongue GO BTO EHDAA2 FMA ZFA MA anterior 2/3 Wikipedia Wikipedia definitional A muscular organ in the floor of the mouth. FEED:rd A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG] 2012-09-17 VHOG:0000419 VHOG Muscular organ in the floor of the mouth.[FEED] 2012-07-02 FEED http://www.feedexp.org The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]. GO:0043586 Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000419 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) UMLS:C0040408 ncithesaurus:Tongue glossus The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis. EMAPA:35264 FMA:54816 MA:0001502 uberon UBERON:0001725 cranial synchondrosis FMA The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis. BIRNLEX:4102 EMAPA:32777 FMA:54819 MA:0001593 NCIT:C33258 UMLS:C0226964 UMLS:C1289183 lingual papilla tongue papilla uberon UBERON:0001726 papilla of tongue FMA-modified UMLS:C0226964 BIRNLEX:4102 UMLS:C0226964 ncithesaurus:Papilla_of_the_Tongue UMLS:C1289183 BIRNLEX:4102 A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. A chemoreceptive organ.[AAO] One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish. arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL) AAO:0010573 BIRNLEX:4101 BTO:0000989 CALOHA:TS-1015 EMAPA:35850 FMA:54825 GAID:815 MA:0001591 MESH:A08.800.550.700.120.800 NCIT:C96518 OpenCyc:Mx4rvVjan5wpEbGdrcN5Y29ycA TAO:0001074 UMLS:C0039337 VHOG:0000130 XAO:0000445 ZFA:0001074 tastebud uberon caliculus gustatorius taste buds taste-bud tastebuds UBERON:0001727 taste bud NIF A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. A chemoreceptive organ.[AAO] 2012-06-20 AAO:0010573 AAO AAO:EJS One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] 2012-09-17 VHOG:0000130 VHOG Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000130 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) UMLS:C0039337 BIRNLEX:4101 UMLS:C0039337 ncithesaurus:Taste_Bud tastebud caliculus gustatorius caliculus gustatorius taste buds taste-bud tastebuds the section of the pharynx that lies above the soft palate The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG] nasopharyngeal In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane BTO:0000662 CALOHA:TS-0663 EHDAA2:0001239 EHDAA:7086 EMAPA:17670 EV:0100066 FMA:54878 GAID:339 MA:0000443 MAT:0000447 MESH:A03.867.557 NCIT:C12423 OpenCyc:Mx4rwUPoDJwpEbGdrcN5Y29ycA UMLS:C0027442 VHOG:0000375 nasal part of pharynx rhinopharynx uberon Nasenrachenraum epipharynx pars nasalis pharyngis UBERON:0001728 nasopharynx the section of the pharynx that lies above the soft palate MGI:cwg MP:0002251 The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG] 2012-09-17 VHOG:0000375 VHOG UMLS:C0027442 ncithesaurus:Nasopharynx Nasenrachenraum BTO:0000662 epipharynx pars nasalis pharyngis A 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 XAO:0000105 lumen of pharynx pharyngeal cavity uberon cavitas pharyngealis cavitas pharyngis UBERON:0001731 cavity of pharynx XAO A anatomical space that is enclosed by a pharynx. OBOL:automatic cavitas pharyngealis cavitas pharyngis BTO:0002097 the circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils FMA:55070 MA:0000752 NCIT:C73468 UMLS:C0459892 Waldeyer's ring Waldeyer's tonsillar ring anulus lymphoideus pharyngis oropharyngeal lymphoid tissue pharyngeal lymphatic ring pharyngeal lymphoid ring uberon UBERON:0001735 tonsillar ring the circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils MGI:cwg MP:0002379 UMLS:C0459892 ncithesaurus:Waldeyers_Tonsillar_Ring anulus lymphoideus pharyngis FMA:55070 FMA:TA Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG] The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG] In humans, they account for 70% of the salivary volume and weigh about 15 grams. [WP,unvetted] In mouse, multilobed and lobulated, on the ventral midline of the neck in mice, submandibular gland development initiates as a thickening of the oral epithelium; around E12 an initial (single) epithelial bud on a stalk grows into a condensing neural crest-derived mesenchyme; clefts in the epithelium result in 3-5 epithelial buds at E13.5, and branching morphogenesis occurs with continued proliferation, successive rounds of cleft formation, duct elongation, and duct lumen formation, so that by E14 the gland is highly branched (multi-lobed); functional differentiation, with the appearance of proacinar cells and secretory products begins after E15 and continues to birth; acinar differentiation continues postnatally with final differentiation of the granular convoluted tubules at puberty[MGI:anna] The submandibular is the first major salivary gland to develop in the embryo, followed by the neighbouring sublingual and then the parotid.[PMID:17336109] The term submandibular as used in humans, is incorrect due the difference in topography of these structures[http://www.avdc.org] BTO:0001316 CALOHA:TS-0988 EFO:0001387 EMAPA:18812 EV:0100061 FMA:55093 GAID:942 MA:0001589 MESH:D013363 NCIT:C12233 UMLS:C0038556 VHOG:0000364 mandibular gland mandibular salivary gland submandibular salivary gland uberon glandula submandibularis maxillary gland submaxillary gland UBERON:0001736 lobular, sexually dimorphic in mouse submandibular gland FMA-abduced-lr Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. MGI:anna Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG] 2012-09-17 VHOG:0000364 VHOG The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG] 2012-09-17 VHOG:0000364 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.525 In mouse, multilobed and lobulated, on the ventral midline of the neck ISBN:0123813611 UMLS:C0038556 ncithesaurus:Submandibular_Gland mandibular gland mandibular salivary gland glandula submandibularis A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] laryngeal AAO:0000268 BTO:0001208 CALOHA:TS-0532 EFO:0000838 EHDAA2:0004063 EMAPA:18333 EV:0100039 FMA:55097 GAID:108 MA:0000414 MAT:0000187 MESH:D007830 MIAA:0000187 NCIT:C12420 OpenCyc:Mx4rvViOnZwpEbGdrcN5Y29ycA UMLS:C0023078 VHOG:0001279 XAO:0003081 galen:Larynx uberon Kehlkopf@de UBERON:0001737 larynx EHDAA2 A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] 2012-07-02 FEED http://www.feedexp.org Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] 2012-06-20 AAO:0000268 AAO AAO:BJB (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001279 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 UMLS:C0023078 ncithesaurus:Larynx Kehlkopf@de BTO:0001208 The cartilaginous structures that support the larynx. (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] BTO:0003660 EHDAA:8157 EMAPA:18697 FMA:55108 GAID:107 MA:0001758 MESH:A02.165.507 NCIT:C12281 UMLS:C0023050 VHOG:0001550 cartilage of larynx cartilagines laryngeales larynx cartilage uberon UBERON:0001739 laryngeal cartilage The cartilaginous structures that support the larynx. MP:0002256 (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001550 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 UMLS:C0023050 ncithesaurus:Laryngeal_Cartilage cartilage of larynx FMA:55108 cartilagines laryngeales larynx cartilage VHOG:0001550 A ligament that is part of a larynx and connexts the cartilages of the larynx EMAPA:37626 FMA:55131 MA:0001755 NCIT:C32933 UMLS:C0458519 laryngeal ligament larynx ligament uberon UBERON:0001743 ligament of larynx FMA A ligament that is part of a larynx and connexts the cartilages of the larynx EMAPA:37626 MA:th UMLS:C0458519 ncithesaurus:Laryngeal_Ligament larynx ligament MA:0001755 Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]. BTO:0000753 CALOHA:TS-0584 FMA:55220 GAID:342 MA:0002436 MESH:D008221 NCIT:C13049 UMLS:C0024296 galen:LymphoidTissue lymphatic tissue lymphocytic tissue uberon UBERON:0001744 lymphoid tissue FMA Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]. lampreys lack organized lymphoid tissue NCBIBook:NBK27108 UMLS:C0024296 ncithesaurus:Lymphoid_Tissue EMAPA:37767 FMA:55513 MA:0002675 NCIT:C33781 UMLS:C0229575 capsula fibrosa glandulae thyroideae fibrous capsule of thyroid gland thyroid capsule thyroid gland capsule uberon UBERON:0001746 capsule of thyroid gland EMAPA:37767 MA:th UMLS:C0229575 ncithesaurus:Thyroid_Gland_Capsule capsula fibrosa glandulae thyroideae FMA:55513 FMA:TA fibrous capsule of thyroid gland FMA:55513 thyroid gland capsule MA:0002675 A parenchyma that is part of a thyroid follicle [Automatically generated definition]. BTO:0004579 EMAPA:37769 FMA:55515 MA:0000730 parenchyma of thyroid parenchyma of thyroid follicle parenchyma of thyroid gland follicle thyroid follicle parenchyma thyroid gland follicle parenchyma thyroid gland parenchyma thyroid parenchyma uberon parenchyma glandulae thyroideae UBERON:0001747 parenchyma of thyroid gland A parenchyma that is part of a thyroid follicle [Automatically generated definition]. OBOL:automatic EMAPA:37769 MA:th parenchyma of thyroid OBOL:accepted parenchyma of thyroid follicle OBOL:automatic parenchyma of thyroid gland follicle OBOL:automatic thyroid follicle parenchyma OBOL:automatic thyroid gland follicle parenchyma OBOL:automatic thyroid parenchyma OBOL:accepted parenchyma glandulae thyroideae BTO:0004579 A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta. TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye EMAPA:35462 FMA:55605 GAID:901 MA:0000274 MESH:D007765 NCIT:C32905 UMLS:C0022903 apparatus lacrimalis lacrymal system uberon lacrimal drainage system nasolacrimal drainage system nasolacrimal system UBERON:0001750 lacrimal apparatus MA HPO:pr ISBN:0781772214 A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta. MGI:anna this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye ncit UMLS:C0022903 ncithesaurus:Lacrimal_Apparatus apparatus lacrimalis lacrymal system MGI:anna lacrimal drainage system nasolacrimal drainage system nasolacrimal system HPO:pr Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[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] 10n AAO:0010475 BAMS:10n BAMS:Xn BIRNLEX:801 BTO:0003472 EFO:0002549 EMAPA:37797 FMA:5731 GAID:721 HBA:9337 MA:0001106 MBA:917 MESH:D014630 NCIT:C12812 OpenCyc:Mx4rviHk2ZwpEbGdrcN5Y29ycA TAO:0000453 UMLS:C0042276 UMLS:C1305910 VHOG:0000737 XAO:0003097 ZFA:0000453 galen:VagusNerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 nervus vagus [x] tenth cranial nerve vagus vagus X nerve vagus nerve [X] vagus nerve tree uberon CN-X cranial nerve X nerve X nervus vagus pneuomgastric nerve vagal nerve vagus nerve or its root UBERON:0001759 vagus nerve motor Wikipedia Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). ISBN:0471209627 Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] 2012-06-20 AAO:0010475 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:0000737 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 10n BIRNLEX:801 NIFSTD:NeuroNames_abbrevSource EMAPA:37797 MA:th UMLS:C0042276 BIRNLEX:801 UMLS:C0042276 ncithesaurus:Vagus_Nerve UMLS:C1305910 BIRNLEX:801 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 BIRNLEX:801 nervus vagus [x] FMA:5731 FMA:TA vagus X nerve MA:0001106 nerve X NeuroNames:702 nervus vagus nervus vagus BTO:0003472 pneuomgastric nerve BTO:0003472 vagus nerve or its root BAMS:10n 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 UMLS:C0003151 VHOG:0001431 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 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 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 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 UMLS:C0042160 tunica vasculosa of eyeball uvea uveal tract uberon pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi vascular layer of eyeball UBERON:0001768 uvea 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 UMLS:C0042160 ncithesaurus:Uvea tunica vasculosa of eyeball FMA:58103 uvea FMA:58103 uveal tract FMA:58103 pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi 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 OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA TAO:0001238 UMLS:C0022077 VHOG:0000101 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 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) 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 TAO:0002187 UMLS:C0459875 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 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 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 OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA UMLS:C0036410 VHOG:0001274 XAO:0000183 ZFA:0005563 uberon scleral capsule UBERON:0001773 Disease notes: implicated in rheumatoid arthritis. sclera FMA ISBN:0781772214 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. 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]. 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 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. 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 UMLS:C0008779 VHOG:0000102 XAO:0000186 ocular ciliary body uberon anterior uvea ciliary bodies corpus ciliare UBERON:0001775 ciliary body 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 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) UMLS:C0008779 ncithesaurus:Ciliary_Body ciliary bodies VHOG:0000102 corpus ciliare corpus ciliare 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 TAO:0005229 UMLS:C0008520 VHOG:0001568 ZFA:0005229 choroid choroid coat choroidea eye choroid posterior uvea uberon chorioid choroidea optic choroid UBERON:0001776 optic choroid 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]. MP treats posterior uvea and optic choroid as distinct MP UMLS:C0008520 ncithesaurus:Choroid choroid MA:0000263 choroid coat choroidea eye choroid VHOG:0001568 posterior uvea chorioid BTO:0001829 choroidea 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 TAO:0002189 UMLS:C0010040 ZFA:0001685 corneal stroma stroma of cornea substantia propria corneae uberon UBERON:0001777 substantia propria of cornea 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 UMLS:C0459736 ciliary body epithelium epithelium of ciliary body ocular ciliary epithelium uberon UBERON:0001778 ciliary epithelium FMA MA Wikipedia A double layer covering the ciliary body that produces aqueous humor. 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 ZFA:0005569 iridial stroma stroma of iris uberon UBERON:0001779 iris stroma The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. 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 OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA UMLS:C0037941 VHOG:0000824 XAO:0003101 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 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 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 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 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 OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA TAO:0000641 UMLS:C0010268 UMLS:C1269897 VHOG:0000279 XAO:0000429 XAO:0003089 ZFA:0000641 cranial neural tree organ uberon cranial nerves nervus cranialis UBERON:0001785 cranial nerve Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. 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 UMLS:C0010268 BIRNLEX:1623 UMLS:C0010268 ncithesaurus:Cranial_Nerve UMLS:C1269897 BIRNLEX:1623 nervus cranialis 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 OpenCyc:Mx4rvdGd-5wpEbGdrcN5Y29ycA UMLS:C0003662 VHOG:0000548 ZFA:0005564 aqueous humor aqueous humour humor aquosus uberon UBERON:0001796 aqueous humor of eyeball 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]. 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 (...) 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 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 UMLS:C0003153 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 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 UMLS:C0003153 ncithesaurus:Anterior_Eye_Segment anterior segment eye ZFA:0005566 segmentum anterius bulbi oculi 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 UMLS:C0278450 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 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 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 TAO:0001326 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. 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 UMLS:C0229232 VHOG:0000550 ZFA:0005574 capsula lentis lens capsule uberon UBERON:0001804 capsule of lens EHDAA2 the elastic, clear, membrane-like structure, that is outer most layer of the lens MGI:smb MP:0003236 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 (...) 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 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 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 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. 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 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 NCIT:C12467 UMLS:C0017071 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 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 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 ganglion sympathicum BTO:0001333 Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. BTO:0001256 EHDAA2:0001400 EMAPA:32813 FMA:5894 MA:0002469 NCIT:C52557 NLXANAT:100303 UMLS:C0017069 uberon ganglion parasympathicum UBERON:0001808 parasympathetic ganglion Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. NLXANAT:100303 UMLS:C0017069 ncithesaurus:Parasympathetic_Ganglion ganglion parasympathicum ganglion parasympathicum BTO:0001256 The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands. The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, they are situated in the upper, outer portion of each orbit Innervation is highly complex and species-specific BTO:0000044 CALOHA:TS-0512 EFO:0001389 EMAPA:35463 EV:0100339 FMA:59101 MA:0001296 NCIT:C12346 UMLS:C0022907 VHOG:0001476 glandula lacrimalis lacrimal-preorbital gland uberon glandula praeorbitalis preorbital gland tear gland UBERON:0001817 lacrimal gland The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands. FMA:59101 The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland]. UMLS:C0022907 ncithesaurus:Lacrimal_Gland glandula lacrimalis lacrimal-preorbital gland glandula praeorbitalis NCBITaxon:91561 preorbital gland NCBITaxon:91561 tear gland BTO:0000044 A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass. Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG] Sebaceous glands are also limited to mammals.[well established][VHOG] BTO:0001980 CALOHA:TS-2384 EMAPA:35754 EV:0100161 FMA:59160 GAID:900 MA:0002565 MESH:D012627 NCIT:C33519 UMLS:C0036505 VHOG:0001468 uberon glandula sebacea glandula sebaceae sebaceous follicle UBERON:0001821 sebaceous gland Wikipedia definitional A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. MP:0000647 Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG] 2012-09-17 VHOG:0001468 VHOG Sebaceous glands are also limited to mammals.[well established][VHOG] 2012-09-17 VHOG:0001468 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102 UMLS:C0036505 ncithesaurus:Sebaceous_Gland glandula sebacea glandula sebaceae BTO:0001980 sebaceous follicle BTO:0001980 One of the cartilage structures in the nose that provide form and support[WP]. CALOHA:TS-0655 EMAPA:37681 FMA:59502 MA:0001883 NCIT:C49593 UMLS:C0225415 cartilage of nose uberon UBERON:0001823 nasal cartilage MA One of the cartilage structures in the nose that provide form and support[WP]. EMAPA:37681 MA:th UMLS:C0225415 ncithesaurus:Nasal_Cartilage The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. EMAPA:18334 FMA:59662 GAID:301 MA:0001766 MESH:D007820 NCIT:C49246 UMLS:C0023053 laryngeal mucosa larynx mucosa larynx mucosa of organ larynx mucous membrane larynx organ mucosa mucosa of organ of larynx mucous membrane of larynx organ mucosa of larynx tunica mucosa laryngis uberon laryngeal mucous membrane UBERON:0001824 mucosa of larynx The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. MP:0002261 UMLS:C0023053 ncithesaurus:Laryngeal_Mucosa larynx mucosa of organ OBOL:automatic larynx mucous membrane OBOL:automatic larynx organ mucosa OBOL:automatic mucosa of organ of larynx OBOL:automatic organ mucosa of larynx OBOL:automatic tunica mucosa laryngis FMA:59662 FMA:TA laryngeal mucous membrane EMAPA:18334 The mucous membrane that lines the nasal cavity[MP]. TODO - check lining vs part of. split olfactory and nasal mucosa? BTO:0000912 CALOHA:TS-0657 EMAPA:36026 FMA:59684 GAID:302 mucosa of nose mucous membrane of nose tunica mucosa nasalis tunica mucosa nasi uberon nasal mucosa UBERON:0001826 nasal cavity mucosa The mucous membrane that lines the nasal cavity[MP]. MP:0002238 mucosa of nose FMA:59684 mucous membrane of nose FMA:59684 tunica mucosa nasi FMA:59684 FMA:TA Aqueous substance secreted by the lacrimal gland. BTO:0001499 CALOHA:TS-1016 EMAPA:36537 ENVO:02000034 FMA:59756 GAID:1173 MA:0002508 MESH:D013666 NCIT:C33739 UMLS:C0039409 galen:Tear galen:Tears lacrimal fluid lacrimal gland secretion lacrimal secretion tear tears uberon tear fluid UBERON:0001827 secretion of lacrimal gland Aqueous substance secreted by the lacrimal gland. UMLS:C0039409 ncithesaurus:Tear tear FMA:59756 tears tear fluid BTO:0001499 One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. There are 3 pairs of major salivary glands in human and mouse FMA:59788 MA:0002478 NCIT:C12999 UMLS:C0930553 galen:MajorSalivaryGland uberon UBERON:0001829 major salivary gland One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. MP:0003792 There are 3 pairs of major salivary glands in human and mouse ISBN:0123813611 UMLS:C0930553 ncithesaurus:Major_Salivary_Gland 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 OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA TAO:0007006 UMLS:C0023759 VHOG:0000677 ZFA:0007006 galen:Lip uberon labia oris lips UBERON:0001833 lip ZFA BTO FMA-implicit VHOG ZFA cjm 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] 2012-08-14 TAO:0007006 TAO ZFIN:curator UMLS:C0023759 ncithesaurus:Lip labia oris 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 OpenCyc:Mx4rv842UpwpEbGdrcN5Y29ycA TAO:0002060 UMLS:C0458583 ZFA:0005225 lower jaw lip uberon labium inferius oris UBERON:0001835 lower lip Lip that covers the lower portion of the mouth.[TAO]. TAO:0002060 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 labium inferius oris A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. salivary We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin BTO:0001202 CALOHA:TS-0891 EMAPA:36536 ENVO:02000036 FMA:59862 GAID:1167 MA:0002507 MAT:0000444 MESH:D012463 NCIT:C13275 OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA UMLS:C0036087 galen:Saliva salivary gland secretion uberon sailva normalis saliva atomaris saliva molecularis UBERON:0001836 saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. GO:0046541 We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin GO UMLS:C0036087 ncithesaurus:Saliva salivary gland secretion FMA:59862 sailva normalis saliva atomaris saliva molecularis The duct of a salivary gland. BTO:0005115 EMAPA:35750 FMA:59908 GAID:939 MA:0001586 MESH:D018987 NCIT:C32486 salivary duct salivary gland duct uberon secretory duct UBERON:0001837 duct of salivary gland The duct of a salivary gland. secretory duct BTO:0005115 A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]. AAO:0011078 BTO:0004685 CALOHA:TS-2080 EMAPA:36580 EV:0100362 FMA:60179 MA:0000238 NCIT:C33227 UMLS:C0458699 VHOG:0001219 XAO:0000193 osseous labyrinth uberon labyrinthus osseus osseus labyrinth UBERON:0001839 Ideally we would place a spatially disjoint from relationship to membranous labyrinth, but there are many parts in common. this should be resolved. bony labyrinth FMA MA FMA A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]. UMLS:C0458699 ncithesaurus:Osseous_Labyrinth labyrinthus osseus the spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]. A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG] Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG] cochlear The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: 'In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)' the cochlea is coiled in most mammals, monotremes being the exceptions. sources vary in connection to bony labyrinth AAO:0000253 BIRNLEX:1190 BTO:0000267 CALOHA:TS-0151 EFO:0000357 EMAPA:17597 EV:0100363 FMA:60201 GAID:724 MA:0000240 MAT:0000144 MESH:D003051 MIAA:0000144 NCIT:C12395 NIFSTD_RETIRED:birnlex_883 OpenCyc:Mx4rvqfJmJwpEbGdrcN5Y29ycA TAO:0000374 UMLS:C0009195 UMLS:C1278895 VHOG:0000691 XAO:0000197 ZFA:0000374 cochlear part of bony labyrinth lagena uberon cochleae cochlear duct cochlear organ lagenas UBERON:0001844 cochlea FMA VHOG XAO ncit the spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]. ISBN:0-683-40008-8 MP:0000031 A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG] 2012-09-17 VHOG:0000691 VHOG Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG] 2012-09-17 VHOG:0000691 VHOG DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998) sources vary in connection to bony labyrinth XAO UMLS:C0009195 BIRNLEX:1190 UMLS:C0009195 ncithesaurus:Cochlea UMLS:C1278895 BIRNLEX:1190 lagena XAO:0000197 cochleae cochlear organ BTO:0000267 lagenas ZFA:0000374 Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] AAO:0000238 BIRNLEX:1196 BTO:0000630 CALOHA:TS-0478 EFO:0001363 EHDAA2:0000831 EHDAA:504 EMAPA:16194 EV:0100361 FMA:60909 GAID:871 MA:0000237 MAT:0000145 MESH:D007758 MIAA:0000145 NCIT:C12499 OpenCyc:Mx4rwJ8SsJwpEbGdrcN5Y29ycA TAO:0000217 UMLS:C0022889 UMLS:C1268973 VHOG:0000284 XAO:0000192 ZFA:0000217 galen:InnerEar inner ear uberon auris interna labyrinth otocyst UBERON:0001846 internal ear definitional Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. ZFIN:curator The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000217 TAO ZFIN:curator The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000284 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366 UMLS:C0022889 BIRNLEX:1196 UMLS:C0022889 ncithesaurus:Internal_Ear UMLS:C1268973 BIRNLEX:1196 auris interna BTO:0000630 A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct. TODO - resolve lacrimal canaliculus vs larcimal duct chelonians lack a lacrimal duct, and lacrimal/harderian secretions remain in or spill from the conjunctival sac[PMID:7559104] EMAPA:19245 FMA:61063 MA:0001295 uberon lacrimal duct tear duct UBERON:0001850 lacrimal drainage system FMA FMA A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct. lacrimal duct FMA:61063 MA:0001295 tear duct MA:0001295 Outermost layer of an organ[WP]. cortical this class is used more generically than in FMA, and includes e.g. cortex of hair EFO:0000383 EHDAA:9344 FMA:61109 galen:Cortex cortex cortex of organ uberon UBERON:0001851 cortex Outermost layer of an organ[WP]. this class is used more generically than in FMA, and includes e.g. cortex of hair FMA cortex FMA:61109 Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP]. The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans. waterproofs skin BTO:0001981 ENVO:02000037 FMA:61304 GAID:1168 MA:0002538 MESH:D012629 NCIT:C13276 UMLS:C0036511 uberon UBERON:0001866 sebum Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP]. BTO:0001981 UMLS:C0036511 ncithesaurus:Sebum A zone of skin that is part of a chest [Automatically generated definition]. check FMA:61415 EMAPA:37279 FMA:61416 MA:0000553 anterior thoracic region zone of skin anterolateral part of thorax zone of skin chest skin chest zone of skin front of thorax zone of skin zone of skin of anterior chest zone of skin of anterior part of thorax zone of skin of anterior thoracic region zone of skin of anterolateral part of thorax zone of skin of chest zone of skin of front of thorax uberon zone of skin of pectoral part of chest UBERON:0001868 skin of chest A zone of skin that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37279 MA:th anterior thoracic region zone of skin OBOL:automatic anterolateral part of thorax zone of skin OBOL:automatic chest zone of skin OBOL:automatic front of thorax zone of skin OBOL:automatic zone of skin of anterior chest FMA:61416 zone of skin of anterior part of thorax FMA:61416 zone of skin of anterior thoracic region OBOL:automatic zone of skin of anterolateral part of thorax OBOL:automatic zone of skin of chest OBOL:automatic zone of skin of front of thorax OBOL:automatic zone of skin of pectoral part of chest FMA:61417 One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA] Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] AAO:0010480 BAMS:HEM BIRNLEX:1042 BTO:0000231 CALOHA:TS-2007 DMBA:15739 EFO:0002521 EMAPA:16653 FMA:61817 MA:0000133 MBA:403 NCIT:C12351 OpenCyc:Mx4rvigx5ZwpEbGdrcN5Y29ycA UMLS:C0228174 UMLS:C0242202 VHOG:0001639 galen:CerebralHemisphere http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=241 uberon cerebrum hemisphere hemispheric regions hemispherium cerebri medial amygdalar nucleus nucleus amygdaloideus medialis nucleus medialis amygdalae UBERON:0001869 cerebral hemisphere FMA-abduced-lr One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA] FMA:61817 Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] 2012-06-20 AAO:0010480 AAO AAO:BJB The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] 2012-09-17 VHOG:0001639 VHOG DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981) UMLS:C0228174 ncithesaurus:Cerebral_Hemisphere UMLS:C0242202 BIRNLEX:1042 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=241 BIRNLEX:1042 cerebrum MA:0000133 VHOG:0001639 hemisphere VHOG:0001639 hemispheric regions BAMS:HEM hemispherium cerebri medial amygdalar nucleus NeuroNames:241 nucleus amygdaloideus medialis NeuroNames:241 nucleus medialis amygdalae NeuroNames:241 Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally. BTO:0000484 DHBA:10161 DMBA:16002 EMAPA:35357 FMA:242199 GAID:674 MA:0000905 NLXANAT:20090601 cortex of frontal lobe frontal lobe cortex gray matter of frontal lobe grey matter of frontal lobe uberon frontal neocortex UBERON:0001870 frontal cortex Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. NLXANAT:20090601 Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally. NLXANAT:20090601 cortex of frontal lobe FMA:242199 frontal lobe cortex FMA:242199 gray matter of frontal lobe FMA:242199 frontal neocortex DHBA:10161 Lower lateral part of the cerebral hemisphere. (MSH) BAMS:TL BAMS:Temporal_lobe BIRNLEX:1160 BTO:0001355 CALOHA:TS-1020 DHBA:12139 EFO:0000917 EMAPA:18797 EV:0100169 FMA:61825 GAID:635 HBA:4132 MAT:0000508 MESH:A08.186.211.730.885.213.863 NCIT:C12353 OpenCyc:Mx4rwQLi-ZwpEbGdrcN5Y29ycA UMLS:C0039485 UMLS:C1268978 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=125 lobus temporalis temporal cortex uberon UBERON:0001871 Boundary notes: It is bounded dorsally by the lateral fissure and posteriorly by an arbitrary border shared with the occipital lobe. [Wikipedia:Temporal_lobe] temporal lobe FMA Lower lateral part of the cerebral hemisphere. (MSH) BIRNLEX:1160 UMLS:C0039485 BIRNLEX:1160 UMLS:C0039485 ncithesaurus:Temporal_Lobe UMLS:C1268978 BIRNLEX:1160 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=125 BIRNLEX:1160 lobus temporalis Upper central part of the cerebral hemisphere. (MSH) parietal region BAMS:Parietal_lobe BIRNLEX:1148 BTO:0001001 CALOHA:TS-0747 DHBA:12131 EFO:0000914 EV:0100168 FMA:61826 GAID:680 HBA:4084 MAT:0000506 MESH:A08.186.211.730.885.213.670 NCIT:C12354 OpenCyc:Mx4rvg-typwpEbGdrcN5Y29ycA UMLS:C0030560 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=95 regio parietalis uberon lobus parietalis UBERON:0001872 parietal lobe FMA Upper central part of the cerebral hemisphere. (MSH) BIRNLEX:1148 UMLS:C0030560 BIRNLEX:1148 UMLS:C0030560 ncithesaurus:Parietal_Lobe_of_the_Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=95 BIRNLEX:1148 regio parietalis FMA:61826 FMA:TA lobus parietalis 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 OpenCyc:Mx4rvtmdUJwpEbGdrcN5Y29ycA UMLS:C0031774 VHOG:0000728 uberon diaphragmatic nerve nervus phrenicus phrenic UBERON:0001884 phrenic nerve 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 UMLS:C0031774 ncithesaurus:Phrenic_Nerve diaphragmatic nerve BTO:0001063 nervus phrenicus nervus phrenicus BTO:0001063 phrenic BTO:0001063 A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces. TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO] Fringe of the tela choroidea of the brain ventricles[MP] choroidal CP BAMS:CHP BAMS:GHP BAMS:chp BAMS:chpl BTO:0000258 CALOHA:TS-0145 EFO:0001915 EMAPA:32741 FMA:61934 GAID:607 MA:0000823 MBA:108 MESH:D002831 NCIT:C12694 TAO:0001443 UMLS:C0008524 VHOG:0001377 ZFA:0001443 chorioid plexus plexus choroideus uberon choroid plexus of cerebral hemisphere plexus choroideus ventricular choroid plexus UBERON:0001886 choroid plexus A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces. ISBN:0471888893 A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO] 2012-08-14 TAO:0001443 TAO ZFIN:curator Fringe of the tela choroidea of the brain ventricles[MP] MP:0000820 CP UMLS:C0008524 ncithesaurus:Choroid_Plexus chorioid plexus FMA:61934 plexus choroideus FMA:61934 FMA:TA choroid plexus of cerebral hemisphere FMA:61934 plexus choroideus The most anterior region the brain including both the telencephalon and diencephalon. Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] prosencephalic FB AAO:0010147 BAMS:FB BAMS:Forebrain BIRNLEX:1509 BTO:0000478 CALOHA:TS-0380 DHBA:10156 DMBA:15566 EFO:0000909 EHDAA2:0000556 EHDAA:3470 EMAPA:16895 FMA:61992 MA:0000170 MAT:0000105 MESH:D016548 MIAA:0000105 NCIT:C40185 TAO:0000109 UMLS:C0085140 VHOG:0000383 XAO:0000011 ZFA:0000109 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 uberon prosencephalon UBERON:0001890 forebrain definitional The most anterior region the brain including both the telencephalon and diencephalon. ZFIN:ZDB-PUB-961014-576 Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] 2012-06-20 AAO:0010147 AAO AAO:BJB The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000109 TAO ZFIN:curator relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] 2012-08-14 TAO:0000109 TAO In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] 2012-09-17 VHOG:0000383 VHOG PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996) FB BIRNLEX:1509 NIFSTD:NeuroNames_abbrevSource UMLS:C0085140 BIRNLEX:1509 UMLS:C0085140 ncithesaurus:Fore-Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 BIRNLEX:1509 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 OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001104 TAO:0000128 UMLS:C0025462 VHOG:0000069 XAO:0000014 ZFA:0000128 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 uberon mesencephalon UBERON:0001891 midbrain 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 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) 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 UMLS:C0025462 ncithesaurus:Mesencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 BIRNLEX:1667 mesencephalon 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 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]. 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) hindbrain segment ZFA:0001064 segment of hindbrain ZFA:0001064 hindbrain neuromeres DHBA:HNM future rhombencephalon MIAA:0000272 rhombomeres VHOG:0000672 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] cerebral telenencephalic In mammals the cortex covers almost the whole of the cerebral hemispheres. In ray-finned fishes and most pronounced in teleosts the roof plate of the embryonic telencephalon extends laterally with the effect that the paired alar plates forming the hemispheric walls roll out lateroventrally in a process called eversion. This is unlike the development in other vertebrate groups. [ZFA:0000079, ISBN:3764351209] In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. supratentorial region AAO:0010479 BAMS:CB BAMS:CH BAMS:IV BAMS:Tel BIRNLEX:1115 BM:Tel BTO:0000239 CALOHA:TS-1018 DHBA:10158 EFO:0000912 EHDAA2:0001982 EMAPA:16910 EV:0100165 FMA:62000 GAID:621 HBA:4007 MA:0000183 MAT:0000421 MBA:567 MESH:D013687 MIAA:0000421 PBA:128011350 TAO:0000079 UMLS:C0039452 VHOG:0000283 XAO:0000012 ZFA:0000079 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 cerebrum endbrain uberon UBERON:0001893 telencephalon Bgee:AN Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. AAO:0010479 XAO:0000012 Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. FMA:62000 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] 2012-06-20 AAO:0010479 AAO AAO:BJB The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000079 TAO ZFIN:curator relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] 2012-08-14 TAO:0000079 TAO From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000283 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) In mammals the cortex covers almost the whole of the cerebral hemispheres. In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. supratentorial region UMLS:C0039452 BIRNLEX:1115 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 BIRNLEX:1115 cerebrum BTO:0000239 EMAPA:16910 FMA:62000 endbrain Swanson:2004 The division of the forebrain that develops from the foremost primary cerebral vesicle. The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] 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] diencephalic in ABA, this is part of the brain stem DiE AAO:0010481 BAMS:DI BAMS:Di BAMS:DiE BAMS:IB BAMS:Zh. BIRNLEX:1503 BM:Die BTO:0000342 CALOHA:TS-0199 DHBA:10389 DMBA:16308 EFO:0000911 EHDAA2:0000385 EHDAA:1969 EHDAA:2645 EHDAA:3472 EMAPA:16896 EV:0100194 FMA:62001 GAID:618 HBA:4391 MA:0000171 MAT:0000420 MBA:1129 MESH:A08.186.211.730.385 MIAA:0000420 NCIT:C12456 OpenCyc:Mx4rwC-V0JwpEbGdrcN5Y29ycA PBA:128013010 TAO:0000101 UMLS:C0012144 VHOG:0000318 XAO:0000013 ZFA:0000101 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=288 between brain interbrain mature diencephalon thalamencephalon uberon betweenbrain diencephalon UBERON:0001894 diencephalon definitional definitional The division of the forebrain that develops from the foremost primary cerebral vesicle. not well differentiated from the cerebrum. (Ariens, p. 868) The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000101 TAO ZFIN:curator Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] 2012-06-20 AAO:0010481 AAO AAO:BJB 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:0000318 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) in ABA, this is part of the brain stem ABA DiE BIRNLEX:1503 NIFSTD:NeuroNames_abbrevSource UMLS:C0012144 BIRNLEX:1503 UMLS:C0012144 ncithesaurus:Diencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=288 BIRNLEX:1503 interbrain Swanson:2004 mature diencephalon FMA:62001 thalamencephalon MGI:anna betweenbrain BTO:0000342 diencephalon 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 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 definitional 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]. 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 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 epencephalon ncithesaurus:Epencephalon UMLS:C0376353 BIRNLEX:965 UMLS:C1516904 ncithesaurus:Epencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA TAO:0000545 UMLS:C0025148 UMLS:C1269575 VHOG:0000181 XAO:0003100 ZFA:0000545 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 bulbus uberon medulla oblonzata metepencephalon UBERON:0001896 medulla oblongata 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 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 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) medulla ABA:MY UMLS:C0025148 BIRNLEX:957 UMLS:C0025148 ncithesaurus:Medulla_Oblongata UMLS:C1269575 BIRNLEX:957 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 BIRNLEX:957 bulbus FMA:62004 FMA:TA medulla oblonzata metepencephalon FMA:62004 Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG] Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO] (...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG] thalamic Th thalamus AAO:0010483 BAMS:TH BAMS:Th BIRNLEX:954 BTO:0001365 CALOHA:TS-1031 DHBA:10390 DMBA:16376 EFO:0000910 EMAPA:17540 EV:0100195 GAID:656 HBA:4392 MA:0000179 MAT:0000109 MBA:549 MESH:A08.186.211.730.385.826 MIAA:0000109 NCIT:C12459 OpenCyc:Mx4rwMPQ65wpEbGdrcN5Y29ycA PBA:128013014 TAO:0001215 UMLS:C0039729 VHOG:0000657 ZFA:0001215 galen:Thalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=300 wider thalamus uberon thalamencephalon thalami thalamus opticus UBERON:0001897 dorsal plus ventral thalamus FMA-abduced-lr Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). BIRNLEX:954 One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG] 2012-09-17 VHOG:0000657 VHOG Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO] 2012-06-20 AAO:0010483 AAO AAO:BJB (...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG] 2012-09-17 VHOG:0000657 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.484 Th BIRNLEX:954 NIFSTD:NeuroNames_abbrevSource thalamus FMA:62007 MA:0000179 UMLS:C0039729 BIRNLEX:954 UMLS:C0039729 ncithesaurus:Thalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=300 BIRNLEX:954 wider thalamus PMCID:PMC3345571 thalamencephalon NeuroNames:300 thalami VHOG:0000657 thalamus opticus NeuroNames:300 A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO] Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO] For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG] hypothalamic all vertebrates contain a hypothalamus Hy AAO:0010484 BAMS:HY BAMS:Hy BIRNLEX:734 BM:Die-Hy BTO:0000614 CALOHA:TS-0469 DHBA:10467 EFO:0000107 EHDAA2:0000802 EHDAA:5446 EMAPA:17536 EV:0100225 FMA:62008 GAID:460 HBA:4540 MA:0000173 MAT:0000112 MBA:1097 MESH:A08.186.211.577.482 MIAA:0000112 NCIT:C12458 OpenCyc:Mx4rwEgr9JwpEbGdrcN5Y29ycA TAO:0000032 UMLS:C0020663 VHOG:0000179 XAO:0004070 ZFA:0000032 galen:Hypothalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=292 preoptico-hypothalamic area preoptico-hypothalamic region uberon hypothalamus UBERON:0001898 hypothalamus FMA EHDAA2 Wikipedia A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. ZFIN:curator Lancelets possess a region similar to the hypothalamus (Murakami, 2005) Ariens, p. 1192 A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000032 TAO ZFIN:curator Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO] 2012-06-20 AAO:0010484 AAO AAO:BJB For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000179 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) all vertebrates contain a hypothalamus WP Hy BIRNLEX:734 NIFSTD:NeuroNames_abbrevSource UMLS:C0020663 BIRNLEX:734 UMLS:C0020663 ncithesaurus:Hypothalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=292 BIRNLEX:734 hypothalamus the epithelial lining of the trachea which contains numerous ciliated cells UBERON:0003227 BTO:0001389 CALOHA:TS-1061 EHDAA2:0002069 EHDAA:5007 EMAPA:16855 EMAPA:18409 FMA:62015 MA:0001862 NCIT:C33797 UMLS:C1179002 VHOG:0001045 epithelial tissue of trachea epithelial tissue of windpipe epithelium of windpipe trachea epithelial tissue trachea epithelium tracheal epithelium windpipe epithelial tissue windpipe epithelium uberon UBERON:0001901 epithelium of trachea the epithelial lining of the trachea which contains numerous ciliated cells ISBN:0-397-51047-0 MGI:cwg MP:0002285 UMLS:C1179002 ncithesaurus:Tracheal_Epithelium epithelial tissue of trachea OBOL:automatic epithelial tissue of windpipe OBOL:automatic epithelium of windpipe OBOL:automatic trachea epithelial tissue OBOL:automatic windpipe epithelial tissue OBOL:automatic windpipe epithelium OBOL:automatic 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 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 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 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 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 TAO:0000160 UMLS:C0039441 VHOG:0001367 XAO:0004271 ZFA:0000160 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 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 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) MTg BIRNLEX:1200 NIFSTD:NeuroNames_abbrevSource tegmentum ISBN:0471888893 UMLS:C0039441 BIRNLEX:1200 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 BIRNLEX:1200 tegmentum mesencephali mesencephalic tegmentum VHOG:0001367 tegmentum mesencephalicum NeuroNames:491 A multi-tissue structure that is part of a spinal cord. BIRNLEX:1496 NCIT:C33969 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 An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN) The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils BAMS:ISO BAMS:Iso-cortex BAMS:NCX BIRNLEX:2547 BTO:0000920 DHBA:10160 EHDAA2:0004662 EMAPA:32842 EMAPA:35589 FMA:62429 GAID:677 MA:0002754 MBA:315 MESH:A08.186.211.730.885.213.420 PBA:294021746 UMLS:C0175173 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 cerebral neocortex homogenetic cortex homotypical cortex isocortex (sensu lato) neocortex (isocortex) neopallial cortex neopallium isocortex uberon iso-cortex nonolfactory cortex nucleus hypoglossalis UBERON:0001950 neocortex An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN) BIRNLEX:2547 OldNeuroNames:754 The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils UMLS:C0175173 BIRNLEX:2547 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 BIRNLEX:2547 homogenetic cortex ISBN:0471888893 homotypical cortex BIRNLEX:2547 isocortex (sensu lato) FMA:62429 neocortex (isocortex) DHBA:10160 isocortex BRAINSPAN:BRAINSPAN iso-cortex BAMS:iso-cortex nonolfactory cortex BTO:0000920 nucleus hypoglossalis NeuroNames:757 An epithelium that is part of a nasopharynx [Automatically generated definition]. UBERON:0003237 BTO:0004480 CALOHA:TS-0662 EHDAA2:0001241 EHDAA:7090 EMAPA:17672 FMA:62452 MA:0001865 NCIT:C49263 UMLS:C1179157 VHOG:0001038 epithelial tissue of nasal part of pharynx epithelial tissue of nasopharynx epithelial tissue of rhinopharynx epithelium of nasal part of pharynx epithelium of rhinopharynx nasal part of pharynx epithelial tissue nasal part of pharynx epithelium nasopharynx epithelial tissue nasopharynx epithelium rhinopharynx epithelial tissue rhinopharynx epithelium uberon nasopharyngeal epithelium UBERON:0001951 epithelium of nasopharynx An epithelium that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic UMLS:C1179157 ncithesaurus:Nasopharynx_Epithelium epithelial tissue of nasal part of pharynx OBOL:automatic epithelial tissue of nasopharynx OBOL:automatic epithelial tissue of rhinopharynx OBOL:automatic epithelium of nasal part of pharynx OBOL:automatic epithelium of rhinopharynx OBOL:automatic nasal part of pharynx epithelial tissue OBOL:automatic nasal part of pharynx epithelium OBOL:automatic nasopharynx epithelial tissue OBOL:automatic rhinopharynx epithelial tissue OBOL:automatic rhinopharynx epithelium OBOL:automatic nasopharyngeal epithelium BTO:0004480 The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]. EMAPA:35192 FMA:62649 MA:0001835 NCIT:C49209 UMLS:C0225604 bronchi cartilage bronchial cartilage bronchial cartilage ring bronchial trunk cartilage bronchus cartilage cartilage of bronchi cartilage of bronchial trunk cartilagines bronchiales uberon UBERON:0001956 cartilage of bronchus MP The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]. MP:0010988 UMLS:C0225604 ncithesaurus:Bronchus_Cartilage bronchi cartilage OBOL:automatic bronchial cartilage ring MP:0010988 bronchial trunk cartilage OBOL:automatic cartilage of bronchi OBOL:automatic cartilage of bronchial trunk OBOL:automatic cartilagines bronchiales A submucosa that is part of a bronchus [Automatically generated definition]. BTO:0002108 EMAPA:37449 FMA:62653 MA:0001837 NCIT:C49214 UMLS:C0225601 bronchi submucosa bronchial submucosa bronchial trunk submucosa bronchus submucosa submucosa of bronchi submucosa of bronchial trunk tela submucosa bronchi uberon submucous layer of bronchi UBERON:0001957 submucosa of bronchus A submucosa that is part of a bronchus [Automatically generated definition]. OBOL:automatic EMAPA:37449 MA:th UMLS:C0225601 ncithesaurus:Bronchus_Submucosa bronchi submucosa OBOL:automatic bronchial trunk submucosa OBOL:automatic submucosa of bronchi OBOL:automatic submucosa of bronchial trunk OBOL:automatic tela submucosa bronchi FMA:62653 FMA:TA submucous layer of bronchi BTO:0002108 An epithelium that lines a terminal bronchiole. 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] EMAPA:36283 FMA:62794 MA:0001774 NCIT:C33755 UMLS:C1179400 bronchiolus terminalis epithelial tissue bronchiolus terminalis epithelium epithelial tissue of bronchiolus terminalis epithelial tissue of terminal bronchiole epithelium of bronchiolus terminalis epithelium of terminal bronchiole terminal bronchiole epithelial tissue terminal bronchiole epithelium uberon UBERON:0001958 terminal bronchiole epithelium An epithelium that lines a terminal bronchiole. UMLS:C1179400 ncithesaurus:Terminal_Bronchiole_Epithelium bronchiolus terminalis epithelial tissue OBOL:automatic bronchiolus terminalis epithelium OBOL:automatic epithelial tissue of bronchiolus terminalis OBOL:automatic epithelial tissue of terminal bronchiole OBOL:automatic epithelium of bronchiolus terminalis OBOL:automatic epithelium of terminal bronchiole FMA:62794 terminal bronchiole epithelial tissue OBOL:automatic diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]. todo - add part relationships to specific layers FMA:62819 MA:0000140 NCIT:C12910 UMLS:C0599921 MALT epithelio-lymphoid tissue mucosa associated lymphatic tissue mucosa associated lymphoid tissue mucosa-associated lymphoid tissue mucosal-associated lymphatic tissue mucosal-associated lymphoid tissue uberon UBERON:0001961 mucosa-associated lymphoid tissue FMA diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]. UMLS:C0599921 ncithesaurus:Mucosa-Associated_Lymphoid_Tissue epithelio-lymphoid tissue FMA:62819 mucosa-associated lymphoid tissue GO:0048537 mucosal-associated lymphatic tissue GO:0048537 mucosal-associated lymphoid tissue GO:0048537 Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]. phylogenetic relationships to be added guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002). FMA:62820 MA:0000136 NCIT:C12936 UMLS:C0596638 gut associated lymphoid tissue uberon GALT UBERON:0001962 gut-associated lymphoid tissue Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]. UMLS:C0596638 ncithesaurus:Gut_Associated_Lymphoid_Tissue A diffuse collection of lymphpoid cells that participate in airway immune responses FMA:62821 MA:0000135 NCIT:C32234 UMLS:C1179418 bronchus associated lymphoid tissue uberon BALT UBERON:0001963 Lymphoid tissue associated with airways in mice has functional similarities to human BALT[ISBN:0123813611] Notes: FMA classifies this as organized, not diffuse bronchial-associated lymphoid tissue ISBN:0123813611 A diffuse collection of lymphpoid cells that participate in airway immune responses ISBN:0123813611 UMLS:C1179418 ncithesaurus:Bronchus-Associated_Lymphoid_Tissue Organism substance that is composed of sperm cells suspended in seminal fluid. seminal Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530). BTO:0001230 CALOHA:TS-0917 EMAPA:31488 FMA:62966 GAID:1169 MA:0002522 MESH:D012661 NCIT:C13277 NCIT:C13713 OpenCyc:Mx4rvgC-zpwpEbGdrcN5Y29ycA UMLS:C1518159 UMLS:C2756969 uberon ejaculate sperm UBERON:0001968 semen Organism substance that is composed of sperm cells suspended in seminal fluid. UMLS:C1518159 ncithesaurus:Male_Genital_System_Fluid_or_Secretion UMLS:C2756969 ncithesaurus:Semen sperm BTO:0001230 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 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw UMLS:C0032105 blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma The liquid component of blood, in which erythrocytes are suspended. 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 ZFA:0005857 galen:Bile uberon fel gall UBERON:0001970 bile 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. UMLS:C0005388 ncithesaurus:Bile fel BTO:0000121 gall BTO:0000121 . BTO:0000501 FMA:62972 GAID:1160 MA:0002519 MESH:D005750 NCIT:C32661 UMLS:C0017133 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 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 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:A07.231.432.952 NCIT:C12818 TAO:0005315 UMLS:C0042520 VHOG:0001765 ZFA:0005315 uberon venula UBERON:0001979 venule 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 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 TAO:0002138 UMLS:C0003847 VHOG:0001763 ZFA:0005255 uberon arteriola UBERON:0001980 arteriole 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 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 OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA TAO:0002137 UMLS:C0005847 VHOG:0001250 XAO:0001011 ZFA:0005314 region of vascular tree organ vascular tree organ region uberon vas sanguineum UBERON:0001981 blood vessel EHDAA2 GO:0072360 A vessel through which blood circulates in the body. BTO:0001102 Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] 2012-09-17 VHOG:0001250 VHOG 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) 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 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:A07.231.432.410 NCIT:C12685 NLXANAT:090902 OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA TAO:0005250 UMLS:C0935624 VHOG:0001253 XAO:0000116 ZFA:0005250 blood capillary capillary vessel uberon UBERON:0001982 capillary FMA MA XAO ZFA Any of the smallest blood vessels connecting arterioles with venules. ISBN:0073040584 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) 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 TAO:0002186 UMLS:C0014259 ZFA:0001687 cornea endothelium endothelium of cornea uberon epithelium posterius corneae UBERON:0001985 corneal endothelium 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]. UMLS:C0014259 ncithesaurus:Corneal_Endothelium cornea endothelium OBOL:automatic endothelium of cornea OBOL:automatic epithelium posterius corneae 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 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 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 UMLS:C0014257 ncithesaurus:Endothelium organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG] placental Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: DOI:10.1002/jmor.11011 BTO:0001078 CALOHA:TS-0799 EFO:0001407 EMAPA:35689 EV:0100119 FMA:63934 GAID:379 MA:0000386 MAT:0000279 MESH:A16.759 MIAA:0000279 NCIT:C13272 OpenCyc:Mx4rvv4zZ5wpEbGdrcN5Y29ycA UMLS:C0032043 VHOG:0001266 allantoic placenta eutherian placenta uberon UBERON:0001987 Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities. placenta ISBN:0073040584 Wikipedia ISBN:0073040584 organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG] 2012-09-17 VHOG:0001266 VHOG DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001) UMLS:C0032043 ncithesaurus:Placenta allantoic placenta ISBN:0073040584 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 OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA UMLS:C0015733 galen:Feces faeces fecal material fecal matter matières fécales@fr merde@fr partie de la merde@fr piece of shit porción de mierda@es portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool teil der fäkalien@de 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] Excretion in semisolid state processed by the intestine.[FMA] FMA:64183 UMLS:C0015733 ncithesaurus:Feces piece of shit portionem cacas cow dung cow pat fewmet frass guano spraint excrement BTO:0000440 Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance. Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]. Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO] EMAPA:35414 FMA:64783 MA:0000109 NCIT:C32746 UMLS:C0225362 VSAO:0000094 XAO:0004029 hyaline cartilage uberon chondroid cartilage UBERON:0001994 hyaline cartilage tissue FMA Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance. GO_REF:0000034 PSPUB:0000170 VSAO:0000094 Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]. FMA:64783 Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO] 2012-08-14 VSAO:0000094 VSAO PSPUB:0000170 UMLS:C0225362 ncithesaurus:Hyaline_Cartilage hyaline cartilage MA:0000109 chondroid cartilage Peripheral portion of the lymph node, underneath the capsule[WP]. EMAPA:35525 FMA:66253 MA:0000740 NCIT:C33029 UMLS:C0933402 lymph node cortex uberon cortex nodi lymphoidei UBERON:0002006 cortex of lymph node Peripheral portion of the lymph node, underneath the capsule[WP]. UMLS:C0933402 ncithesaurus:Lymph_Node_Cortex cortex nodi lymphoidei The mdeullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells. EMAPA:35529 FMA:66254 MA:0000745 lymph node medulla uberon medulla nodi lymphoidei UBERON:0002007 medulla of lymph node The mdeullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells. medulla nodi lymphoidei 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 OpenCyc:Mx4rvVjbIpwpEbGdrcN5Y29ycA UMLS:C0034052 VHOG:0000982 XAO:0004162 galen:PulmonaryArtery pulmonary arterial tree pulmonary arterial tree organ part uberon arteria pulmonalis pulmonary arterial subtree truncus pulmonalis UBERON:0002012 pulmonary artery 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.. 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 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 UMLS:C0034052 ncithesaurus:Pulmonary_Artery pulmonary arterial tree FMA:66326 pulmonary arterial tree organ part FMA:66326 arteria pulmonalis pulmonary arterial subtree FMA:66326 truncus pulmonalis the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage provides some protection from trauma and damage. The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule] EMAPA:18679 FMA:66610 MA:0000370 NCIT:C12885 UMLS:C0227637 galen:CapsuleOfKidney capsula fibrosa renis capsule of kidney fibrous capsule of kidney renal capsule uberon UBERON:0002015 kidney capsule the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage MGI:anna MP:0011383 UMLS:C0227637 ncithesaurus:Renal_Capsule capsula fibrosa renis FMA:66610 FMA:TA fibrous capsule of kidney FMA:66610 renal capsule GO:0072127 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 UMLS:C0034090 VHOG:0001133 XAO:0000394 galen:PulmonaryVein pulmonary venous tree organ part uberon venae pulmonales UBERON:0002016 pulmonary vein 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 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 UMLS:C0034090 ncithesaurus:Pulmonary_Vein venae pulmonales 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 OpenCyc:Mx4rv_bem5wpEbGdrcN5Y29ycA UMLS:C0032718 VHOG:0000656 XAO:0000392 galen:PortalVein portal venous tree organ part uberon UBERON:0002017 portal vein 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 cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] AAO:0010476 BAMS:11n BAMS:XIn BIRNLEX:812 EHDAA2:0000106 EHDAA:2855 EMAPA:17265 FMA:6720 FMA:80284 GAID:825 HBA:9340 MA:0001088 MBA:717 MESH:D000055 NCIT:C32041 OpenCyc:Mx4rwTEwI5wpEbGdrcN5Y29ycA UMLS:C0000905 UMLS:C1305777 VHOG:0000699 XAO:0004214 Willis' nerve accessory XI accessory XI nerve accessory nerve accessory nerve [XI] cervical accessory nerve cranial nerve XI eleventh cranial nerve nervus accessorius [XI] pars spinalis nervus accessorius radix spinalis nervus accessorius spinal accessory nerve spinal accessory nerve tree spinal part of accessory nerve uberon CN-XI accessory spinal nerve UBERON:0002019 accessory XI nerve A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. BIRNLEX:812 http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7 VHOG Wikipedia A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. ISBN:080184780X XAO:0004214 Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000699 VHOG Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] 2012-06-20 AAO:0010476 AAO AAO:EJS Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] 2012-09-17 VHOG:0000699 VHOG In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve GO FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] FMA UMLS:C0000905 BIRNLEX:812 UMLS:C0000905 ncithesaurus:Accessory_Nerve UMLS:C1305777 BIRNLEX:812 accessory XI EHDAA2:0000106 cranial nerve XI BIRNLEX:812 eleventh cranial nerve BIRNLEX:812 nervus accessorius [XI] FMA:6720 FMA:TA pars spinalis nervus accessorius FMA:6720 FMA:TA radix spinalis nervus accessorius FMA:6720 FMA:TA spinal accessory nerve FMA:6720 CN-XI VHOG:0000699 accessory spinal nerve BAMS:XIn 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 NCIT:C32695 OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA TAO:0002197 UMLS:C0018220 VHOG:0001768 ZFA:0001681 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 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] 2012-08-14 TAO:0002197 TAO ZFIN:curator EMAPA:37596 MA:th 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 TAO:0000029 UMLS:C0035507 UMLS:C1522180 VHOG:0000070 XAO:0000015 ZFA:0000029 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 uberon rhombencephalon UBERON:0002028 hindbrain 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]. ZFA:0000029 ZFIN:curator 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) 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 UMLS:C0035507 ncithesaurus:Hind-Brain UMLS:C1522180 BIRNLEX:942 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 An epithelium that is part of a bronchus [Automatically generated definition]. BTO:0001845 CALOHA:TS-1240 EFO:0000307 EMAPA:32691 FMA:67782 MA:0001839 NCIT:C32231 UMLS:C0599333 bronchi epithelial tissue bronchi epithelium bronchial epithelium bronchial trunk epithelial tissue bronchial trunk epithelium bronchus epithelial tissue bronchus epithelium epithelial tissue of bronchi epithelial tissue of bronchial trunk epithelial tissue of bronchus epithelium of bronchi epithelium of bronchial trunk uberon UBERON:0002031 epithelium of bronchus An epithelium that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C0599333 ncithesaurus:Bronchial_Epithelium bronchi epithelial tissue OBOL:automatic bronchi epithelium OBOL:automatic bronchial trunk epithelial tissue OBOL:automatic bronchial trunk epithelium OBOL:automatic bronchus epithelial tissue OBOL:automatic epithelial tissue of bronchi OBOL:automatic epithelial tissue of bronchial trunk OBOL:automatic epithelial tissue of bronchus OBOL:automatic epithelium of bronchi OBOL:automatic epithelium of bronchial trunk OBOL:automatic A tiny smooth muscle that connects the hair follicle with the dermis. When contracted the arrector pili causes the raising of the hair BTO:0005132 EMAPA:26775 FMA:67821 MA:0000778 arrector pili arrector pili muscle arrector pili smooth muscle arrector pilli arrector pilli muscle arrector pilorum arrector pilorum muscle of hair uberon arectores pilorum erector pili erectores pilorum pilomotor muscle UBERON:0002033 arrector muscle of hair FMA FMA A tiny smooth muscle that connects the hair follicle with the dermis. arrector pili FMA:67821 MA:0000778 arrector pili muscle EMAPA:26779 MP:0010679 arrector pili smooth muscle MA:0000778 arrector pilli MP:0010679 arrector pilli muscle MP:0010679 arrector pilorum ISBN:0123813611 arrector pilorum muscle of hair ISBN:0123813611 arectores pilorum BTO:0005132 erector pili BTO:0005132 erectores pilorum BTO:0005132 pilomotor muscle BTO:0005132 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 OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA UMLS:C1331262 WBbt:0005779 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 Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO] Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO] However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG] cerebellar The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full] almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem infratentorial region AAO:0010485 BAMS:CB BAMS:Cb BIRNLEX:1489 BM:CB BTO:0000232 CALOHA:TS-0125 DHBA:10656 EFO:0000327 EHDAA2:0000232 EMAPA:17787 EV:0100293 FMA:67944 GAID:595 HBA:4696 MA:0000198 MAT:0000110 MBA:512 MESH:D002531 MIAA:0000110 NCIT:C12445 OpenCyc:Mx4rvl1eipwpEbGdrcN5Y29ycA TAO:0000100 UMLS:C0007765 UMLS:C1268981 VHOG:0000024 XAO:0003098 ZFA:0000100 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=643 epencephalon-1 uberon corpus cerebelli parencephalon UBERON:0002037 cerebellum FMA MA definitional Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. BTO:0000232 ISBN:3764351209 MESH:A08.186.211.132.810.428.200 ZFA:0000100 ISBN:0471888893 Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO] 2012-06-20 AAO:0010485 AAO AAO:BJB Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000100 TAO ZFIN:curator However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG] 2012-09-17 VHOG:0000024 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) almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem ABA infratentorial region UMLS:C0007765 BIRNLEX:1489 UMLS:C0007765 ncithesaurus:Cerebellum UMLS:C1268981 BIRNLEX:1489 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=643 BIRNLEX:1489 epencephalon-1 FMA:67944 corpus cerebelli NeuroNames:643 parencephalon NeuroNames:643 A systemic artery that supplies the lung with with oxygenated blood. EMAPA:18608 FMA:68109 GAID:477 MA:0001923 MESH:D001981 NCIT:C32230 OpenCyc:Mx4r4sy0UiNbEd2AAAACs6hRXg UMLS:C0006257 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 A systemic artery that supplies the lung with with oxygenated blood. UBERON:cjm UMLS:C0006257 ncithesaurus:Bronchial_Artery arteriae bronchiales rami bronchiales partis thoracicae aortae An endothelium that is part of a lymphatic vessel [Automatically generated definition]. The vascular endothelium that lines the lymph vessels.[TAO] BTO:0004303 CALOHA:TS-2156 EMAPA:35533 FMA:68444 MA:0000750 MESH:D004729 NCIT:C49258 TAO:0005258 UMLS:C1180786 ZFA:0005258 endothelium of lymph vessel endothelium of lymphatic vessel lymph vessel endothelium lymphatic endothelium lymphatic vessel endothelium uberon UBERON:0002042 lymphatic vessel endothelium An endothelium that is part of a lymphatic vessel [Automatically generated definition]. OBOL:automatic The vascular endothelium that lines the lymph vessels.[TAO] 2012-08-14 TAO:0005258 TAO ZFIN:curator UMLS:C1180786 ncithesaurus:Lymphatic_Vessel_Endothelium endothelium of lymph vessel OBOL:automatic endothelium of lymphatic vessel FMA:68444 lymph vessel endothelium OBOL:automatic lymphatic endothelium BTO:0004303 A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species AAO:0010544 BTO:0001379 CALOHA:TS-1047 EFO:0000861 EHDAA2:0002028 EHDAA:2148 EHDAA:2975 EMAPA:17068 EV:0100133 FMA:9603 GAID:465 MA:0000129 MAT:0000081 MESH:D013961 MIAA:0000081 NCIT:C12400 OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA UMLS:C0040132 VHOG:0000418 XAO:0000162 galen:ThyroidGland thyroid uberon glandula thyroidea UBERON:0002046 thyroid gland A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. BTO:0001379 Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] 2012-06-20 AAO:0010544 AAO AAO:BJB (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] 2012-09-17 VHOG:0000418 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes NCBITaxon:32443 Romer In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) NCBITaxon:7746 Romer In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species NCBITaxon:32523 Romer UMLS:C0040132 ncithesaurus:Thyroid_Gland glandula thyroidea 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 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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]. UMLS:C0175423 BIRNLEX:1110 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=589 BIRNLEX:1110 raphe pontis FMA:68875 FMA:TA nucleus raphe pontis NeuroNames:589 nucleus raphes pontis raphe (mediana pontina) NeuroNames:589 Respiration organ that develops as an oupocketing of the esophagus. lung http://langual.org 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 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0024109 VHOG:0000310 XAO:0000119 galen:Lung http://www.langual.org/langual_thesaurus.asp?termid=C0187 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 some species only have a single lung Respiration organ that develops as an oupocketing of the esophagus. 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) 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 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 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 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 epithelium that is part of a bronchiole [Automatically generated definition]. in FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however there are two distinct terms for the corresponding epithelium. BTO:0001866 CALOHA:TS-0570 EMAPA:32693 FMA:62497 FMA:69077 MA:0001772 NCIT:C48942 UMLS:C1181296 bronchiolar epithelium bronchiole epithelial tissue bronchiole epithelium epithelial tissue of bronchiole epithelial tissue of lobular bronchiole epithelium of lobular bronchiole lobular bronchiole epithelial tissue lobular bronchiole epithelium uberon UBERON:0002051 epithelium of bronchiole An epithelium that is part of a bronchiole [Automatically generated definition]. OBOL:automatic in FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however there are two distinct terms for the corresponding epithelium. FMA UMLS:C1181296 ncithesaurus:Bronchiole_Epithelium bronchiolar epithelium BTO:0001866 bronchiole epithelial tissue OBOL:automatic epithelial tissue of bronchiole OBOL:automatic epithelial tissue of lobular bronchiole OBOL:automatic epithelium of lobular bronchiole OBOL:automatic lobular bronchiole epithelial tissue OBOL:automatic lobular bronchiole epithelium OBOL:automatic the thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. FMA:69087 MA:0000117 NCIT:C32050 UMLS:C1181304 capsule of adrenal gland uberon adrenal capsule UBERON:0002052 adrenal gland capsule the thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. MP:0013565 UMLS:C1181304 ncithesaurus:Adrenal_Gland_Capsule capsule of adrenal gland FMA:69087 Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted]. EMAPA:37088 FMA:69264 MA:0002056 NCIT:C52737 UMLS:C0226334 uberon arteria suprarenalis inferior UBERON:0002056 inferior suprarenal artery Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted]. EMAPA:37088 MA:th UMLS:C0226334 ncithesaurus:Inferior_Suprarenal_Artery arteria suprarenalis inferior 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 EMAPA:37108 MA:th UMLS:C1181536 ncithesaurus:Phrenic_Artery the ganglion associated with the lingual nerve that provides postsynaptic fibers to the submandibular and sublingual glands BTO:0001318 EHDAA2:0001942 EHDAA:6710 EMAPA:36276 FMA:6966 MA:0002470 NCIT:C52558 UMLS:C0229063 mandibular ganglion uberon Blandin`s ganglion ganglion submandibulare lingual ganglion maxillary ganglion submaxillary ganglion UBERON:0002059 submandibular ganglion the ganglion associated with the lingual nerve that provides postsynaptic fibers to the submandibular and sublingual glands ISBN:0-683-40008-8 MP:0001035 UMLS:C0229063 ncithesaurus:Submandibular_Ganglion mandibular ganglion UBERON:cjm Blandin`s ganglion BTO:0001318 ganglion submandibulare ganglion submandibulare BTO:0001318 lingual ganglion MA:0002470 maxillary ganglion MA:0002470 submaxillary ganglion MA:0002470 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 OpenCyc:Mx4rquH9YKgNEdudWQACs5b6Bw UMLS:C1519589 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. assume spelling error for ncit ncit UMLS:C1519589 ncithesaurus:Trancus_Arteriosus 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 TAO:0001119 UMLS:C0011646 VHOG:0000108 XAO:0000217 ZFA:0001119 vertebrate dermis uberon corium cutis UBERON:0002067 dermis 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]. 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 UMLS:C0011646 ncithesaurus:Dermis corium corium BTO:0000294 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 NCIT:C33645 TAO:0001136 UMLS:C0278403 ZFA:0001136 hypoderm vertebrate hypodermis uberon sub-tegumental tissue subcutaneous tissue subcutis subtegumental tissue superficial fascia tela subcutanea UBERON:0002072 hypodermis 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]. 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 UMLS:C0278403 ncithesaurus:Subcutis sub-tegumental tissue BTO:0004525 subcutaneous tissue subtegumental tissue BTO:0004525 superficial fascia tela subcutanea A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]. The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG] BTO:0000554 CALOHA:TS-0432 EFO:0002464 EMAPA:18771 EMAPA:29741 EV:0100156 FMA:70660 GAID:934 MA:0000154 MESH:D018859 NCIT:C13317 OpenCyc:Mx4rvVjOI5wpEbGdrcN5Y29ycA UMLS:C0221971 VHOG:0001268 uberon folliculus pili UBERON:0002073 Development notes:Formation largely takes place during fetal and perinatal skin development. However, after skin wounding de novo hair follicle formation may also occur in adult mouse and rabbit skin[DOI:10.1016/j.cub.2008.12.005]. hair follicle FMA A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]. The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG] 2012-09-17 VHOG:0001268 VHOG ISBN:978-4431998051 Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3 UMLS:C0221971 ncithesaurus:Hair_Follicle folliculus pili The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla. TODO - add distinct subclasses for coat hair vs vibrissa hair TODO - check definition of trichocyte in CL BTO:0004672 EMAPA:36498 FMA:70728 MA:0000159 NCIT:C33543 UMLS:C0221961 shaft of hair uberon scapus pili UBERON:0002074 hair shaft The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla. UMLS:C0221961 ncithesaurus:Shaft_of_the_Hair scapus pili BTO:0004672 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 UMLS:C0042779 XAO:0003034 visceral organ visceral organ system uberon Organsystem@de 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 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 Organsystem@de BTO:0001491 splanchnic tissue BTO:0001491 visceral tissue BTO:0001491 A cortex that is part of a hair [Automatically generated definition]. EMAPA:35387 FMA:70934 MA:0000156 coat hair cortex coat/hair cortex cortex of coat hair cortex of coat/hair hair cortex uberon UBERON:0002077 cortex of hair A cortex that is part of a hair [Automatically generated definition]. OBOL:automatic coat hair cortex OBOL:automatic coat/hair cortex OBOL:automatic cortex of coat hair OBOL:automatic cortex of coat/hair OBOL:automatic 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 OpenCyc:Mx4rRMlc0KgNEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA UMLS:C0225883 VHOG:0000717 galen:RightVentricle cardiac right ventricle right ventricle right ventricle of heart uberon right cardiac ventricle ventriculus dexter UBERON:0002080 heart right ventricle cjm 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] 2012-09-17 VHOG:0000717 VHOG UMLS:C0225883 ncithesaurus:Right_Ventricle right ventricle FMA:7098 right cardiac ventricle EMAPA:17340 ventriculus dexter 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 OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA TAO:0000009 UMLS:C0018827 VHOG:0000435 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. 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 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 OpenCyc:Mx4rtW8v46gEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA UMLS:C0225897 VHOG:0000718 galen:LeftVentricle cardiac left ventricle left cardiac ventricle left ventricle left ventricle of heart uberon ventriculus sinister cordis UBERON:0002084 heart left ventricle GO 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] 2012-09-17 VHOG:0000718 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] 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) UMLS:C0225897 ncithesaurus:Left_Ventricle left ventricle FMA:7101 ventriculus sinister cordis 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 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 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) axial skeleton FMA:71221 EMAPA:37721 MA:th 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 UMLS:C0222646 VHOG:0001666 VSAO:0000076 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 Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. UBERONREF:0000003 Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] 2012-08-14 VSAO:0000076 VSAO PSPUB:0000170 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 paired fin skeleton skeleton appendiculare The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer. The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32668 EV:0100313 FMA:71236 MA:0000815 NCIT:C49332 UMLS:C0459393 VHOG:0000270 cranial dura mater dura mater cranialis dura mater encephali dura mater of brain uberon UBERON:0002092 brain dura mater The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer. MP:0009025 The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000270 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000270 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C0459393 ncithesaurus:Cerebral_Dura_Mater cranial dura mater FMA:71236 dura mater cranialis FMA:71236 FMA:TA A dura mater that is part of a spinal cord [Automatically generated definition]. The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17806 FMA:71237 MA:0001132 NCIT:C49799 UMLS:C0228124 VHOG:0000411 dura mater of neuraxis of spinal cord dura mater of spinal cord spinal cord dura mater spinal cord dura mater of neuraxis uberon UBERON:0002093 spinal dura mater A dura mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000411 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000411 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C0228124 ncithesaurus:Spinal_Cord_Dura_Mater dura mater of neuraxis of spinal cord OBOL:automatic spinal cord dura mater of neuraxis OBOL:automatic 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 OpenCyc:Mx4rwA7lp5wpEbGdrcN5Y29ycA UMLS:C0225870 VHOG:0000386 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 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 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 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 s. interventriculare cordis septum inferius septum membranaceum ventricular septum ventricular septum MA:0000085 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:A01.047.025.600.451 NCIT:C33103 UMLS:C0025474 galen:Mesentery generic mesentery mesentery (generic) uberon UBERON:0002095 mesentery 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 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 mesentery (generic) The organ covering the body that consists of the dermis and epidermis. skin, animal consider 'integumentary system' for invertebrates http://langual.org 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 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA UMLS:C1123023 XAO:0000023 galen:Skin http://www.langual.org/langual_thesaurus.asp?termid=C0193 entire skin skin organ uberon entire integument integument integumental organ pelt skin animal skin UBERON:0002097 skin of body 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 UMLS:C0018819 XAO:0004141 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 OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA TAO:0001115 UMLS:C0460005 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 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 A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO] 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] AAO:0010336 AEO:0000172 CALOHA:TS-0552 EFO:0000876 EHDAA2:0003172 EHDAA:1697 EHDAA:8273 EMAPA:16405 FMA:24875 GAID:36 MA:0000007 MAT:0000090 MIAA:0000090 NCIT:C12429 OpenCyc:Mx4rvn1uSZwpEbGdrcN5Y29ycA UMLS:C0015385 VHOG:0000336 VSAO:0000121 XAO:0003027 galen:Extremity free limb limb sensu Vertebrata pentadactyl limb tetrapod limb flipper uberon extremities extremity UBERON:0002101 limb Sarcopterygians A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. UBERONREF:0000003 Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO] 2012-06-20 AAO:0010336 AAO AAO:BJB 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:0000336 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 UMLS:C0015385 ncithesaurus:Limb free limb FMA:24875 limb sensu Vertebrata MAT:0000090 flipper extremities A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts. Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm Upper limb, which connects the manus with the pectoral girdle.[AAO] note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb AAO:0000205 BTO:0001729 CALOHA:TS-2214 EFO:0000882 EHDAA2:0002133 EHDAA:6208 EMAPA:17412 EV:0100014 FMA:24878 GAID:1215 GAID:51 MA:0000025 MAT:0000394 MESH:D005552 MIAA:0000394 NCIT:C12671 UMLS:C1140618 VHOG:0000338 VSAO:0000148 XAO:0003030 galen:UpperExtremity anteriormost limb fore limb forelimb free part of upper limb free upper limb membrum superius pectoral limb superior member upper extremity upper limb pectoral flipper uberon foreleg UBERON:0002102 forelimb A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts. UBERONREF:0000003 Upper limb, which connects the manus with the pectoral girdle.[AAO] 2012-06-20 AAO:0000205 AAO AAO:LAP note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb FMA UMLS:C1140618 ncithesaurus:Upper_Extremity free part of upper limb FMA:24878 free upper limb FMA:24878 UBERONREF:0000003 membrum superius FMA:7183 FMA:TA pectoral flipper A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. Lower limb, which connects the pes with the pelvic girdle.[AAO] 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] crural note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton AAO:0000219 BTO:0002345 CALOHA:TS-2215 EFO:0000883 EHDAA2:0001033 EHDAA:6094 EMAPA:17458 EV:0100015 FMA:24879 GAID:1221 GAID:38 MA:0000026 MAT:0000395 MESH:D006614 MIAA:0000395 NCIT:C12742 NCIT:C77625 UMLS:C0023216 UMLS:C1522391 VHOG:0000337 VSAO:0000150 XAO:0003031 galen:LowerExtremity free lower limb hind limb hind-limb hindlimb inferior member lower limb membrum inferius uberon free part of lower limb lower extremity membrum inferius pelvic appendage UBERON:0002103 hindlimb A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. UBERONREF:0000003 Lower limb, which connects the pes with the pelvic girdle.[AAO] 2012-06-20 AAO:0000219 AAO AAO:LAP 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:0000337 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton FMA UMLS:C0023216 ncithesaurus:Lower_Extremity UMLS:C1522391 ncithesaurus:Hind_Limb free lower limb FMA:24879 UBERONREF:0000003 hind-limb VSAO:0000150 membrum inferius FMA:7184 FMA:TA free part of lower limb FMA:24879 membrum inferius 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 OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA TAO:0001127 UMLS:C0587900 XAO:0003198 ZFA:0001127 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 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 spleen http://langual.org 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:A15.382.520.604.713 MIAA:0000085 NCIT:C12432 OpenCyc:Mx4rvVjgw5wpEbGdrcN5Y29ycA TAO:0000436 UMLS:C0037993 VHOG:0000120 XAO:0000328 ZFA:0000436 galen:Spleen http://www.langual.org/langual_thesaurus.asp?termid=C0191 uberon lien UBERON:0002106 spleen 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 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) UMLS:C0037993 ncithesaurus:Spleen lien 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]. http://langual.org 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 OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA TAO:0000123 UMLS:C0023884 VHOG:0000257 XAO:0000133 ZFA:0000123 galen:Liver http://www.langual.org/langual_thesaurus.asp?termid=C0176 uberon iecur jecur UBERON:0002107 liver BTO EHDAA2 GO-def ZFA ZFA-weakened EHDAA2 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 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 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 jecur 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:A03.492.411.620 MIAA:0000047 NCIT:C12386 OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA TAO:0001323 UMLS:C0021852 VHOG:0000055 XAO:0000130 ZFA:0001323 galen:SmallIntestine small bowel small intestine uberon anterior intestine intestinum tenue mid intestine UBERON:0002108 small intestine 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 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 UMLS:C0021852 ncithesaurus:Small_Intestine intestinum tenue intestinum tenue BTO:0000651 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 OpenCyc:Mx4rvVkGr5wpEbGdrcN5Y29ycA TAO:0000208 UMLS:C0016976 VHOG:0000221 XAO:0000135 ZFA:0000208 galen:Gallbladder gall bladder gallbladder 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) gall bladder BTO MA ZFA cjm definitional 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] 2012-09-17 VHOG:0000221 VHOG 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) UMLS:C0016976 ncithesaurus:Gallbladder gallbladder FMA:7202 vesica biliaris vesica fellea 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 A paired organ of the urinary tract which has the production of urine as its primary function. kidney http://langual.org One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] renal AAO:0000250 BTO:0000671 CALOHA:TS-0510 EFO:0000929 EMAPA:17373 EV:0100096 FMA:7203 GAID:423 MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 NCIT:C12415 OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA UMLS:C0022646 XAO:0003267 galen:Kidney http://www.langual.org/langual_thesaurus.asp?termid=C0196 reniculate kidney uberon UBERON:0002113 kidney FMA definitional A paired organ of the urinary tract which has the production of urine as its primary function. One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] 2012-06-20 AAO:0000250 AAO AAO:BJB UMLS:C0022646 ncithesaurus:Kidney reniculate kidney 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:A03.492.411.620.270 MIAA:0000044 NCIT:C12263 OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA UMLS:C0013303 VHOG:0000052 XAO:0000236 galen:Duodenum uberon proximal intestine upper intestine UBERON:0002114 duodenum 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 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 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 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 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 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 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 EMAPA:37366 MA:th UMLS:C0227874 ncithesaurus:Left_Ovary In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] pronephric UBERON:0005794 AAO:0011089 BTO:0001541 EFO:0000927 EHDAA2:0001570 EHDAA:1017 EMAPA:16579 FMA:72170 MAT:0000117 MIAA:0000117 NCIT:C34280 TAO:0000151 UMLS:C0231048 VHOG:0000037 XAO:0002000 ZFA:0000151 pronephric kidney uberon archinephron embryonic kidney pronephron UBERON:0002120 Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros GO OG ZFA In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. GO:0048793 A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] 2012-09-17 VHOG:0000037 VHOG Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] 2012-06-20 AAO:0011089 AAO XAO:curator The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000151 TAO ZFIN:curator In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] 2012-09-17 VHOG:0000037 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637 UMLS:C0231048 ncithesaurus:Pronephros pronephric kidney XAO:0002000 archinephron BTO:0001541 embryonic kidney BTO:0001541 pronephron BTO:0001541 The fibrous connective tissue surrounding the thymus. EMAPA:19306 FMA:72204 MA:0000766 NCIT:C33770 UMLS:C0229945 thymic capsule thymus capsule uberon UBERON:0002122 capsule of thymus The fibrous connective tissue surrounding the thymus. MP:0002368 UMLS:C0229945 ncithesaurus:Thymic_Capsule the outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes Histologically, the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. The cortex and medulla play different roles in the development of T cells. Cells in the thymus can be divided into thymic stromal cells and cells of hematopoietic origin[WP] BTO:0002934 EMAPA:35863 FMA:72205 MA:0000767 NCIT:C33774 UMLS:C0229948 thymic cortex thymus cortex uberon UBERON:0002123 cortex of thymus the outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes ISBN:0-683-40008-8 MP:0002371 UMLS:C0229948 ncithesaurus:Thymus_Cortex thymic cortex BTO:0002934 thymus cortex MA:0000767 Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. BTO:0004560 EFO:0001969 EMAPA:19305 FMA:72206 MA:0000771 NCIT:C33775 UMLS:C0229949 medulla of thymus gland thymus gland medulla thymus medulla uberon UBERON:0002124 medulla of thymus Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. UMLS:C0229949 ncithesaurus:Thymus_Medulla medulla of thymus gland OBOL:automatic thymus gland medulla OBOL:automatic A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified]. in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP] Lymphocytes, reticular cells and macrophages are found in the lobules FMA:72215 MA:0000770 NCIT:C33772 UMLS:C1522462 lobule of thymus thymic lobule thymus lobule uberon UBERON:0002125 thymus lobule A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified]. ncithesaurus:Thymic_Lobule UMLS:C1522462 ncithesaurus:Thymic_Lobule lobule of thymus FMA:72215 thymus lobule MA:0000770 A 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 UMLS:C0175427 VHOG:0001381 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 NIFSTD A 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 UMLS:C0175427 BIRNLEX:1307 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695]. BAMS:CB BAMS:CBX BAMS:CbCx BIRNLEX:1566 BM:CB-Cbx BTO:0000043 CALOHA:TS-2000 DHBA:10657 DMBA:16939 EMAPA:35211 EV:0100294 FMA:72248 GAID:596 HBA:4697 MA:0000199 MBA:528 MESH:D002525 NCIT:C49216 UMLS:C0007759 UMLS:C1284087 VHOG:0001597 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=647 cortex of cerebellar hemisphere uberon cortex cerebellaris cortex cerebelli UBERON:0002129 The circuits in the cerebellar cortex look similar across all classes of vertebrates, including fish, reptiles, birds, and mammals (e.g., Fig. 2). This has been taken as evidence that the cerebellum performs functions important to all vertebrate species. (Wikipedia) cerebellar cortex The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer. BIRNLEX:1566 The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695]. GO:0021695 UMLS:C0007759 BIRNLEX:1566 UMLS:C0007759 ncithesaurus:Cerebellar_Cortex UMLS:C1284087 BIRNLEX:1566 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=647 BIRNLEX:1566 cortex of cerebellar hemisphere DMBA:CbHCx cortex cerebellaris BTO:0000043 cortex cerebelli NeuroNames:647 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 TAO:0000539 UMLS:C0023951 ZFA:0000539 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=583 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 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 UMLS:C0023951 BIRNLEX:905 UMLS:C0023951 ncithesaurus:Locus_Coeruleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=583 BIRNLEX:905 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 UMLS:C0175447 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=590 superior salivary nucleus uberon nucleus salivarius superior nucleus salivatorius cranialis nucleus salivatorius rostralis nucleus salivatorius superior UBERON:0002149 superior salivatory nucleus 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 EMAPA:37756 MA:th UMLS:C0175447 BIRNLEX:1131 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw TAO:0001320 UMLS:C0014124 VHOG:0000084 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 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 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 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225706 VHOG:0000301 uberon UBERON:0002167 right lung Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] FMA:FMA 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 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 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225730 VHOG:0000618 uberon UBERON:0002168 left lung Lung which consists of the left upper lobe and left lower lobe.[FMA] FMA:FMA 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 UMLS:C0225730 ncithesaurus:Left_Lung the upper conducting airways of the lung; these airways arise from the terminus of the trachea Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] bronchial In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue BTO:0001340 CALOHA:TS-1229 EFO:0000932 EMAPA:32689 EV:0100041 FMA:7409 GAID:346 MA:0000436 MAT:0000133 MESH:D001980 MIAA:0000133 NCIT:C12683 UMLS:C0006255 VHOG:0000262 XAO:0000121 bronchi bronchial trunk uberon bronchial tissue UBERON:0002185 bronchus the upper conducting airways of the lung; these airways arise from the terminus of the trachea ISBN:0-397-51047-0 MESH:A04.411.125 MGI:cwg MP:0002264 Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000262 VHOG UMLS:C0006255 ncithesaurus:Bronchus bronchi bronchial trunk FMA:7409 bronchial tissue BTO:0001340 the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching bronchiolar lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer BTO:0002375 CALOHA:TS-2003 EHDAA:8171 EHDAA:8183 EHDAA:8199 EHDAA:8221 EMAPA:32697 FMA:7410 MA:0000422 NCIT:C12684 OpenCyc:Mx4rvl9iDpwpEbGdrcN5Y29ycA UMLS:C0006270 VHOG:0000675 lobular bronchiole uberon bronchioli bronchiolus UBERON:0002186 bronchiole ncit the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching ISBN:0-397-51047-0 MGI:cwg MP:0002267 lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer ISBN:0123813611 UMLS:C0006270 ncithesaurus:Bronchiole lobular bronchiole FMA:7410 bronchioli bronchiolus BTO:0002375 the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls BTO:0003223 EMAPA:36282 FMA:7411 MA:0000424 NCIT:C33754 OpenCyc:Mx4rwS7IU5wpEbGdrcN5Y29ycA UMLS:C0225666 bronchiolus terminalis uberon bronchioli terminalis terminal bronchiole tube UBERON:0002187 terminal bronchiole the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls ISBN:0-397-51047-0 MGI:cwg MP:0002268 UMLS:C0225666 ncithesaurus:Terminal_Bronchiole bronchiolus terminalis bronchioli terminalis 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 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. the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] MP:0011156 panniculus adiposus MP:0011156 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. Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers. from its internal surface are given off a number of membranous processes or trabeculae, consisting, in man, of connective tissue, with a small admixture of plain muscle fibers; but in many of the lower animals composed almost entirely of involuntary muscle[WP] EMAPA:35524 FMA:74604 MA:0000739 NCIT:C33028 UMLS:C0229699 capsula nodi lymphoidei lymph node capsule uberon UBERON:0002194 capsule of lymph node Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers. UMLS:C0229699 ncithesaurus:Lymph_Node_Capsule capsula nodi lymphoidei FMA:74604 FMA:TA The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA]. Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO] The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head[NCBIBook:NBK53175]. AHP AAO:0010540 BAMS:AHY BAMS:AL BAMS:APit BIRNLEX:1581 BM:AHy BTO:0000040 CALOHA:TS-0794 EFO:0000230 EHDAA2:0000109 EMAPA:17514 FMA:74627 MA:0000177 MESH:A06.407.747.608 NCIT:C12772 TAO:0001282 UMLS:C0032008 UMLS:C1280369 VHOG:0000141 ZFA:0001282 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=407 anterior hypophysis anterior lobe (hypophysis) anterior lobe of hypophysis anterior lobe of pituitary anterior lobe of pituitary gland anterior pituitary lobus anterior (glandula pituitaria) lobus anterior hypophysis pituitary gland, anterior lobe uberon anterior lobe of the pituitary anterior pituitary gland cranial lobe lobus anterior pituitary anterior lobe pituitary glandanterior lobe rostral lobe UBERON:0002196 adenohypophysis NCBIBook:NBK53175 ZFA lexical The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA]. ZFIN:curator Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO] 2012-06-20 AAO:0010540 AAO AAO:BJB The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO] 2012-08-14 TAO:0001282 TAO ZFIN:curator It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5 In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish ZFA AHP BIRNLEX:1581 NIFSTD:NeuroNames_abbrevSource UMLS:C0032008 BIRNLEX:1581 UMLS:C0032008 ncithesaurus:Anterior_Lobe_of_the_Pituitary_Gland UMLS:C1280369 BIRNLEX:1581 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=407 BIRNLEX:1581 anterior hypophysis ZFA:0001282 lobus anterior (glandula pituitaria) FMA:74627 FMA:TA lobus anterior hypophysis FMA:74627 FMA:TA anterior lobe of the pituitary BAMS:APit anterior pituitary gland BTO:0000040 cranial lobe BTO:0000496 lobus anterior NeuroNames:407 pituitary anterior lobe EMAPA:17514 pituitary glandanterior lobe BAMS:AL rostral lobe BTO:0000496 The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon. request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon' The infundibular part of the pituitary gland consisting of two regions.[AAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19) NHP AAO:0010537 BAMS:NHP BAMS:NHY BAMS:NL BAMS:PPit BIRNLEX:1586 BM:NY BTO:0000937 CALOHA:TS-0815 DMBA:15691 EHDAA2:0001271 EHDAA:7536 EMAPA:17519 FMA:74628 MA:0000178 MESH:A06.407.747.734 NCIT:C12773 TAO:0001271 UMLS:C0032009 UMLS:C1280368 VHOG:0000142 ZFA:0001271 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=401 infundibular process lobus nervosus neurohypophysis lobus posterior (glandula pituitaria) lobus posterior hypophysis neural lobe neural lobe of pituitary neural lobe of pituitary gland neuro hypophysis neurohypophysis pituitary gland, posterior lobe posterior lobe of pituitary posterior lobe of pituitary gland posterior pituitary uberon lobus nervosus lobus posterior pituitary gland neural lobe pituitary gland, neural lobe posterior lobe of hypophysis posterior pituitary gland UBERON:0002198 neurohypophysis MA ZFA lexical The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon. MP:0004164 request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon' Ariens, p. 1192 The infundibular part of the pituitary gland consisting of two regions.[AAO] 2012-06-20 AAO:0010537 AAO AAO:BJB It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000142 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5 todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19) EMAPA NHP BIRNLEX:1586 NIFSTD:NeuroNames_abbrevSource UMLS:C0032009 BIRNLEX:1586 UMLS:C0032009 ncithesaurus:Posterior_Lobe_of_the_Pituitary_Gland UMLS:C1280368 BIRNLEX:1586 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=401 BIRNLEX:1586 infundibular process FMA:74628 lobus nervosus neurohypophysis FMA:74628 FMA:TA lobus posterior (glandula pituitaria) FMA:74628 FMA:TA lobus posterior hypophysis FMA:74628 FMA:TA neural lobe FMA:74628 neural lobe of pituitary BIRNLEX:1586 neural lobe of pituitary gland FMA:74628 posterior lobe of pituitary gland FMA:74628 lobus nervosus NeuroNames:401 lobus posterior NeuroNames:401 pituitary gland neural lobe BAMS:NL pituitary gland, neural lobe NeuroNames:401 posterior lobe of hypophysis NeuroNames:401 posterior pituitary gland BTO:0000937 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 ZFA:0000368 galen:Integument dermis plus epidermis plus hypodermis integumentum commune skin and subcutaneous tissue skin plus hypodermis the integument uberon Hautsystem@de dermal system dermoid system skin tegument vertebrate integument UBERON:0002199 integument FMA FMA The dermis, epidermis and hypodermis. 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 Hautsystem@de BTO:0000634 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 A submucosa that is part of a trachea. BTO:0002115 EMAPA:35879 FMA:7472 MA:0001860 NCIT:C49307 UMLS:C0225586 submucosa of windpipe trachea submucosa tracheal submucosa windpipe submucosa uberon submucous layer of trachea UBERON:0002202 submucosa of trachea A submucosa that is part of a trachea. OBOL:automatic UMLS:C0225586 ncithesaurus:Trachea_Submucosa submucosa of windpipe OBOL:automatic windpipe submucosa OBOL:automatic submucous layer of trachea BTO:0002115 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 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 ISBN:0781772214 Vasculature that is part of the eye region. OBOL:automatic 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 OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g UMLS:C0026860 VHOG:0001275 VSAO:0000031 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 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) UMLS:C0026860 ncithesaurus:Musculoskeletal_System Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA] A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO] AEO:0000178 EHDAA2:0003178 EMAPA:35344 FMA:7492 MA:0000321 TAO:0005156 ZFA:0005156 articulatio fibrosa uberon junctura fibrosa UBERON:0002209 fibrous joint FMA Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA] FMA:FMA A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO] 2012-08-14 TAO:0005156 TAO ZFIN:curator junctura fibrosa 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 TAO:0005155 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 junctura cartilaginea Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA] WP considers epiphyseal plates as subtypes of this consider adding link to hyaline cartilage EMAPA:35846 FMA:7497 MA:0001501 cartilago epiphysialis primary cartilaginous joint uberon epiphysial cartilage UBERON:0002215 synchondrosis Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA] FMA:FMA cartilago epiphysialis FMA:7497 FMA:TA primary cartilaginous joint FMA:7497 epiphysial cartilage FMA:7497 Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA] consider adding fibrocartilage class EMAPA:37758 FMA:7498 MA:0001504 secondary cartilaginous joint uberon UBERON:0002216 symphysis MA FMA Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA] FMA:FMA EMAPA:37758 MA:th secondary cartilaginous joint FMA:7498 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 OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA TAO:0005153 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 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:A01.911.800 NCIT:C12905 OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA UMLS:C0230139 cavitas thoracis cavity of chest cavity of thorax chest cavity pectoral cavity space of thoracic compartment thoracic lumen uberon UBERON:0002224 thoracic cavity The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. UBERON:cjm UMLS:C0230139 ncithesaurus:Thoracic_Cavity cavitas thoracis 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 OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA TAO:0000075 UMLS:C0037925 VHOG:0000601 XAO:0000020 ZFA:0000075 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 uberon SpC cerebro-cerebellar fissure cerebrocerebellar fissure fissura cerebro-cerebellaris fissura cerebrocerebellaris medulla spinalis spinal cord structure spinal medulla UBERON:0002240 spinal cord 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 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 UMLS:C0037925 BIRNLEX:1709 UMLS:C0037925 ncithesaurus:Spinal_Cord http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 BIRNLEX:1709 SpC cerebro-cerebellar fissure NeuroNames:22 cerebrocerebellar fissure NeuroNames:22 fissura cerebro-cerebellaris NeuroNames:22 fissura cerebrocerebellaris NeuroNames:22 medulla spinalis medulla spinalis BTO:0001279 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 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]. 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 An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint AAO:0010180 BTO:0001772 FBbt:00005158 FMA:77659 VHOG:0000287 XAO:0000273 olfactory organ olfactory sense organ olfactory sensory organ main olfactory organ primary olfactory organ uberon olfactory neuroepithelium organ olfactus organum olfactorium UBERON:0002268 olfactory organ An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. UBERON:cjm olfactory organ BTO:0001772 olfactory sensory organ FBbt:00005158 olfactory neuroepithelium BTO:0001772 organ olfactus BTO:0001772 organum olfactorium BTO:0001772 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 brain stem reticular formation brainstem reticular formation reticular formation (classical) reticular formation of the brainstem uberon UBERON:0002275 reticular formation 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 brainstem reticular formation NeuroNames:1223 reticular formation (classical) NeuroNames:1223 reticular formation of the brainstem NeuroNames:1223 A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]. The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]. 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] BAMS:LV BAMS:Tel-V BIRNLEX:1263 BM:Tel-LV BTO:0000879 CALOHA:TS-1230 DHBA:10596 DMBA:126651562 EFO:0001961 EHDAA2:0001984 EHDAA:3502 EHDAA:6576 EMAPA:16914 EV:0100307 FMA:78448 GAID:611 HBA:9419 MA:0000192 MBA:81 MESH:D020547 NCIT:C12834 OpenCyc:Mx4rvYsFdZwpEbGdrcN5Y29ycA TAO:0000696 UMLS:C0152279 VHOG:0000643 ZFA:0000696 lateral ventricle lateral ventricles telencephalic ventricle telencephalon lateral ventricle uberon forebrain ventricle lateral ventricle of brain tectal ventricle telencephalic ventricles telencephalic vesicle UBERON:0002285 modeled as space in EHDAA2 telencephalic ventricle material to immaterial EHDAA2 A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]. The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]. GO:0021670 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:0000643 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 UMLS:C0152279 BIRNLEX:1263 UMLS:C0152279 ncithesaurus:Lateral_Ventricle lateral ventricle MA:0000192 lateral ventricles telencephalic ventricle VHOG:0000643 ZFA:0000696 telencephalon lateral ventricle EHDAA2:0001984 lateral ventricle of brain BTO:0000879 telencephalic ventricles BAMS:Tel-V telencephalic vesicle ZFA:0000696 Choroid plexus of the fourth ventricle BAMS:chp4 BAMS:cp4v DHBA:12808 EMAPA:32742 FMA:78492 HBA:9710 MA:0000983 NCIT:C32308 NLX:27388 TAO:0001446 UMLS:C0152293 VHOG:0001375 ZFA:0001446 chorioid plexus of cerebral hemisphere of fourth ventricle chorioid plexus of fourth ventricle choroid plexus fourth ventricle fourth ventricle chorioid plexus of cerebral hemisphere fourth ventricle choroid plexus uberon 4th ventricle choroid plexus UBERON:0002290 choroid plexus of fourth ventricle Choroid plexus of the fourth ventricle NLX:27388 UMLS:C0152293 ncithesaurus:Choroid_Plexus_of_the_Fourth_Ventricle chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic choroid plexus fourth ventricle ZFA:0001446 fourth ventricle chorioid plexus of cerebral hemisphere OBOL:automatic 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 biliary apparatus uberon biliary tract UBERON:0002294 biliary system 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). 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 TAO:0005130 ZFA:0005130 uberon dorsal mesogastrium mesenterium dorsale commune UBERON:0002296 dorsal mesentery EHDAA2 The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]. 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 mesenterium dorsale commune 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 TAO:0002156 UMLS:C0006121 VHOG:0001457 ZFA:0001707 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 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 ZFA:0001707 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 UMLS:C0006121 ncithesaurus:Brain_Stem http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 BIRNLEX:1565 brain stem ABA:BS truncus encephali 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 One of the layers of the neocortex. cortical layer ABA:CTX1-6b EMAPA:35588 FMA:83138 MA:0000186 layer of neocortex neocortex layer uberon cerebral cortex layer lamina of neocortex UBERON:0002301 layer of neocortex One of the layers of the neocortex. layer of neocortex FMA:83138 neocortex layer MA:0000186 cerebral cortex layer MA:0000186 lamina of neocortex FMA:83138 Part of choroid plexus contained in the lateral ventricle BAMS:cplv DHBA:10601 EHDAA2:0004449 EMAPA:17769 FMA:83711 HBA:9708 MA:0000961 NCIT:C32309 NLX:32548 TAO:0001447 UMLS:C0152289 VHOG:0001376 ZFA:0001447 chorioid plexus of cerebral hemisphere of lateral ventricle chorioid plexus of lateral ventricle choroid plexus telencephalic ventricle lateral ventricle chorioid plexus of cerebral hemisphere lateral ventricle choroid plexus uberon UBERON:0002307 choroid plexus of lateral ventricle Part of choroid plexus contained in the lateral ventricle NLX:32548 UMLS:C0152289 ncithesaurus:Choroid_Plexus_of_the_Lateral_Ventricle chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic choroid plexus telencephalic ventricle ZFA:0001447 lateral ventricle chorioid plexus of cerebral hemisphere OBOL:automatic A neural nucleus that is part of the brain. EMAPA:35185 FMA:83840 MA:0000811 NCIT:C49346 UMLS:C1706993 ZFA:0005575 brain nucleus uberon brain nuclei UBERON:0002308 nucleus of brain A neural nucleus that is part of the brain. 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 UMLS:C0475853 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. check the FMA placement here; ncit placement of body cavity here probably not correct 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 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 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 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 The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. EMAPA:31518 FMA:85275 MA:0001686 NCIT:C49309 UMLS:C1710584 epithelial tissue of urethra urethra epithelial tissue urethra epithelium uberon urethral epithelium urethral plate urethral seam UBERON:0002325 epithelium of urethra GO The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. GO:0061071 UMLS:C1710584 ncithesaurus:Urethra_Epithelium epithelial tissue of urethra OBOL:automatic urethra epithelial tissue OBOL:automatic urethral plate EMAPA:31518 urethral seam EMAPA:31518 A lamina propria that is part of a urethra [Automatically generated definition]. EMAPA:37785 FMA:85276 MA:0001689 lamina propria mucosa of urethra lamina propria mucosae of urethra urethra lamina propria urethra lamina propria mucosa urethra lamina propria mucosae uberon urethral lamina propria UBERON:0002326 lamina propria of urethra A lamina propria that is part of a urethra [Automatically generated definition]. OBOL:automatic EMAPA:37785 MA:th lamina propria mucosa of urethra OBOL:automatic lamina propria mucosae of urethra OBOL:automatic urethra lamina propria mucosa OBOL:automatic urethra lamina propria mucosae 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:A16.254.610 NCIT:C12463 TAO:0000135 UMLS:C0028439 VHOG:0000199 VSAO:0000032 XAO:0000055 ZFA:0000135 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 VSAO 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 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 UMLS:C0028439 ncithesaurus:Notochord notocord ZFA:0000135 notochorda 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. 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:A16.254.425.660.750 MIAA:0000068 NCIT:C34302 TAO:0000155 UMLS:C0376449 VHOG:0000191 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 EHDAA2 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. 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) mesodermal cluster GO:0001756 UMLS:C0376449 ncithesaurus:Somite epimere ISBN:0073040584 epithelial somite somites somitus 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 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]. UMLS:C1516995 ncithesaurus:Exocrine_System exocrine glandular system EHDAA2:0002225 The connecting cord from the developing embryo to the placenta. The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP]. umbilical BTO:0001415 CALOHA:TS-1078 EFO:0001415 EHDAA2:0000312 EHDAA:158 EMAPA:26115 EV:0100127 FMA:85541 GAID:517 MAT:0000280 MESH:A16.254.789 MIAA:0000280 NCIT:C34320 OpenCyc:Mx4rvyewDJwpEbGdrcN5Y29ycA UMLS:C0041633 chorda umbilicalis funiculus umbilicalis uberon birth cord connecting stalk funiculus umbilicalis yolk stalk UBERON:0002331 See notes for connecting stalk umbilical cord The connecting cord from the developing embryo to the placenta. ISBN:0-683-40008-8 MP:0001725 The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP]. UMLS:C0041633 ncithesaurus:Umbilical_Cord chorda umbilicalis MP:0012134 funiculus umbilicalis MP:0012134 birth cord funiculus umbilicalis yolk stalk BTO:0001415 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 OpenCyc:Mx4rv-6d0ZwpEbGdrcN5Y29ycA VHOG:0001134 galen:PulmonaryTrunk pulmonary artery (trunk) trunk of pulmonary arterial tree uberon main pulmonary artery UBERON:0002333 pulmonary trunk MA 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] 2012-09-17 VHOG:0001134 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] 2012-09-17 VHOG:0001134 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 main pulmonary artery the duct of the submadibular gland that opens at the sublingual papilla near the frenulum of the tongue FMA also has 'main submandibular duct' (FMA:59899) BTO:0004556 EMAPA:35833 FMA:86266 MA:0002698 NCIT:C33649 UMLS:C0227472 uberon Wharton's duct ductus submandibularis ductus submaxillaris submandibular salivary duct submaxillar gland duct submaxillary duct UBERON:0002334 submandibular duct the duct of the submadibular gland that opens at the sublingual papilla near the frenulum of the tongue ISBN:0-683-40008-8 MP:0009525 FMA also has 'main submandibular duct' (FMA:59899) FMA UMLS:C0227472 ncithesaurus:Submandibular_Duct Wharton's duct FMA:59899 ductus submandibularis BTO:0004556 ductus submaxillaris submaxillar gland duct BTO:0004556 The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle. CALOHA:TS-1266 EMAPA:35310 FMA:86487 MA:0002734 NCIT:C32516 UMLS:C0227849 endometrium stroma stroma of endometrium uberon UBERON:0002337 endometrial stroma The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle. ncithesaurus:Endometrial_Stroma UMLS:C0227849 ncithesaurus:Endometrial_Stroma A lamina propria that is part of a bronchus [Automatically generated definition]. EMAPA:35194 FMA:86619 MA:0001836 NCIT:C49212 UMLS:C1707054 bronchi lamina propria bronchi lamina propria mucosa bronchi lamina propria mucosae bronchial trunk lamina propria bronchial trunk lamina propria mucosa bronchial trunk lamina propria mucosae bronchus lamina propria bronchus lamina propria mucosa bronchus lamina propria mucosae lamina propria mucosa of bronchi lamina propria mucosa of bronchial trunk lamina propria mucosa of bronchus lamina propria mucosae of bronchi lamina propria mucosae of bronchial trunk lamina propria mucosae of bronchus lamina propria of bronchi lamina propria of bronchial trunk uberon bronchial lamina propria UBERON:0002338 lamina propria of bronchus true A lamina propria that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707054 ncithesaurus:Bronchus_Lamina_Propria bronchi lamina propria OBOL:automatic bronchi lamina propria mucosa OBOL:automatic bronchi lamina propria mucosae OBOL:automatic bronchial trunk lamina propria OBOL:automatic bronchial trunk lamina propria mucosa OBOL:automatic bronchial trunk lamina propria mucosae OBOL:automatic bronchus lamina propria mucosa OBOL:automatic bronchus lamina propria mucosae OBOL:automatic lamina propria mucosa of bronchi OBOL:automatic lamina propria mucosa of bronchial trunk OBOL:automatic lamina propria mucosa of bronchus OBOL:automatic lamina propria mucosae of bronchi OBOL:automatic lamina propria mucosae of bronchial trunk OBOL:automatic lamina propria mucosae of bronchus OBOL:automatic lamina propria of bronchi OBOL:automatic lamina propria of bronchial trunk OBOL:automatic bronchial lamina propria EMAPA:35194 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]. 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:A16.254.600 MIAA:0000066 NCIT:C34222 TAO:0000045 UMLS:C0027789 VHOG:0000057 XAO:0000048 ZFA:0000045 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 XAO BTO 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 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] 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) UMLS:C0027789 ncithesaurus:Neural_Crest NC XAO:0000048 crista neuralis 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 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:00001061 FMA:87657 MAT:0000176 MIAA:0000176 NCIT:C34228 TAO:0001120 UMLS:C1518271 VHOG:0000150 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. (...) 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) UMLS:C1518271 ncithesaurus:Neuroectoderm epithelium tubi neuralis; neuroectoderma 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 OpenCyc:Mx4rvdZIBpwpEbGdrcN5Y29ycA UMLS:C0039987 dorsal vertebra thorax vertebra vertebra of thorax vertebra thoracica uberon UBERON:0002347 thoracic vertebra 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. 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. 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 XAO:0000316 ZFA:0005057 galen:Epicardium heart epicardium visceral serous pericardium of heart visceral serous pericardium proper uberon pericardium visceral mesothelium UBERON:0002348 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. 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 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 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 OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw RETIRED_EHDAA2:0001220 TAO:0001319 UMLS:C0027061 VHOG:0000083 XAO:0000065 ZFA:0001319 galen:Myocardium heart myocardium muscle of heart uberon cardiac muscle heart muscle UBERON:0002349 myocardium 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 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 heart muscle 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 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 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) 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 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:A01.673 NCIT:C12767 OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA UMLS:C0030797 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. 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 serous portion of pericardium uberon pericardium serosum UBERON:0002357 serous pericardium FMA FMA Serous membrane which is divided into parietal and visceral serous pericardium. serous portion of pericardium FMA:9582 pericardium serosum 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:A01.047.025.600 NCIT:C12770 OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA TAO:0005120 UMLS:C0031153 VHOG:0001257 XAO:0000139 ZFA:0005120 galen:Peritoneum uberon peritonaeum UBERON:0002358 peritoneum 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 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 Membrane organ that surrounds the brain and the spinal cord. Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] meningeal Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx). Not consider part of the CNS/neuraxis in FMA BTO:0000144 CALOHA:TS-1177 EFO:0000867 EMAPA:32660 EV:0100312 FMA:9589 GAID:687 MA:0001113 MAT:0000113 MESH:D008578 NCIT:C12348 NLXANAT:090204 OpenCyc:Mx4rwDOl8JwpEbGdrcN5Y29ycA TAO:0001355 UMLS:C0025285 VHOG:0001295 ZFA:0001355 layer of meninges meningeal layer meninx primitiva uberon UBERON:0002360 meninx FMA Bgee:AN Membrane organ that surrounds the brain and the spinal cord. FMA:9589 Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG] 2012-09-17 VHOG:0001295 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0001295 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 Not consider part of the CNS/neuraxis in FMA FMA https://github.com/obophenotype/uberon/issues/1261 UMLS:C0025285 ncithesaurus:Meninges meninx primitiva VHOG:0001295 The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals. consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater]. BTO:0001635 EHDAA2:0004318 EHDAA:1367 EHDAA:1961 EHDAA:2001 EHDAA:2099 EHDAA:2685 EHDAA:2833 EHDAA:2867 EHDAA:3692 EHDAA:3710 EHDAA:6566 EHDAA:6583 EMAPA:32663 EV:0100315 FMA:9590 GAID:693 MA:0001116 MESH:D010841 NCIT:C33321 NLXANAT:090209 OpenCyc:Mx4rvtesBZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001464 UMLS:C0031869 pia mater of neuraxis pial membrane uberon pia UBERON:0002361 pia mater The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals. NLXANAT:090209 delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater]. UMLS:C0031869 ncithesaurus:Pia_Mater pial membrane NLXANAT:090209 pia NLXANAT:090209 A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space. BTO:0001636 CALOHA:TS-0052 EMAPA:32659 EV:0100314 FMA:9591 GAID:688 MA:0001114 MESH:D001099 NCIT:C32136 NLXANAT:090208 OpenCyc:Mx4rve5HlJwpEbGdrcN5Y29ycA UMLS:C1510935 arachnoid arachnoid mater of neuraxis arachnoid membrane uberon arachnoidea mater UBERON:0002362 arachnoid mater A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space. ISBN:0471888893 UMLS:C1510935 ncithesaurus:Arachnoid_Membrane arachnoid membrane NLXANAT:090208 arachnoidea mater BTO:0001636 Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections. the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater]. capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288 some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. DOI:10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261] BTO:0001637 CALOHA:TS-2008 EMAPA:32664 EV:0100313 FMA:9592 GAID:691 MA:0001115 MESH:D004388 NCIT:C32488 NLXANAT:090206 OpenCyc:Mx4rvvmzqZwpEbGdrcN5Y29ycA UMLS:C0013313 dura mater of neuraxis pachymeninges uberon dura UBERON:0002363 dura mater definitional Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections. NLXANAT:090206 the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater]. UMLS:C0013313 ncithesaurus:Dura_Mater pachymeninges NLXANAT:090206 dura BTO:0001637 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 UMLS:C0015282 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 UMLS:C0015282 ncithesaurus:Exocrine_Gland ducted gland AEO:0000097 glandula exocrina The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. TODO - FMA treats the gland as part of the prostate - see also FMA:74119. prostatic BTO:0001129 CALOHA:TS-0828 EFO:0000858 EMAPA:19287 EV:0100104 FMA:9600 GAID:392 MA:0000404 MAT:0000078 MESH:D011467 MIAA:0000078 NCIT:C12410 OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA UMLS:C0033572 VHOG:0001261 galen:ProstateGland male prostate prostate uberon prostata UBERON:0002367 prostate gland The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. GO:0030850 UMLS:C0033572 ncithesaurus:Prostate_Gland male prostate prostata 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 OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA UMLS:C0014133 ductless gland glandula endocrina uberon ductless gland glandulae endocrinae UBERON:0002368 endocrine 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]. UMLS:C0014133 ncithesaurus:Endocrine_Gland ductless gland AEO:0000098 ductless gland glandulae endocrinae Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. AAO:0010551 BTO:0000047 CALOHA:TS-0016 EFO:0000238 EMAPA:18426 EV:0100135 FMA:9604 GAID:446 MA:0000116 MAT:0000071 MESH:D000311 MIAA:0000071 NCIT:C12666 OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA UMLS:C0001625 VHOG:0001141 XAO:0000164 galen:AdrenalGland glandula adrenalis glandula suprarenalis uberon adrenal adrenal capsule adrenal medulla cell atrabiliary capsule epinephric gland epinephros glandula suprarenalis interrenal gland suprarenal capsule suprarenal gland UBERON:0002369 adrenal gland FMA-abduced-lr Wikipedia Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. BTO:0000047 Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] 2012-06-20 AAO:0010551 AAO AAO:BJB All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 UMLS:C0001625 ncithesaurus:Adrenal_Gland glandula adrenalis glandula suprarenalis adrenal BTO:0000047 adrenal capsule BTO:0000047 atrabiliary capsule BTO:0000047 epinephric gland epinephros BTO:0000047 glandula suprarenalis BTO:0000047 interrenal gland GO:0030325 suprarenal capsule BTO:0000047 suprarenal gland Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland. thymus http://langual.org Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO] A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG] thymic AAO:0010548 BTO:0001374 CALOHA:TS-1043 EFO:0000860 EHDAA2:0002017 EHDAA:9119 EMAPA:18768 EV:0100138 FMA:9607 GAID:464 MA:0000142 MAT:0000080 MESH:A06.407.850 MIAA:0000080 NCIT:C12433 OpenCyc:Mx4rvpIympwpEbGdrcN5Y29ycA TAO:0001078 UMLS:C0040113 VHOG:0000253 XAO:0000163 ZFA:0001078 http://www.langual.org/langual_thesaurus.asp?termid=C0273 thymus gland thymus organ uberon UBERON:0002370 thymus EHDAA2 ZFA Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. NLM:thymus Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO] 2012-06-20 AAO:0010548 AAO AAO:BJB A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG] 2012-09-17 VHOG:0000253 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.558 UMLS:C0040113 ncithesaurus:Thymus_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 bone marrow http://langual.org 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 OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA UMLS:C0005953 VHOG:0001218 XAO:0000123 galen:BoneMarrow http://www.langual.org/langual_thesaurus.asp?termid=C0149 medulla ossea medulla ossium uberon medulla of bone medullary bone UBERON:0002371 bone marrow 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) UMLS:C0005953 ncithesaurus:Bone_Marrow medulla ossea BTO:0000141 FMA:9608 medulla ossium BTO:0000141 medulla of bone BTO:0000141 either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region BTO:0001387 CALOHA:TS-1053 EFO:0001401 EMAPA:35871 EV:0100052 FMA:9609 GAID:341 MA:0000143 MESH:A03.867.603.925 NCIT:C12802 OpenCyc:Mx4rvVivrZwpEbGdrcN5Y29ycA UMLS:C0836921 UMLS:C1519547 UMLS:C1519548 VHOG:0001139 uberon Mandel UBERON:0002372 tonsil cjm either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx MGI:cwg MP:0002380 UMLS:C0836921 ncithesaurus:Tonsil UMLS:C1519547 ncithesaurus:Tonsilar_Tissue UMLS:C1519548 ncithesaurus:Tonsillar_Lymphoid_Tissue Mandel BTO:0001387 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 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 EHDAA2-abduced Any skeletal muscle that is part of the head region. 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. 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 OpenCyc:Mx4rvlygNJwpEbGdrcN5Y29ycA UMLS:C0000739 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. 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 OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA 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 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 UMLS:C2328219 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 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 TAO:0005023 UMLS:C0018957 VHOG:0001624 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. 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) In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes WP UMLS:C0018957 ncithesaurus:Hematopoietic_System Blutbildungssystem BTO:0000570 Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. BTO:0000855 CALOHA:TS-0580 EFO:0000871 ENVO:02000041 EV:0100049 FMA:9671 GAID:1186 MA:0002520 MAT:0000055 MESH:A12.207.630 MIAA:0000055 NCIT:C13252 OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA UMLS:C0024202 VHOG:0001590 ZFA:0005658 galen:Lymph uberon lympha UBERON:0002391 lymph Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. UMLS:C0024202 ncithesaurus:Lymph lympha the paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG] the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue nasolacrimal duct - posterior naris AAO:0000643 EHDAA2:0001237 EHDAA:7849 EHDAA:9094 EMAPA:17853 FMA:9703 GAID:902 MA:0001299 MESH:D009301 NCIT:C33161 OpenCyc:Mx4rv6PJy5wpEbGdrcN5Y29ycA UMLS:C0027437 VHOG:0000664 uberon d. nasolacrimalis tear duct UBERON:0002392 nasolacrimal duct the paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity ISBN:0-683-40008-8 MP:0008969 The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG] 2012-09-17 VHOG:0000664 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256 nasolacrimal duct - posterior naris VHOG:0000664 UMLS:C0027437 ncithesaurus:Nasolacrimal_Duct d. nasolacrimalis tear duct 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 OpenCyc:Mx4rvdCds5wpEbGdrcN5Y29ycA TAO:0001100 UMLS:C0005400 VHOG:0000212 XAO:0000134 ZFA:0001100 uberon bile tube biliary duct gall duct hepatic duct UBERON:0002394 bile duct EMAPA MA XAO 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. 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 (...) 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) 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 outer serous membrane of the pulmonary pleural. EMAPA:16776 FMA:9733 MA:0002488 NCIT:C33273 OpenCyc:Mx4rvv2Uq5wpEbGdrcN5Y29ycA UMLS:C0225777 VHOG:0001495 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 UMLS:C0225777 ncithesaurus:Parietal_Pleura pleura parietalis 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 OpenCyc:Mx4rwNFqppwpEbGdrcN5Y29ycA 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 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 FMA UMLS:C0225776 ncithesaurus:Visceral_Pleura pleura pulmonalis FMA:9734 FMA:TA pleura visceralis 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:A01.911.800.650 NCIT:C12840 OpenCyc:Mx4rwCKAppwpEbGdrcN5Y29ycA UMLS:C0178802 VHOG:0000581 cavitas pleuralis uberon cavitum pleuralae cavitum pleurale UBERON:0002402 pleural cavity Wikipedia 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] 2012-09-17 VHOG:0000581 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 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 cavitum pleuralae cavitum pleurale 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 OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA TAO:0001159 UMLS:C0020962 VHOG:0001247 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. 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) UMLS:C0020962 ncithesaurus:Immune_System a double-walled sac containing the heart and the roots of the great vessels. FMA:9868 RETIRED_EHDAA2:0001443 TAO:0000054 uberon pericardium UBERON:0002406 pericardial sac FMA a double-walled sac containing the heart and the roots of the great vessels. 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 OpenCyc:Mx4rvoCLgJwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001443 TAO:0000054 UMLS:C0031050 VHOG:0001280 XAO:0004182 ZFA:0000054 galen:Pericardium uberon UBERON:0002407 pericardium MA 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] 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 UMLS:C0225969 VHOG:0000537 lamina parietalis (pericardii serosum) lamina parietalis pericardii parietal layer of serous pericardium parietal pericardium uberon pericardial sac UBERON:0002408 parietal serous pericardium Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. UMLS:C0225969 ncithesaurus:Parietal_Pericardium lamina parietalis pericardii FMA:9870 FMA:TA parietal pericardium VHOG:0000537 pericardial sac Transudate contained in the pericardial cavity.[FMA] BTO:0001016 FMA:9887 MA:0002530 uberon UBERON:0002409 pericardial fluid FMA Transudate contained in the pericardial cavity.[FMA] FMA:9887 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 MA:0000219 MESH:D001341 NCIT:C12673 TAO:0001574 UMLS:C0004388 UMLS:C1305381 VHOG:0000396 ZFA:0001574 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 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 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) FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib FMA UMLS:C0004388 BIRNLEX:1123 UMLS:C0004388 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 the small, erectile body located at the anterior end of the vulva clitoral BTO:0002020 EHDAA2:0000255 EHDAA:9360 EMAPA:30819 FMA:9909 GAID:385 MA:0000382 MESH:D002987 NCIT:C12308 OpenCyc:Mx4rvVjr6ZwpEbGdrcN5Y29ycA UMLS:C0008984 VHOG:0000700 galen:Clitoris uberon UBERON:0002411 clitoris Wikipedia MA EHDAA2 Wikipedia the small, erectile body located at the anterior end of the vulva ISBN:0-683-40008-8 MP:0003127 UMLS:C0008984 ncithesaurus:Clitoris 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 CALOHA:TS-2352 EFO:0001371 EMAPA:32740 FMA:9914 MA:0000309 NCIT:C12933 OpenCyc:Mx4rvt2Dh5wpEbGdrcN5Y29ycA TAO:0001189 UMLS:C0549207 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 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 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 XAO:0003076 galen:CervicalVertebra cervical vertebrae uberon vertebrae cervicales UBERON:0002413 cervical vertebra true A vertebra that is located in the cervical region of the vertebral column. cervical vertebrae vertebrae cervicales Large vertebra of the movable part of the vertebral column, characterized by the absence of the foramen transversarium within the transverse process, and by the absence of facets on the sides of the body. Whereas all rats had six lumbar vertebrae, variable patterns in mice included mostly five vertebrae in DBA/2J, mostly six vertebrae in C57BL/6J, and a mix in B6129PF2/J CALOHA:TS-2364 EMAPA:18007 FMA:9921 GAID:240 MA:0000312 MESH:D008159 NCIT:C12744 OpenCyc:Mx4rvaOek5wpEbGdrcN5Y29ycA UMLS:C0024091 galen:LumbarVertebra uberon UBERON:0002414 lumbar vertebra Large vertebra of the movable part of the vertebral column, characterized by the absence of the foramen transversarium within the transverse process, and by the absence of facets on the sides of the body. Whereas all rats had six lumbar vertebrae, variable patterns in mice included mostly five vertebrae in DBA/2J, mostly six vertebrae in C57BL/6J, and a mix in B6129PF2/J PMCID:PMC2700063 UMLS:C0024091 ncithesaurus:Lumbar_Vertebra 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 OpenCyc:Mx4rvVjiC5wpEbGdrcN5Y29ycA WBbt:0005741 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 caudal subdivision 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 TADS:0000108 UMLS:C0037267 VHOG:0000403 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 (...) 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) UMLS:C0037267 ncithesaurus:Integumentary_System integumentary system FMA:72979 dermal system MIAA:0000033 integumentum commune organism surface EHDAA2:0003154 surface BILA:0000118 The abdominal segment of the torso. EMAPA:35104 FMA:259211 MA:0000021 uberon abdomen/pelvis/perineum lower body lower trunk lumbar region UBERON:0002417 abdominal segment of trunk FMA The abdominal segment of the torso. abdomen/pelvis/perineum MA:0000021 lower body MA:0000021 lower trunk FMA:259211 lumbar region 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 OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA TAO:0001501 UMLS:C0007301 VHOG:0001207 VSAO:0000040 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 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 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) 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 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 Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures. Fluid-filled brain cavity. Kimmel et al, 1995.[TAO] Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO] The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592]. 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] AAO:0011043 BAMS:4V BAMS:V4 BIRNLEX:1256 BM:Pons-4V BTO:0003426 CALOHA:TS-2015 DHBA:10669 DHBA:12805 DMBA:126651782 EHDAA2:0000100 EHDAA:896 EMAPA:16917 EV:0100310 FMA:78469 GAID:610 HBA:9421 MA:0000196 MBA:145 MESH:D020546 NCIT:C12828 OpenCyc:Mx4rv-7Q6pwpEbGdrcN5Y29ycA TAO:0000110 UMLS:C0149556 VHOG:0000006 XAO:0003099 ZFA:0000110 ventricle IV rhombencephalic vesicle uberon 4th ventricle IVth ventricle fourth ventricle proper hindbrain ventricle rhombencephalic ventricle ventricle of hindbrain ventricle of rhombencephalon ventriculus quartus UBERON:0002422 fourth ventricle EHDAA2 Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures. BIRNLEX:1256 Fluid-filled brain cavity. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000110 TAO ZFIN:curator Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO] 2012-06-20 AAO:0011043 AAO UBERON:0002422 The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592]. GO:0021592 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:0000006 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 UMLS:C0149556 ncithesaurus:Fourth_Ventricle_of_the_Brain ventricle IV ZFA:0000110 rhombencephalic vesicle ZFA:0000110 4th ventricle MA:0000196 IVth ventricle VHOG:0000006 fourth ventricle proper BAMS:V4 hindbrain ventricle VHOG:0000006 rhombencephalic ventricle VHOG:0000006 ventricle of hindbrain BTO:0003426 ventricle of rhombencephalon BTO:0003426 ventriculus quartus 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 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 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 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 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 VHOG:0000538 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]. lamina visceralis pericardii serosi visceral pericardium VHOG:0000538 epicardium MA:0000484 pericardium visceral mesothelium EMAPA:16589 Any muscle organ that is part of a chest [Automatically generated definition]. BTO:0000508 CALOHA:TS-1037 EMAPA:17747 EMAPA:17748 FMA:9619 MA:0000548 anterior thoracic region muscle organ anterolateral part of thorax muscle organ chest muscle organ front of thorax muscle organ muscle of thorax muscle organ of anterior thoracic region muscle organ of anterolateral part of thorax muscle organ of chest muscle organ of front of thorax musculus thoracicus thoracic muscle uberon UBERON:0002426 chest muscle Any muscle organ that is part of a chest [Automatically generated definition]. OBOL:automatic anterior thoracic region muscle organ OBOL:automatic anterolateral part of thorax muscle organ OBOL:automatic chest muscle organ OBOL:automatic front of thorax muscle organ OBOL:automatic muscle of thorax FMA:9619 muscle organ of anterior thoracic region OBOL:automatic muscle organ of anterolateral part of thorax OBOL:automatic muscle organ of chest OBOL:automatic muscle organ of front of thorax OBOL:automatic A bone that is part of a limb [Automatically generated definition]. the formal definition is very inclusive, and includes sesamoids NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle EFO:0000945 MAT:0000151 MIAA:0000151 NCIT:C32223 UMLS:C0582791 bone of extremity bone of limb free limb bone uberon UBERON:0002428 limb bone A bone that is part of a limb [Automatically generated definition]. OBOL:automatic NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle NCIT UMLS:C0582791 ncithesaurus:Bone_of_the_Extremity bone of limb OBOL:automatic free limb bone UBERONREF:0000003 Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted]. FMA:61213 MA:0000736 NCIT:C32298 UMLS:C0588054 lymph node of neck uberon UBERON:0002429 cervical lymph node Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted]. UMLS:C0588054 ncithesaurus:Cervical_Lymph_Node 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 mucous secreting gland associated with the mucuous membrane lining the uterus. simple or branched tubular BTO:0003433 BTO:0004518 EMAPA:29919 MA:0001726 NCIT:C33842 UMLS:C1183035 endometrial gland endometrial mucuous gland endometrium gland glandulae uterinae uterine gland uberon glandulae uterinae UBERON:0002451 endometrial gland MP The mucous secreting gland associated with the mucuous membrane lining the uterus. UMLS:C1183035 ncithesaurus:Uterine_Gland endometrial gland BTO:0003433 glandulae uterinae FMA:71647 FMA:TA glandulae uterinae An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted]. MA has both mammary and thoracic EHDAA2:0000880 EHDAA:8585 EMAPA:18617 FMA:3960 MA:0001982 MA:0001984 NCIT:C52941 OpenCyc:Mx4rMe0MIao8EduQrwACs5b6Bw UMLS:C0226276 internal mammary artery internal thoracic mammary artery uberon arteria mammaria interna arteria thoracica interna mammary artery UBERON:0002456 internal thoracic artery An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted]. MA has both mammary and thoracic MA UMLS:C0226276 ncithesaurus:Internal_Mammary_Artery internal mammary artery MA:0001982 arteria mammaria interna arteria thoracica interna mammary artery EMAPA:18617 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 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 intersegmental artery ZFA:0001061 intersegmental arteries ZFA:0001061 Arteries that supply the spinal cord. EHDAA2:0001890 EHDAA:4355 EMAPA:18241 MA:0002043 NCIT:C33587 TAO:0000682 UMLS:C0447043 ZFA:0000682 spinal arteries uberon UBERON:0002458 spinal artery Arteries that supply the spinal cord. UMLS:C0447043 ncithesaurus:Spinal_Artery spinal arteries ZFA:0000682 A tributary of the iliac vein that drains the urinary bladder. EMAPA:37205 MA:0002263 venae vesicales vesical veins vesical veins set uberon UBERON:0002460 vesical vein A tributary of the iliac vein that drains the urinary bladder. UBERON:cjm EMAPA:37205 MA:th venae vesicales FMA:70911 FMA:TA vesical veins The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] lymphoid The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013] The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013] We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. UBERON:0002096 EHDAA2:0001043 EHDAA:8677 EMAPA:37664 FMA:74594 GAID:931 MA:0002435 MAT:0000197 MIAA:0000197 NCIT:C12746 OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA TAO:0000385 UMLS:C0024235 VHOG:0000842 XAO:0003199 ZFA:0000385 lymphatic system uberon lymphatic circulatory system lymphatic drainage system systema lymphoideum UBERON:0002465 lymphoid system FMA The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] 2012-06-20 AAO:0010522 AAO AAO:BJB Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] 2012-09-17 VHOG:0000842 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627 We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. EMAPA:37664 MA:th UMLS:C0024235 ncithesaurus:Lymphatic_System lymphatic system ZFA:0000385 lymphatic circulatory system lymphatic drainage system systema lymphoideum 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 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. UMLS:C0021849 ncithesaurus:Intestinal_Secretion intestinal secretion FMA:62974 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 NCIT:C32538 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 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 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 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 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 The minute canals that pass the prostatic secretions to the urethra. EMAPA:36568 FMA:19580 MA:0002785 NCIT:C13102 UMLS:C0227965 duct of prostate duct of prostate gland prostate duct prostate gland duct prostatic duct uberon UBERON:0002485 prostate duct The minute canals that pass the prostatic secretions to the urethra. MP:0009734 UMLS:C0227965 ncithesaurus:Prostatic_Duct 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 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 A lymph node that is part of an abdomen [Automatically generated definition]. EMAPA:35992 FMA:12787 MA:0002827 abdomen lymph node lymph node of abdomen uberon parietal abdominal lymph node UBERON:0002507 abdominal lymph node A lymph node that is part of an abdomen [Automatically generated definition]. OBOL:automatic abdomen lymph node OBOL:automatic parietal abdominal lymph node FMA:12787 The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. BTO:0000767 EMAPA:35561 FMA:12795 MA:0002829 NCIT:C77641 UMLS:C0229792 mesenteric node uberon nodi lymphoidei mesenterici UBERON:0002509 mesenteric lymph node FMA The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. MP:0005232 UMLS:C0229792 ncithesaurus:Mesenteric_Lymph_Node nodi lymphoidei mesenterici BTO:0000767 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 VSAO VSAO Replacement bone that forms within cartilage. GO:0001958 GO_REF:0000034 VSAO:0000145 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 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 UMLS:C0149543 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 The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof. UMLS:C0149543 ncithesaurus:Base_of_the_Skull base of skull FMA:52801 basis cranii FMA:52801 FMA:TA cranial base FMA:52801 MA:0002840 Connective tissue composed of elastic fibers. FMA:20113 GAID:926 MA:0002853 MESH:D004547 NCIT:C32495 elastic connective tissue textus connectivus elasticus elastic fiber uberon UBERON:0002521 elastic tissue Connective tissue composed of elastic fibers. 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 UMLS:C0162867 uberon tunica media vasorum UBERON:0002522 May be composed of smooth muscle and elastic tissue tunica media MA cjm cjm The middle layer of an artery or vein. [WP,unvetted]. UMLS:C0162867 ncithesaurus:Tunica_Media tunica media vasorum tunica media vasorum BTO:0002011 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 UMLS:C0162864 uberon Bichat's tunic intima tunica intima vasorum UBERON:0002523 tunica intima 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 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 UMLS:C0162864 ncithesaurus:Tunica_Intima Bichat's tunic BTO:0002012 intima BTO:0002012 tunica intima vasorum BTO:0002012 A lymph node that is part of a pancreas [Automatically generated definition]. FMA:16626 MA:0002881 NCIT:C77642 UMLS:C0229783 lymph node of pancreas pancreas lymph node pancreatic node uberon aJCC level 19 node pyloric lymph node UBERON:0002527 pancreatic lymph node A lymph node that is part of a pancreas [Automatically generated definition]. OBOL:automatic UMLS:C0229783 ncithesaurus:Pancreatic_Lymph_Node lymph node of pancreas OBOL:automatic pancreas lymph node OBOL:automatic aJCC level 19 node FMA:16626 pyloric lymph node MA:0002881 an organ that functions as a secretory or excretory organ glandular UBERON:MIAA_0000021 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 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UMLS:C1285092 WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland an organ that functions as a secretory or excretory organ MGI:csmith MP:0002163 UMLS:C1285092 ncithesaurus:Gland glandular organ Druese BTO:0000522 glandula glandula BTO:0000522 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 epiblast uberon blastocyst ectoblast epiblastus primitive ectoderm UBERON:0002532 epiblast (generic) 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] 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) epiblast VHOG:0000243 ectoblast MP:0003886 epiblastus 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 tail bud ZFA:0000077 end bud BTO:0001445 tail bud mesenchyme ZFA:0000077 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:A16.254.160 MIAA:0000242 NCIT:C34249 TAO:0001306 UMLS:C0080322 VHOG:0000155 XAO:0000096 ZFA:0001306 pharyngeal arches branchial arch uberon arcus pharyngei visceral arch UBERON:0002539 pharyngeal arch EHDAA2 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. ZFA:yb 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) UMLS:C0080322 ncithesaurus:Pharyngeal_Arch pharyngeal arches branchial arch BTO:0001785 MP:0002884 arcus pharyngei 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 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. 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 ectodermal placode FMA:293966 placode ectodermal cranial placode UBERON:cjm cranial placodes XAO:0000305 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 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 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 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 NCIT:C12892 UMLS:C0581619 UMLS:C1278837 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 UMLS:C0581619 BIRNLEX:1499 UMLS:C0581619 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 regional part of brain that is part of a cerebellar cortex [Automatically generated definition]. BIRNLEX:1571 FMA:76924 cerebellar cortical segment segment of cerebellar cortex uberon UBERON:0002749 regional part of cerebellar cortex A regional part of brain that is part of a cerebellar cortex [Automatically generated definition]. OBOL:automatic cerebellar cortical segment FMA:76924 segment of cerebellar cortex BIRNLEX:1571 . BIRNLEX:1704 FMA:71168 MA:0003083 NCIT:C12895 UMLS:C0581620 UMLS:C0581621 UMLS:C1278838 lumbar segment of spinal cord lumbar segments of spinal cord [1-5] lumbar spinal cord pars lumbalis medullae spinalis segmenta lumbalia medullae spinalis [1-5] spinal cord lumbar segment uberon UBERON:0002792 lumbar spinal cord . UMLS:C0581620 BIRNLEX:1704 UMLS:C0581621 ncithesaurus:Lumbar_Spinal_Cord UMLS:C1278838 BIRNLEX:1704 lumbar segment of spinal cord FMA:71168 lumbar segments of spinal cord [1-5] FMA:71168 lumbar spinal cord FMA:71168 pars lumbalis medullae spinalis FMA:71168 FMA:TA segmenta lumbalia medullae spinalis [1-5] FMA:71168 FMA:TA spinal cord lumbar segment MA:0003083 Parietal lobe of the left hemisphere of the brain BIRNLEX:1728 FMA:72974 UMLS:C1281960 uberon UBERON:0002802 left parietal lobe Parietal lobe of the left hemisphere of the brain BIRNLEX:1728 UMLS:C1281960 BIRNLEX:1728 Parietal lobe of the right hemisphere of the brain BIRNLEX:1729 FMA:72973 UMLS:C1281959 uberon UBERON:0002803 right parietal lobe Parietal lobe of the right hemisphere of the brain BIRNLEX:1729 UMLS:C1281959 BIRNLEX:1729 A temporal lobe that is part of a left cerebral hemisphere. BIRNLEX:1784 FMA:72972 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rwQLi-ZwpEbGdrcN5Y29ycA UMLS:C1281971 uberon UBERON:0002808 left temporal lobe A temporal lobe that is part of a left cerebral hemisphere. OBOL:automatic UMLS:C1281971 BIRNLEX:1784 A temporal lobe that is part of a right cerebral hemisphere. BIRNLEX:1785 FMA:72971 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rwQLi-ZwpEbGdrcN5Y29ycA UMLS:C1281970 uberon UBERON:0002809 right temporal lobe A temporal lobe that is part of a right cerebral hemisphere. OBOL:automatic UMLS:C1281970 BIRNLEX:1785 A frontal cortex that is part of a right cerebral hemisphere. BIRNLEX:1786 FMA:72969 UMLS:C1281954 uberon UBERON:0002810 right frontal lobe A frontal cortex that is part of a right cerebral hemisphere. OBOL:automatic UMLS:C1281954 BIRNLEX:1786 A frontal cortex that is part of a left cerebral hemisphere. BIRNLEX:1787 FMA:72970 UMLS:C1281955 uberon UBERON:0002811 left frontal lobe A frontal cortex that is part of a left cerebral hemisphere. OBOL:automatic UMLS:C1281955 BIRNLEX:1787 A cerebral hemisphere that is in the left side of a brain. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern BIRNLEX:1795 FMA:61819 NCIT:C32955 UMLS:C0228176 left hemisphere uberon UBERON:0002812 left cerebral hemisphere A cerebral hemisphere that is in the left side of a brain. OBOL:automatic UMLS:C0228176 ncithesaurus:Left_Cerebral_Hemisphere left hemisphere BIRNLEX:1795 A cerebral hemisphere that is in the right side of a brain. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern BIRNLEX:1797 FMA:67292 NCIT:C33472 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvigx5ZwpEbGdrcN5Y29ycA UMLS:C0228175 right hemisphere uberon UBERON:0002813 right cerebral hemisphere A cerebral hemisphere that is in the right side of a brain. OBOL:automatic UMLS:C0228175 ncithesaurus:Right_Cerebral_Hemisphere right hemisphere BIRNLEX:1797 Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453) BAMS:12 BAMS:12N BAMS:XII BIRNLEX:2644 BM:XII DHBA:12545 EHDAA2:0004635 EMAPA:35416 EV:0100286 FMA:54505 HBA:9557 MA:0001039 MBA:773 NCIT:C12899 UMLS:C0228802 VHOG:0001358 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 ncithesaurus:Nucleus_of_the_Hypoglossal_Nerve hypoglossal XII nucleus hypoglossal nerve nucleus hypoglossal nucleus nucleus nervi hypoglossi nucleus of hypoglossal nerve twelfth cranial nerve nucleus uberon nucleus hypoglossalis nucleus nervi hypoglossi UBERON:0002871 hypoglossal nucleus Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453) BIRNLEX:2644 UMLS:C0228802 BIRNLEX:2644 UMLS:C0228802 ncithesaurus:Hypoglossal_Nucleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 BIRNLEX:2644 hypoglossal XII nucleus MA:0001039 hypoglossal nerve nucleus FMA:54505 hypoglossal nucleus FMA:54505 nucleus nervi hypoglossi FMA:54505 FMA:TA nucleus of hypoglossal nerve FMA:54505 twelfth cranial nerve nucleus FMA:54505 nucleus hypoglossalis NeuroNames:757 nucleus nervi hypoglossi The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted]. LF BAMS:lf BAMS:lfh BIRNLEX:4041 DHBA:10622 FMA:83727 HBA:9401 NCIT:C33005 OpenCyc:Mx4rwJlWu5wpEbGdrcN5Y29ycA UMLS:C0228186 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=35 fissura interhemispherica fissura longitudinalis cerebrales fissura longitudinalis cerebri fissura longitudinalis magna hemispheric sulcus interhemispheric fissure longitudinal cerebral fissure longitudinal fissure of hemisphere longitudinal fissure of the cerebrum longitudinal sulcus medial longitudinal fissure sagittal fissure uberon UBERON:0002921 longitudinal fissure FMA The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted]. LF BIRNLEX:4041 NIFSTD:NeuroNames_abbrevSource UMLS:C0228186 BIRNLEX:4041 UMLS:C0228186 ncithesaurus:Longitudinal_Fissure http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=35 BIRNLEX:4041 fissura interhemispherica BIRNLEX:4041 fissura longitudinalis cerebrales BIRNLEX:4041 fissura longitudinalis cerebri BIRNLEX:4041 fissura longitudinalis magna BIRNLEX:4041 hemispheric sulcus FMA:83727 interhemispheric fissure FMA:83727 longitudinal cerebral fissure FMA:83727 longitudinal fissure of hemisphere BIRNLEX:4041 longitudinal fissure of the cerebrum BIRNLEX:4041 longitudinal sulcus FMA:83727 medial longitudinal fissure FMA:83727 sagittal fissure FMA:83727 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 UMLS:C0040999 VHOG:0001353 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 A sensory epithelium that is part of a gustatory system. FMA:62412 uberon UBERON:0002926 gustatory epithelium NIFSTD A sensory epithelium that is part of a gustatory system. OBOL:automatic 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 UMLS:C0228426 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 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 UMLS:C0228426 BIRNLEX:923 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=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 A wall, dividing a cavity or structure into smaller ones[WP]. septal AAO:0011127 FMA:86461 OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ septa uberon UBERON:0003037 general anatomical term in FMA septum A wall, dividing a cavity or structure into smaller ones[WP]. septa The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. BIRNLEX:966 FMA:71167 MA:0003082 NCIT:C12894 UMLS:C0581620 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 The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. UMLS:C0581620 BIRNLEX:966 UMLS:C0581620 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 A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] AAO:0011076 EFO:0003420 EHDAA2:0001232 EHDAA:1504 EMAPA:16543 FMA:293971 TAO:0000048 VHOG:0000186 XAO:0000005 ZFA:0000048 olfactory placodes placoda nasalis placoda olfactoria uberon nasal I placode nasal placode UBERON:0003050 Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic olfactory placode NCBIBook:NBK53171 ZFA EHDAA2 A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. XAO:0000005 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] 2012-09-17 VHOG:0000186 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 olfactory placodes placoda nasalis placoda olfactoria An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP] Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305 UBERON:0004373 AAO:0011080 BTO:0002661 EHDAA2:0001342 EMAPA:16669 FMA:302920 NCIT:C34240 TAO:0000051 UMLS:C1518678 VHOG:0001148 XAO:0000006 ZFA:0000051 otic vesicle uberon OV acoustic vesicle auditory vesicle otocyst UBERON:0003051 ear vesicle An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP] MP:0009806 Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000051 TAO ZFIN:curator One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] 2012-09-17 VHOG:0001148 VHOG The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] 2012-09-17 VHOG:0001148 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413 MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305 MP UMLS:C1518678 ncithesaurus:Otic_Vesicle otic vesicle MP:0004311 acoustic vesicle VHOG:0001148 auditory vesicle BTO:0002661 otocyst MP:0004311 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 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 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) 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) 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 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 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 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) unsegmented paraxial mesoderm somitomeric mesoderm GO:0002075 unsegmented mesenchyme VHOG:0000559 In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0011088 NCIT:C34279 TAO:0000150 UMLS:C1283945 VHOG:0000082 XAO:0000063 ZFA:0000150 uberon archinephric duct ductus pronephricus pronephric ducts UBERON:0003060 The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct GO Wikipedia XAO In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000150 TAO ZFIN:curator The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000082 VHOG (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] 2012-09-17 VHOG:0000082 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 UMLS:C1283945 ncithesaurus:Pronephric_Duct archinephric duct VHOG:0000082 ductus pronephricus pronephric ducts ZFA:0000150 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 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]. 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) 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 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 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) 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 TAO:0001206 UMLS:C1284010 VHOG:0000087 XAO:0000085 ZFA:0001206 uberon IM intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium UBERON:0003064 intermediate mesoderm 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 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 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 intermediate plate EMAPA:16178 intermediate plate mesoderm mesenchyma intermedium The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. The second of the 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. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, develops from visceral pouch 2 2 AAO:0010363 EHDAA2:0000050 EHDAA:611 EMAPA:16272 FMA:293017 NCIT:C34288 TAO:0001596 VHOG:0000297 XAO:0000098 ZFA:0001611 2nd pharyngeal arch arcus pharyngeus secundus branchial arch 2 hyoid arch pharyngeal arch 2 second branchial arch second pharyngeal arch second visceral arch visceral arch 2 uberon 2nd arch 2nd visceral arch hyoid bars pharyngeal arches 2 UBERON:0003066 pharyngeal arch 2 The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. ZFIN:yb The second 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:0010363 AAO XAO:EJS 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:0000297 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) in XAO, develops from visceral pouch 2 XAO arcus pharyngeus secundus branchial arch 2 hyoid arch XAO:0000098 second branchial arch second visceral arch visceral arch 2 2nd arch EHDAA2:0000050 2nd visceral arch VHOG:0000297 pharyngeal arches 2 VHOG:0000297 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) 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 XAO:0000205 ZFA:0001204 uberon chordamesoderm UBERON:0003068 axial mesoderm The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. GO:0048318 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 chordamesoderm A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK] Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). AAO:0011079 EFO:0003429 EHDAA2:0001339 EHDAA:506 EMAPA:16195 FMA:293973 NCIT:C34239 TAO:0000138 UMLS:C1518677 VHOG:0000235 XAO:0000223 ZFA:0000138 placoda otica uberon auditory placode ear placode ear/otic placode octaval VIII placode octaval placode UBERON:0003069 otic placode invaginates NCBIBook:NBK53175 A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK] NCBIBook:NBK53175 Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000138 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] 2012-09-17 VHOG:0000235 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). NCBIBook:NBK53175 UMLS:C1518677 ncithesaurus:Otic_Placodes placoda otica octaval VIII placode ISBN:0471888893 octaval placode ISBN:0471888893 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. 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) 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 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 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 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 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 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 XAO:0000240 ZFA:0000122 uberon lens placodes placoda lentis UBERON:0003073 lens placode NCBIBook:NBK53175 A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. 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 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 Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. AAO:0000637 EHDAA2:0001243 EHDAA:1590 EMAPA:16577 GAID:1315 MESH:A16.254.940 NCIT:C26469 TAO:0000546 UMLS:C0043204 VHOG:0000082 XAO:0000242 ZFA:0000546 Wolffian duct uberon Leydig's duct archinephric duct ductus mesonephricus; ductus Wolffi renal duct UBERON:0003074 mesonephric duct GO EHDAA2 Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. ZFIN:curator Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] 2012-06-20 AAO:0000637 AAO AAO:BJB The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000082 VHOG (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] 2012-09-17 VHOG:0000082 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 UMLS:C0043204 ncithesaurus:Mesonephric_Duct Wolffian duct GOC:yaf ZFA:0000546 Leydig's duct archinephric duct VHOG:0000082 ductus mesonephricus; ductus Wolffi 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 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 UMLS:C0920623 VHOG:0000068 XAO:0000249 ZFA:0000132 uberon lamina neuralis presumptive central nervous system UBERON:0003075 neural plate 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 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 UMLS:C0920623 ncithesaurus:Neural_Plate lamina neuralis (...) 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 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 TAO:0000255 UMLS:C1284009 VHOG:0000114 XAO:0000259 ZFA:0000255 paraxial mesenchyme somitic mesoderm uberon mesoderma paraxiale UBERON:0003077 paraxial mesoderm EHDAA2 Bgee:AN The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] GO:0048339 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) 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 somitic mesoderm ISBN:9780878932504 mesoderma paraxiale 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 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) 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 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 TAO:0000121 UMLS:C1517749 VHOG:0000118 XAO:0000311 ZFA:0000121 LPM lateral mesoderm uberon lateral plate lateral plate mesenchyme mesoderma laminae lateralis UBERON:0003081 lateral plate mesoderm 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 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 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) 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 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 TAO:0001056 UMLS:C1513802 VHOG:0001244 XAO:0000315 ZFA:0001056 myomeres uberon muscle plate myomere myotome region myotomes myotomus UBERON:0003082 myotome 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) UMLS:C1513802 ncithesaurus:Myotome_Region myomeres TAO:0001056 myotomus 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 XAO:0000319 ZFA:0001024 TNC uberon trunk crest UBERON:0003083 trunk neural crest 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 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 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 XAO:0000364 ZFA:0000011 uberon CA UBERON:0003086 caudal artery Extension of the dorsal aorta in the tail. 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 EHDAA2:0003439 EMAPA:31159 FMA:295652 NCIT:C34287 TAO:0001080 UMLS:C0183176 VHOG:0000680 XAO:0000397 ZFA:0001080 sclerotomes uberon sclerotomus UBERON:0003089 sclerotome EHDAA2 EHDAA2 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]. XB:curator 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) part_of somite in XAO XAO UMLS:C0183176 ncithesaurus:Sclerotome sclerotomes TAO:0001080 sclerotomus The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus. Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]. In all vertebrates the thyroid arises from the ventral aspect of the second pouch Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm AAO:0011106 BTO:0004709 EHDAA2:0002033 EHDAA:952 EMAPA:16361 NCIT:C34312 TAO:0001081 UMLS:C1519512 XAO:0000444 ZFA:0001081 uberon thyroid primordia UBERON:0003091 thyroid primordium ZFA ZFA VHOG ISBN:0073040584 The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus. Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]. ZFIN:curator In all vertebrates the thyroid arises from the ventral aspect of the second pouch Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm EHDAA2 UMLS:C1519512 ncithesaurus:Thyroid_Primordium thyroid primordia ZFA:0001081 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 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 CNC XAO:0001001 cephalic neural crest EMAPA:16091 crista neuralis cranialis Gonochoristic organism that can produce female gametes. AAO:0010030 BILA:0000028 CARO:0000028 FBbt:00007011 FMA:67812 HAO:0000028 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 female human body FMA:67812 female TAO:0000303 Gonochoristic organism that can produce male gametes. AAO:0010033 BILA:0000027 CARO:0000027 FBbt:00007004 FMA:67811 HAO:0000027 TAO:0000242 TGMA:0001838 WBbt:0007850 XAO:0003006 ZFA:0000242 male human body uberon male UBERON:0003101 male organism Gonochoristic organism that can produce male gametes. CARO:0000027 male human body FMA:67811 male TAO:0000242 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 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. 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 consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. 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 XAO:0003046 ZFA:0000393 mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue uberon mesenchyma UBERON:0003104 mesenchyme Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. BTO:0001393 ZFIN:curator 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 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 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]. ZFA:0000863 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 roof of skull skull roof dermal bone cranium ZFA:0000863 roofing bones of the skull The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[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 1 and df VP3 3 AAO:0010365 EHDAA2:0000069 EHDAA:1080 EMAPA:16399 FMA:293029 TAO:0001598 VHOG:0000298 XAO:0000447 ZFA:0001606 3rd pharyngeal arch first gill arch gill arch 1 third pharyngeal arch third visceral arch visceral arch 3 uberon 3rd arch 3rd visceral arch branchial arch 1 first branchial arch UBERON:0003114 pharyngeal arch 3 The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. MP:0006339 The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] 2012-06-20 AAO:0010365 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:0000298 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) in XAO, called branchial arch 1 and df VP3 XAO first gill arch ZFA:0001606 gill arch 1 ZFA:0001606 3rd arch EHDAA2:0000069 3rd visceral arch VHOG:0000298 branchial arch 1 AAO:0010365 ZFA:0001606 first branchial arch ZFA:0001606 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 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) 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 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) 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 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 second pair of branchial arches in embryogenesis The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]. The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO] UBERON:0004372 AAO:0010418 EHDAA2:0000051 EMAPA:16203 EMAPA:16686 TAO:0005006 VHOG:0000148 XAO:0000343 ZFA:0005006 2nd arch artery AA2 aortic arch 2 hyoid aortic arch second aortic arch second branchial arch artery uberon 2nd aortic arch artery 2nd branchial arch artery 2nd pharyngeal arch artery UBERON:0003119 pharyngeal arch artery 2 The vessels formed within the second pair of branchial arches in embryogenesis MP:0010356 The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]. The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO] 2012-06-20 AAO:0010418 AAO ISBN:0-02-377110-0 2nd arch artery EHDAA2:0000051 AA2 ZFA:0005006 aortic arch 2 ZFA:0005006 hyoid aortic arch ZFA:0005006 second aortic arch XAO:0000343 2nd aortic arch artery EMAPA:16686 2nd branchial arch artery EMAPA:16686 2nd pharyngeal arch artery EMAPA:16686 The vessels formed within the third 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 third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]. The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches 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] UBERON:0004352 AAO:0010419 EHDAA2:0000070 EMAPA:16687 TAO:0005007 VHOG:0000147 XAO:0000344 ZFA:0005007 3rd arch artery AA3 aortic arch 3 carotid arch third aortic arch third branchial arch artery uberon 3rd aortic arch artery 3rd branchial arch artery 3rd pharyngeal arch artery UBERON:0003120 pharyngeal arch artery 3 The vessels formed within the third pair of branchial arches in embryogenesis MP:0006356 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:0005007 TAO ZFIN:curator The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]. The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches 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:0010419 AAO ISBN:0-02-377110-0 3rd arch artery EHDAA2:0000070 AA3 ZFA:0005007 aortic arch 3 ZFA:0005007 carotid arch third aortic arch XAO:0000344 3rd aortic arch artery EMAPA:16687 3rd branchial arch artery EMAPA:16687 3rd pharyngeal arch artery EMAPA:16687 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 TAO:0005008 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]. 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 TAO:0005016 VHOG:0000144 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]. the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries 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 the outermost extraembryonic membrane The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG] The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]. Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] chorionic The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN:0073040584] Extra-embryonic ectoderm BTO:0000252 CALOHA:TS-0144 EFO:0002780 EHDAA2:0000245 EHDAA:150 EMAPA:16112 EV:0100121 FMA:80224 GAID:1299 MESH:A16.254.403.473 NCIT:C34122 NCIT:C34124 UMLS:C0008503 UMLS:C1516505 VHOG:0000200 chorion (vertebrates) embryonic chorion fetal chorion uterine chorion uberon chorion frondosum chorionic sac UBERON:0003124 chorion ISBN:0073040584 the outermost extraembryonic membrane MESH:A10.615.284.473 MP:0002836 The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG] 2012-09-17 VHOG:0000200 VHOG The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]. BTO:0000252 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:0000200 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 Extra-embryonic ectoderm UMLS:C0008503 ncithesaurus:Chorion UMLS:C1516505 ncithesaurus:Chorionic_Sac uterine chorion ZFIN:curator chorion frondosum chorionic sac The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. An elongated tube which carries air to and from the lungs.[AAO] The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] tracheal In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx. in mouse 15-18 C-rings, 15-20 in human. AAO:0010140 BTO:0001388 CALOHA:TS-1060 EFO:0000935 EHDAA2:0002066 EHDAA:3078 EMAPA:16853 EV:0100040 FMA:7394 GAID:361 MA:0000441 MAT:0000137 MESH:D014132 MIAA:0000137 NCIT:C12428 OpenCyc:Mx4rvViOX5wpEbGdrcN5Y29ycA UMLS:C0040578 VHOG:0000371 XAO:0000118 cartilaginous trachea vertebrate trachea windpipe uberon tracheal tubule UBERON:0003126 trachea EHDAA2 The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. GO:0060438 An elongated tube which carries air to and from the lungs.[AAO] 2012-06-20 AAO:0010140 AAO AAO:BJB The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000371 VHOG In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] 2012-09-17 VHOG:0000371 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409 in mouse 15-18 C-rings, 15-20 in human. ISBN:0123813611 UMLS:C0040578 ncithesaurus:Trachea vertebrate trachea tracheal tubule BTO:0001388 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 MIAA:0000340 OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA VHOG:0000334 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). 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 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 OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA UMLS:C0037303 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]. 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 OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA 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 A male organ involved in reproduction MA:0000545 male organism reproductive organ male organism reproductive structure male organism reproductive system organ male organism sex organ male reproductive gland/organ male reproductive system organ male sex organ reproductive organ of male organism reproductive structure of male organism reproductive system organ of male organism sex organ of male organism uberon UBERON:0003135 male reproductive organ A male organ involved in reproduction UBERON:xp male organism reproductive organ OBOL:automatic male organism reproductive structure OBOL:automatic male organism reproductive system organ OBOL:automatic male organism sex organ OBOL:automatic male reproductive gland/organ MA:0000545 reproductive organ of male organism OBOL:automatic reproductive structure of male organism OBOL:automatic reproductive system organ of male organism OBOL:automatic sex organ of male organism OBOL:automatic Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBbt:00005159 FMA:77853 gustatory organ system organ gustatory system organ organ of gustatory organ system organ of gustatory system organ of taste system taste organ taste system organ uberon UBERON:0003212 gustatory organ Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBC:auto_generated_definition gustatory organ system organ OBOL:automatic gustatory system organ OBOL:automatic organ of gustatory organ system OBOL:automatic organ of gustatory system OBOL:automatic organ of taste system OBOL:automatic taste system organ 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 one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO] A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] EHDAA2:0004062 EHDAA:4041 EHDAA:5021 EHDAA:5915 EMAPA:17375 VHOG:0000540 metanephric blastema metanephric mesoderm metanephrogenic mesenchyme metanephros associated mesenchyme uberon UBERON:0003220 Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme ISBN:9780878932504 one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO] GO:0072075 A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] 2012-09-17 VHOG:0000540 VHOG When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] 2012-09-17 VHOG:0000540 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462 metanephric blastema metanephric mesoderm metanephrogenic mesenchyme EHDAA:5021 metanephros associated mesenchyme RETIRED_EHDAA2:0001139 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 An epithelium that is part of a otic placode [Automatically generated definition]. check ZFA, placemeant, appears to refer to both adult structures and primordium EHDAA2:0001341 EHDAA:510 EMAPA:16197 VHOG:0000636 ZFA:0007068 epithelial tissue of otic placode otic epithelium otic placode epithelial tissue otic placode epithelium uberon UBERON:0003249 epithelium of otic placode An epithelium that is part of a otic placode [Automatically generated definition]. OBOL:automatic epithelial tissue of otic placode OBOL:automatic otic epithelium otic placode epithelial tissue OBOL:automatic otic placode 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 An endoderm that is part of a thyroid primordium. UBERON:0005235 EHDAA:956 EMAPA:25357 RETIRED_EHDAA2:0002035 VHOG:0001089 endoderm of thyroid primordium uberon UBERON:0003261 thyroid primordium endoderm ZFA-propagated An endoderm that is part of a thyroid primordium. OBOL:automatic endoderm of thyroid primordium OBOL:automatic A mesenchyme that is part of a chorion. TODO - check UBERON:0003423 EHDAA2:0003245 EHDAA:154 EMAPA:16114 EMAPA:16266 RETIRED_EHDAA2:0000247 VHOG:0000620 chorion mesenchyme chorion mesoderm chorionic mesenchyme mesenchyme of chorion mesenchyme of chorion (vertebrates) uberon UBERON:0003265 chorionic mesenchyme EHDAA2 EHDAA2 ISBN:0073040584 A mesenchyme that is part of a chorion. OBOL:automatic chorion mesenchyme OBOL:automatic chorion mesoderm RETIRED_EHDAA2:0000247 chorionic mesenchyme EHDAA2:0003245 mesenchyme of chorion (vertebrates) 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 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. 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 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 lower jaw ZFA:0001273 mandible ZFA:0001273 lower jaw skeleton AAO:0000274 mandibles TAO:0001273 mandibular series ZFA:0001273 An endothelium that is part of a trachea. EHDAA:3082 RETIRED_EHDAA2:0002068 endothelium of windpipe trachea endothelium windpipe endothelium uberon UBERON:0003279 endothelium of trachea An endothelium that is part of a trachea. OBOL:automatic endothelium of windpipe OBOL:automatic trachea endothelium OBOL:automatic windpipe endothelium OBOL:automatic 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 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. 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 mesentery of ventriculus OBOL:automatic mesogaster mesogastium MA:0001617 mesogastrium 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 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 midgut mesentery OBOL:automatic A meninx that is part of a midbrain [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001174 EHDAA:3708 EMAPA:17791 MA:0001058 RETIRED_EHDAA2:0001109 VHOG:0000012 meninges of midbrain midbrain meninges midbrain meninx uberon mesencephalon meninges UBERON:0003288 meninx of midbrain A meninx that is part of a midbrain [Automatically generated definition]. OBOL:automatic Meninges that are part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000012 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000012 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 meninges of midbrain OBOL:automatic midbrain meninges OBOL:automatic midbrain meninx OBOL:automatic mesencephalon meninges VHOG:0000012 A meninx that is part of a telencephalon [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the telencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001990 EHDAA:5476 EMAPA:17774 MA:0000979 VHOG:0000010 meninges of telencephalon telencephalon meninges telencephalon meninx uberon UBERON:0003289 meninx of telencephalon A meninx that is part of a telencephalon [Automatically generated definition]. OBOL:automatic Meninges that are part of the telencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000010 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000010 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 meninges of telencephalon OBOL:automatic telencephalon meninges OBOL:automatic telencephalon meninx OBOL:automatic A meninx that is part of a diencephalon [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000399 EHDAA:5458 EMAPA:17764 MA:0000826 VHOG:0000009 between brain meninges between brain meninx diencephalon meninges diencephalon meninx interbrain meninges interbrain meninx mature diencephalon meninges mature diencephalon meninx meninges of between brain meninges of diencephalon meninges of interbrain meninges of mature diencephalon meninx of between brain meninx of interbrain meninx of mature diencephalon uberon UBERON:0003290 meninx of diencephalon A meninx that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Meninges that are part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000009 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000009 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 between brain meninges OBOL:automatic between brain meninx OBOL:automatic diencephalon meninges OBOL:automatic diencephalon meninx OBOL:automatic interbrain meninges OBOL:automatic interbrain meninx OBOL:automatic mature diencephalon meninges OBOL:automatic mature diencephalon meninx OBOL:automatic meninges of between brain OBOL:automatic meninges of diencephalon OBOL:automatic meninges of interbrain OBOL:automatic meninges of mature diencephalon OBOL:automatic meninx of between brain OBOL:automatic meninx of interbrain OBOL:automatic meninx of mature diencephalon OBOL:automatic A meninx that is part of a hindbrain [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000770 EHDAA:3688 EMAPA:17783 MA:0000987 VHOG:0000011 hindbrain meninges hindbrain meninx meninges of hindbrain uberon rhomencephalon meninges UBERON:0003291 meninx of hindbrain definitional A meninx that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Meninges that are part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000011 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000011 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 hindbrain meninges OBOL:automatic hindbrain meninx OBOL:automatic meninges of hindbrain OBOL:automatic rhomencephalon meninges VHOG:0000011 A meninx that is part of a spinal cord [Automatically generated definition]. Meninges that are part of the spinal cord. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] CALOHA:TS-2148 EHDAA2:0001895 EHDAA:2865 EMAPA:17804 MA:0001130 NCIT:C12350 UMLS:C0037938 VHOG:0000443 menines of spinal cord meninges of spinal cord spinal cord meninges spinal cord meninx spinal meninges spinal meninx uberon UBERON:0003292 meninx of spinal cord A meninx that is part of a spinal cord [Automatically generated definition]. OBOL:automatic Meninges that are part of the spinal cord. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000443 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000443 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C0037938 ncithesaurus:Spinal_Meninges menines of spinal cord meninges of spinal cord OBOL:automatic spinal cord meninges OBOL:automatic spinal cord meninx OBOL:automatic spinal meninges 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. pharynx gland EHDAA2:0001461 glandulae pharyngeae BTO:0004849 Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. EHDAA2:0000395 EHDAA:4475 EMAPA:16897 VHOG:0000653 diencephalon gland interbrain gland uberon UBERON:0003296 gland of diencephalon Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. diencephalon gland OBOL:automatic interbrain gland OBOL:automatic 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 integumental system gland integumentary gland 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 testis [Automatically generated definition]. EHDAA2:0002010 EHDAA:8150 EMAPA:35858 VHOG:0001442 testis mesenchyme uberon UBERON:0003312 mesenchyme of testis Mesenchyme that is part of a developing testis [Automatically generated definition]. OBOL:automatic testis mesenchyme 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 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 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 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 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 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 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 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 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 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 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 midgut epithelium 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 tongue [Automatically generated definition]. BTO:0000992 CALOHA:TS-1051 EHDAA2:0004598 EMAPA:17881 FMA:284658 MA:0001592 NCIT:C49300 UMLS:C1710436 epithelial tissue of tongue tongue epithelial tissue tongue epithelium uberon lingual epithelium UBERON:0003357 examples: tongue squamous epithelium, keratined, non-keratinized and parakeratinized epithelium, as well as gustatory epithelium. Note that not all these subtypes are named in individual anatomy ontologies. epithelium of tongue An epithelium that is part of a tongue [Automatically generated definition]. OBOL:automatic UMLS:C1710436 ncithesaurus:Tongue_Epithelium epithelial tissue of tongue OBOL:automatic tongue epithelial tissue OBOL:automatic tongue epithelium OBOL:automatic lingual epithelium BTO:0000992 An epithelium that is part of a submandibular gland [Automatically generated definition]. BTO:0004557 EMAPA:18813 VHOG:0000989 epithelial tissue of submandibular gland submandibular gland epithelial tissue submandibular gland epithelium uberon submandibular duct epithelium submandibular gland duct epithelium submaxillary gland epithelium UBERON:0003359 epithelium of submandibular gland An epithelium that is part of a submandibular gland [Automatically generated definition]. OBOL:automatic epithelial tissue of submandibular gland OBOL:automatic submandibular gland epithelial tissue OBOL:automatic submandibular gland epithelium OBOL:automatic submandibular duct epithelium BTO:0004557 submandibular gland duct epithelium BTO:0004557 submaxillary gland epithelium EMAPA:18813 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 bud ectoderm 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 bud ectoderm 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 extraembryonic structure that develops_from a ectoderm and is part of a chorion. BTO:0005145 EMAPA:16113 chorion ectoderm uberon chorion epithelium chorionic epithelium UBERON:0003374 chorionic ectoderm ISBN:0073040584 A extraembryonic structure that develops_from a ectoderm and is part of a chorion. OBOL:automatic chorion ectoderm OBOL:automatic chorionic epithelium BTO:0005145 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 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 portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]. UBERON:0004244 BTO:0001391 EMAPA:19192 FMA:262010 MA:0001863 NCIT:C49306 UMLS:C1710458 trachea smooth muscle tracheal smooth muscle uberon UBERON:0003387 smooth muscle of trachea A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]. OBOL:automatic UMLS:C1710458 ncithesaurus:Trachea_Smooth_Muscle_Tissue trachea smooth muscle MA:0001863 tracheal smooth muscle BTO:0001391 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 colon mesentery large bowel mesentery large intestinal mesentery mesentery of large bowel mesentery of large intestine 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 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 Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue. EMAPA:25097 lingual gland tongue gland uberon UBERON:0003409 gland of tongue Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue. lingual gland OBOL:automatic tongue 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 Mesenchyme that is part of a developing tongue [Automatically generated definition]. TODO - develops_from EHDAA2:0004614 EMAPA:17882 tongue mesenchyme uberon UBERON:0003416 mesenchyme of tongue Mesenchyme that is part of a developing tongue [Automatically generated definition]. OBOL:automatic tongue mesenchyme EHDAA2:0004614 Mesenchyme that is part of a developing submandibular gland [Automatically generated definition]. EMAPA:18814 VHOG:0001110 submandibular gland mesenchyme uberon submaxillary gland mesenchyme UBERON:0003418 mesenchyme of submandibular gland Mesenchyme that is part of a developing submandibular gland [Automatically generated definition]. OBOL:automatic submandibular gland mesenchyme OBOL:automatic submaxillary gland mesenchyme EMAPA:18814 A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP] TODO - check EMAPA:26127 EMAPA:35925 Wharton's jelly umbilical cord mesenchyme uberon UBERON:0003422 mesenchyme of umbilical cord A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP] Wharton's jelly EMAPA:26127 umbilical cord mesenchyme OBOL:automatic A lymph node that is located in a kidney [Automatically generated definition]. Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland FMA:276799 MA:0002882 NCIT:C77646 UMLS:C2699031 kidney lymph node lymph node of kidney uberon UBERON:0003425 renal lymph node A lymph node that is located in a kidney [Automatically generated definition]. OBOL:automatic Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland NCBITaxon:10090 UMLS:C2699031 ncithesaurus:Renal_Lymph_Node kidney lymph node OBOL:automatic lymph node of kidney 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 A nerve that is part of a chest [Automatically generated definition]. EMAPA:37266 MA:0000551 anterior thoracic region nerve anterolateral part of thorax nerve front of thorax nerve nerve of anterior thoracic region nerve of anterolateral part of thorax nerve of chest nerve of front of thorax uberon UBERON:0003432 chest nerve A nerve that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37266 MA:th anterior thoracic region nerve OBOL:automatic anterolateral part of thorax nerve OBOL:automatic front of thorax nerve OBOL:automatic nerve of anterior thoracic region OBOL:automatic nerve of anterolateral part of thorax OBOL:automatic nerve of chest OBOL:automatic nerve of front of thorax 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). 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 part of a limb [Automatically generated definition]. EMAPA:37291 MA:0000693 nerve of limb uberon UBERON:0003440 limb nerve A nerve that is part of a limb [Automatically generated definition]. OBOL:automatic EMAPA:37291 MA:th nerve of limb OBOL:automatic A nerve that is part of a forelimb [Automatically generated definition]. EMAPA:37334 MA:0000616 fore limb nerve nerve of fore limb nerve of forelimb nerve of superior member nerve of upper extremity wing nerve uberon UBERON:0003441 forelimb nerve A nerve that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37334 MA:th fore limb nerve OBOL:automatic nerve of fore limb OBOL:automatic nerve of forelimb OBOL:automatic nerve of superior member OBOL:automatic nerve of upper extremity OBOL:automatic wing nerve NCBITaxon:8782 OBOL:automatic A nerve that is part of a hindlimb [Automatically generated definition]. EMAPA:37342 MA:0000664 hind limb nerve nerve of hind limb nerve of hindlimb nerve of inferior member nerve of lower extremity uberon UBERON:0003442 hindlimb nerve A nerve that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37342 MA:th hind limb nerve OBOL:automatic nerve of hind limb OBOL:automatic nerve of hindlimb OBOL:automatic nerve of inferior member OBOL:automatic nerve of lower extremity OBOL:automatic 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 lymphatic vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:37580 MA:0001824 apparatus respiratorius lymph vessel apparatus respiratorius lymphatic vessel lymph vessel of apparatus respiratorius lymph vessel of respiratory system lymphatic vessel of apparatus respiratorius lymphatic vessel of respiratory system respiratory system lymph vessel uberon UBERON:0003456 respiratory system lymphatic vessel A lymphatic vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37580 MA:th apparatus respiratorius lymph vessel OBOL:automatic apparatus respiratorius lymphatic vessel OBOL:automatic lymph vessel of apparatus respiratorius OBOL:automatic lymph vessel of respiratory system OBOL:automatic lymphatic vessel of apparatus respiratorius OBOL:automatic lymphatic vessel of respiratory system OBOL:automatic respiratory system lymph vessel OBOL:automatic A bone that is part of a head [Automatically generated definition]. EMAPA:35996 MA:0000576 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 A bone that is part of a neck [Automatically generated definition]. EMAPA:37246 MA:0000584 OpenCyc:Mx4rvnpJSJwpEbGdrcN5Y29ycA 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 chest [Automatically generated definition]. EMAPA:18025 MA:0000547 anterior thoracic region bone anterior thoracic region bone organ anterolateral part of thorax bone anterolateral part of thorax bone organ bone of anterior thoracic region bone of anterolateral part of thorax bone of chest bone of front of thorax bone organ of anterior thoracic region bone organ of anterolateral part of thorax bone organ of chest bone organ of front of thorax chest bone organ front of thorax bone front of thorax bone organ uberon UBERON:0003459 chest bone A bone that is part of a chest [Automatically generated definition]. OBOL:automatic anterior thoracic region bone OBOL:automatic anterior thoracic region bone organ OBOL:automatic anterolateral part of thorax bone OBOL:automatic anterolateral part of thorax bone organ OBOL:automatic bone of anterior thoracic region OBOL:automatic bone of anterolateral part of thorax OBOL:automatic bone of chest OBOL:automatic bone of front of thorax OBOL:automatic bone organ of anterior thoracic region OBOL:automatic bone organ of anterolateral part of thorax OBOL:automatic bone organ of chest OBOL:automatic bone organ of front of thorax OBOL:automatic chest bone organ OBOL:automatic front of thorax bone OBOL:automatic front of thorax 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 NCIT:C63706 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 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 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 A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle) the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc EFO:0003842 GAID:198 NCIT:C12982 UMLS:C0448188 bone of hind limb bone of hindlimb bone of inferior member bone of lower extremity bone organ of hind limb bone organ of hindlimb bone organ of lower extremity hind limb bone hind limb bone organ hindlimb bone organ uberon UBERON:0003464 hindlimb bone A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle) the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc MA UMLS:C0448188 ncithesaurus:Bone_of_the_Lower_Extremity bone of hind limb OBOL:automatic bone of hindlimb OBOL:automatic bone of inferior member OBOL:automatic bone of lower extremity OBOL:automatic bone organ of hind limb OBOL:automatic bone organ of hindlimb OBOL:automatic bone organ of lower extremity OBOL:automatic hind limb bone OBOL:automatic hind limb bone organ OBOL:automatic hindlimb bone organ OBOL:automatic The ureteral branches of renal artery are small branches which supply the ureter. ureteric artery EMAPA:37676 FMA:70491 MA:0002074 uberon UBERON:0003468 ureteric segment of renal artery FMA FMA The ureteral branches of renal artery are small branches which supply the ureter. ureteric artery MA:0002074 EMAPA:37676 MA:th 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 Iinferior 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 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 Iinferior 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 MA:th arteria labialis inferior 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 An artery that supplies blood to the cerebellum. EHDAA2:0000228 EHDAA:5290 EMAPA:37074 MA:0001933 NCIT:C52845 UMLS:C0226246 uberon UBERON:0003472 cerebellar artery An artery that supplies blood to the cerebellum. EMAPA:37074 MA:th UMLS:C0226246 ncithesaurus:Cerebellar_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]. 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 One of the arteries supplying a meninix[Automatically generated definition]. EMAPA:37104 GAID:499 MA:0002001 MESH:D008576 uberon UBERON:0003474 meningeal artery One of the arteries supplying a meninix[Automatically generated definition]. EMAPA:37104 MA:th A vein that is part of a ureter [Automatically generated definition]. EMAPA:37679 MA:0002250 ureter vein vein of ureter uberon UBERON:0003475 ureteric vein A vein that is part of a ureter [Automatically generated definition]. OBOL:automatic EMAPA:37679 MA:th ureter vein OBOL:automatic vein of ureter OBOL:automatic 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 lower lip. EMAPA:37202 FMA:52541 MA:0002253 inferior labial vein lower lip vein vena labialis inferior uberon venae labiales inferiores UBERON:0003478 vein of lower lip The inferior labial vein is the vein receiving blood from the lower lip. EMAPA:37202 MA:th inferior labial vein FMA:52541 lower lip vein OBOL:automatic vena labialis inferior venae labiales inferiores 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 clitoris [Automatically generated definition]. EMAPA:37201 MA:0002252 clitoris vein uberon UBERON:0003480 vein of clitoris A vein that is part of a clitoris [Automatically generated definition]. OBOL:automatic EMAPA:37201 MA:th clitoris vein OBOL:automatic A vein that is part of a tail [Automatically generated definition]. see also caudal vein AAO:0011105 EMAPA:37761 MA:0002233 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 EMAPA:37761 MA:th post-vent region vein OBOL:automatic vein of post-vent region OBOL:automatic vein of tail OBOL:automatic caudal vein A portion of lymphoid tissue that is part of a thymus [Automatically generated definition]. EMAPA:37766 MA:0002673 MESH:A06.407.850 NCIT:C38515 UMLS:C1515429 lymphoid tissue of thymus lymphoid tissue of thymus gland thymus gland lymphoid tissue uberon UBERON:0003483 thymus lymphoid tissue A portion of lymphoid tissue that is part of a thymus [Automatically generated definition]. OBOL:automatic EMAPA:37766 MA:th UMLS:C1515429 ncithesaurus:Thymic_Lymphoid_Tissue lymphoid tissue of thymus OBOL:automatic lymphoid tissue of thymus gland OBOL:automatic thymus gland lymphoid tissue OBOL:automatic A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland. EMAPA:37531 MA:0002452 camera-type eye sebaceous gland sebaceous gland of camera-type eye sebaceous gland of vertebrate eye vertebrate eye sebaceous gland uberon UBERON:0003484 eye sebaceous gland MA A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland. EMAPA:37531 MA:th camera-type eye sebaceous gland OBOL:automatic sebaceous gland of camera-type eye OBOL:automatic sebaceous gland of vertebrate eye OBOL:automatic vertebrate eye sebaceous gland OBOL:automatic A sebaceous gland that is part of a vagina [Automatically generated definition]. EMAPA:37793 MA:0001732 sebaceous gland of vagina uberon UBERON:0003485 vagina sebaceous gland A sebaceous gland that is part of a vagina [Automatically generated definition]. OBOL:automatic EMAPA:37793 MA:th sebaceous gland of vagina OBOL:automatic A holocrine gland of the dermis that secretes sebum into hair follicles. MA:0000149 cutaneous sebaceous gland sebaceous gland of skin uberon UBERON:0003487 skin sebaceous gland A holocrine gland of the dermis that secretes sebum into hair follicles. MP:0009535 sebaceous gland of skin OBOL:automatic 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 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 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 adult head blood vessel blood vessel of adult head blood vessel of head uberon UBERON:0003496 head blood vessel true 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]. 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 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 a trachea. UBERON:0003525 EMAPA:35874 MA:0001852 blood vessel of trachea uberon UBERON:0003505 trachea blood vessel A blood vessel that is part of a trachea. OBOL:automatic blood vessel of trachea OBOL:automatic A blood vessel that is part of a chest [Automatically generated definition]. EMAPA:37239 MA:0000549 anterior thoracic region blood vessel anterolateral part of thorax blood vessel blood vessel of anterior thoracic region blood vessel of anterolateral part of thorax blood vessel of chest blood vessel of front of thorax front of thorax blood vessel uberon UBERON:0003506 chest blood vessel A blood vessel that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37239 MA:th anterior thoracic region blood vessel OBOL:automatic anterolateral part of thorax blood vessel OBOL:automatic blood vessel of anterior thoracic region OBOL:automatic blood vessel of anterolateral part of thorax OBOL:automatic blood vessel of chest OBOL:automatic blood vessel of front of thorax OBOL:automatic front of thorax blood vessel 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. 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 limb [Automatically generated definition]. EMAPA:36598 MA:0000687 blood vessel of limb uberon UBERON:0003514 limb blood vessel A blood vessel that is part of a limb [Automatically generated definition]. OBOL:automatic blood vessel of limb OBOL:automatic A blood vessel that is part of a forelimb [Automatically generated definition]. EMAPA:37292 MA:0000611 anteriormost limb blood vessel blood vessel of anteriormost limb blood vessel of fore limb blood vessel of forelimb blood vessel of upper extremity fore limb blood vessel wing blood vessel uberon UBERON:0003515 forelimb blood vessel A blood vessel that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37292 MA:th anteriormost limb blood vessel OBOL:automatic blood vessel of anteriormost limb OBOL:automatic blood vessel of fore limb OBOL:automatic blood vessel of forelimb OBOL:automatic blood vessel of upper extremity OBOL:automatic fore limb blood vessel OBOL:automatic wing blood vessel NCBITaxon:8782 OBOL:automatic A blood vessel that is part of a hindlimb [Automatically generated definition]. EMAPA:37298 MA:0000659 blood vessel of hind limb blood vessel of hindlimb blood vessel of lower extremity hind limb blood vessel uberon UBERON:0003516 hindlimb blood vessel A blood vessel that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37298 MA:th blood vessel of hind limb OBOL:automatic blood vessel of hindlimb OBOL:automatic blood vessel of lower extremity OBOL:automatic hind limb blood vessel OBOL:automatic A blood vessel that is part of a kidney [Automatically generated definition]. EMAPA:28457 MA:0001682 TAO:0005306 ZFA:0005306 blood vessel of kidney renal blood vessel uberon UBERON:0003517 kidney blood vessel A blood vessel that is part of a kidney [Automatically generated definition]. OBOL:automatic blood vessel of kidney OBOL:automatic renal 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 capillary that is part of a kidney [Automatically generated definition]. EMAPA:31443 MA:0002586 blood capillary of kidney capillary of kidney capillary vessel of kidney kidney blood capillary kidney capillary vessel renal capillary uberon UBERON:0003527 kidney capillary A capillary that is part of a kidney [Automatically generated definition]. OBOL:automatic blood capillary of kidney OBOL:automatic capillary of kidney OBOL:automatic capillary vessel of kidney OBOL:automatic kidney blood capillary OBOL:automatic kidney capillary vessel OBOL:automatic renal capillary 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 An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition]. EMAPA:37581 MA:0001825 apparatus respiratorius endothelium of lymph vessel apparatus respiratorius lymph vessel endothelium apparatus respiratorius lymphatic vessel endothelium endothelium of lymph vessel of apparatus respiratorius endothelium of lymph vessel of respiratory system lymph vessel endothelium of apparatus respiratorius lymph vessel endothelium of respiratory system lymphatic vessel endothelium of apparatus respiratorius lymphatic vessel endothelium of respiratory system respiratory system endothelium of lymph vessel respiratory system lymph vessel endothelium respiratory system lymphatic vessel endothelium uberon UBERON:0003529 respiratory system lymphatic vessel endothelium An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37581 MA:th apparatus respiratorius endothelium of lymph vessel OBOL:automatic apparatus respiratorius lymph vessel endothelium OBOL:automatic apparatus respiratorius lymphatic vessel endothelium OBOL:automatic endothelium of lymph vessel of apparatus respiratorius OBOL:automatic endothelium of lymph vessel of respiratory system OBOL:automatic lymph vessel endothelium of apparatus respiratorius OBOL:automatic lymph vessel endothelium of respiratory system OBOL:automatic lymphatic vessel endothelium of apparatus respiratorius OBOL:automatic lymphatic vessel endothelium of respiratory system OBOL:automatic respiratory system endothelium of lymph vessel OBOL:automatic respiratory system lymph vessel endothelium OBOL:automatic respiratory system lymphatic vessel endothelium OBOL:automatic A zone of skin that is part of a forelimb [Automatically generated definition]. TODO - check free limb vs pectoral complex EMAPA:32612 FMA:23101 MA:0000617 NCIT:C12296 UMLS:C0222212 anteriormost limb skin fore limb skin skin of fore limb skin of forelimb skin of upper limb upper limb skin wing skin uberon UBERON:0003531 forelimb skin A zone of skin that is part of a forelimb [Automatically generated definition]. OBOL:automatic UMLS:C0222212 ncithesaurus:Skin_of_the_Upper_Limb_and_Shoulder anteriormost limb skin OBOL:automatic fore limb skin OBOL:automatic skin of fore limb OBOL:automatic skin of forelimb OBOL:automatic skin of upper limb FMA:23101 upper limb skin FMA:23101 wing skin NCBITaxon:8782 OBOL:automatic A zone of skin that is part of a hindlimb [Automatically generated definition]. TODO - check free limb vs pelvic complex EMAPA:32620 FMA:23102 MA:0000665 NCIT:C12297 UMLS:C0222268 hind limb skin lower limb skin skin of hind limb skin of hindlimb skin of lower extremity skin of lower limb uberon UBERON:0003532 hindlimb skin A zone of skin that is part of a hindlimb [Automatically generated definition]. OBOL:automatic UMLS:C0222268 ncithesaurus:Skin_of_the_Lower_Limb_and_Hip hind limb skin OBOL:automatic lower limb skin FMA:23102 skin of hind limb OBOL:automatic skin of hindlimb OBOL:automatic skin of lower extremity OBOL:automatic skin of lower limb FMA:23102 A zone of skin that is part of a tail [Automatically generated definition]. EMAPA:36502 MA:0000700 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 bronchiole that is part of a right lung [Automatically generated definition]. EMAPA:35425 MA:0001787 NCIT:C49279 UMLS:C0225670 bronchiole of right lung lobular bronchiole of right lung right lung lobular bronchiole uberon UBERON:0003538 right lung bronchiole A bronchiole that is part of a right lung [Automatically generated definition]. OBOL:automatic UMLS:C0225670 ncithesaurus:Right_Lung_Bronchiole bronchiole of right lung OBOL:automatic lobular bronchiole of right lung OBOL:automatic right lung lobular bronchiole OBOL:automatic A bronchiole that is part of a left lung [Automatically generated definition]. EMAPA:19000 MA:0001778 NCIT:C49252 UMLS:C0225674 bronchiole of left lung left lung lobular bronchiole lobular bronchiole of left lung uberon UBERON:0003539 left lung bronchiole A bronchiole that is part of a left lung [Automatically generated definition]. OBOL:automatic UMLS:C0225674 ncithesaurus:Left_Lung_Bronchiole bronchiole of left lung OBOL:automatic left lung lobular bronchiole OBOL:automatic lobular bronchiole of left lung OBOL:automatic A terminal bronchiole that is part of a right lung [Automatically generated definition]. EMAPA:36638 MA:0001789 NCIT:C49294 UMLS:C1709961 bronchiolus terminalis of right lung right lung bronchiolus terminalis terminal bronchiole of right lung uberon UBERON:0003540 right lung terminal bronchiole A terminal bronchiole that is part of a right lung [Automatically generated definition]. OBOL:automatic UMLS:C1709961 ncithesaurus:Right_Lung_Terminal_Bronchiole bronchiolus terminalis of right lung OBOL:automatic right lung bronchiolus terminalis OBOL:automatic terminal bronchiole of right lung OBOL:automatic A terminal bronchiole that is part of a left lung [Automatically generated definition]. EMAPA:36636 MA:0001780 NCIT:C49255 UMLS:C1708675 bronchiolus terminalis of left lung left lung bronchiolus terminalis terminal bronchiole of left lung uberon UBERON:0003541 left lung terminal bronchiole A terminal bronchiole that is part of a left lung [Automatically generated definition]. OBOL:automatic UMLS:C1708675 ncithesaurus:Left_Lung_Terminal_Bronchiole bronchiolus terminalis of left lung OBOL:automatic left lung bronchiolus terminalis OBOL:automatic terminal bronchiole of left lung OBOL:automatic A meninx that is part of a brain [Automatically generated definition]. Meninges that are part of the brain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] CALOHA:TS-2147 EMAPA:32662 EV:0100312 MA:0000813 VHOG:0000013 brain meninges meninges of brain meninx of brain uberon UBERON:0003547 brain meninx A meninx that is part of a brain [Automatically generated definition]. OBOL:automatic Meninges that are part of the brain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000013 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000013 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 brain meninges OBOL:automatic meninges of brain OBOL:automatic meninx of brain OBOL:automatic A meninx that is part of a forebrain [Automatically generated definition]. EMAPA:17764 EMAPA:17774 EMAPA:37543 MA:0000883 forebrain meninx meninges of forebrain meninx of forebrain uberon UBERON:0003548 forebrain meninges A meninx that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37543 MA:th forebrain meninx OBOL:automatic meninges of forebrain OBOL:automatic meninx of forebrain OBOL:automatic The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule. The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32667 EV:0100315 MA:0000816 NCIT:C49335 UMLS:C1706994 VHOG:0000470 brain pia mater of neuraxis pia mater of brain pia mater of neuraxis of brain uberon UBERON:0003549 brain pia mater The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule. MP:0009026 The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000470 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000470 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C1706994 ncithesaurus:Brain_Pia_Mater brain pia mater of neuraxis OBOL:automatic pia mater of brain OBOL:automatic pia mater of neuraxis of brain OBOL:automatic A pia mater that is part of a forebrain [Automatically generated definition]. EMAPA:17767 EMAPA:17777 EMAPA:37546 MA:0000886 forebrain pia mater of neuraxis pia mater of forebrain pia mater of neuraxis of forebrain uberon UBERON:0003550 forebrain pia mater A pia mater that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37546 MA:th forebrain pia mater of neuraxis OBOL:automatic pia mater of forebrain OBOL:automatic pia mater of neuraxis of forebrain OBOL:automatic A pia mater that is part of a midbrain [Automatically generated definition]. Pia mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001175 EMAPA:17794 MA:0001061 RETIRED_EHDAA2:0001110 VHOG:0000467 midbrain pia mater of neuraxis pia mater of midbrain pia mater of neuraxis of midbrain uberon mesencephalon pia mater UBERON:0003551 midbrain pia mater A pia mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Pia mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000467 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000467 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 midbrain pia mater of neuraxis OBOL:automatic pia mater of midbrain OBOL:automatic pia mater of neuraxis of midbrain OBOL:automatic mesencephalon pia mater VHOG:0000467 A pia mater that is part of a telencephalon [Automatically generated definition]. Pia mater that is part of the telencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001992 EMAPA:17777 MA:0000982 VHOG:0000476 pia mater of neuraxis of telencephalon pia mater of telencephalon telencephalon pia mater of neuraxis uberon UBERON:0003552 telencephalon pia mater A pia mater that is part of a telencephalon [Automatically generated definition]. OBOL:automatic Pia mater that is part of the telencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000476 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000476 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 pia mater of neuraxis of telencephalon OBOL:automatic pia mater of telencephalon OBOL:automatic telencephalon pia mater of neuraxis OBOL:automatic A pia mater that is part of a diencephalon [Automatically generated definition]. Pia mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000400 EMAPA:17767 MA:0000829 VHOG:0000475 between brain pia mater between brain pia mater of neuraxis diencephalon pia mater of neuraxis interbrain pia mater interbrain pia mater of neuraxis mature diencephalon pia mater mature diencephalon pia mater of neuraxis pia mater of between brain pia mater of diencephalon pia mater of interbrain pia mater of mature diencephalon pia mater of neuraxis of between brain pia mater of neuraxis of diencephalon pia mater of neuraxis of interbrain pia mater of neuraxis of mature diencephalon uberon UBERON:0003553 diencephalon pia mater A pia mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Pia mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000475 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000475 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 between brain pia mater OBOL:automatic between brain pia mater of neuraxis OBOL:automatic diencephalon pia mater of neuraxis OBOL:automatic interbrain pia mater OBOL:automatic interbrain pia mater of neuraxis OBOL:automatic mature diencephalon pia mater OBOL:automatic mature diencephalon pia mater of neuraxis OBOL:automatic pia mater of between brain OBOL:automatic pia mater of diencephalon OBOL:automatic pia mater of interbrain OBOL:automatic pia mater of mature diencephalon OBOL:automatic pia mater of neuraxis of between brain OBOL:automatic pia mater of neuraxis of diencephalon OBOL:automatic pia mater of neuraxis of interbrain OBOL:automatic pia mater of neuraxis of mature diencephalon OBOL:automatic A pia mater that is part of a hindbrain [Automatically generated definition]. Pia mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000772 EMAPA:17786 MA:0000990 VHOG:0000466 hindbrain pia mater of neuraxis pia mater of hindbrain pia mater of neuraxis of hindbrain uberon rhombencephalon pia mater UBERON:0003554 hindbrain pia mater A pia mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Pia mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000466 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000466 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 hindbrain pia mater of neuraxis OBOL:automatic pia mater of hindbrain OBOL:automatic pia mater of neuraxis of hindbrain OBOL:automatic rhombencephalon pia mater VHOG:0000466 A pia mater that is part of a spinal cord [Automatically generated definition]. The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001896 EMAPA:17807 MA:0001133 NCIT:C49800 UMLS:C1710148 VHOG:0000468 pia mater of neuraxis of spinal cord pia mater of spinal cord spinal cord pia mater of neuraxis uberon UBERON:0003555 spinal cord pia mater A pia mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000468 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000468 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C1710148 ncithesaurus:Spinal_Cord_Pia_Mater pia mater of neuraxis of spinal cord OBOL:automatic pia mater of spinal cord OBOL:automatic spinal cord pia mater of neuraxis OBOL:automatic An arachnoid mater that is part of a forebrain [Automatically generated definition]. EMAPA:17765 EMAPA:17775 EMAPA:37544 MA:0000884 arachnoid mater of forebrain arachnoid mater of neuraxis of forebrain arachnoid of forebrain forebrain arachnoid forebrain arachnoid mater of neuraxis uberon UBERON:0003556 forebrain arachnoid mater An arachnoid mater that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37544 MA:th arachnoid mater of forebrain OBOL:automatic arachnoid mater of neuraxis of forebrain OBOL:automatic arachnoid of forebrain OBOL:automatic forebrain arachnoid OBOL:automatic forebrain arachnoid mater of neuraxis OBOL:automatic An arachnoid mater that is part of a midbrain [Automatically generated definition]. Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17792 MA:0001059 VHOG:0000233 arachnoid mater of midbrain arachnoid mater of neuraxis of midbrain arachnoid of midbrain midbrain arachnoid midbrain arachnoid mater of neuraxis uberon mesencephalon arachnoid mater UBERON:0003557 midbrain arachnoid mater An arachnoid mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000233 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000233 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoid mater of midbrain OBOL:automatic arachnoid mater of neuraxis of midbrain OBOL:automatic arachnoid of midbrain OBOL:automatic midbrain arachnoid OBOL:automatic midbrain arachnoid mater of neuraxis OBOL:automatic mesencephalon arachnoid mater VHOG:0000233 An arachnoid mater that is part of a diencephalon [Automatically generated definition]. Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17765 MA:0000827 VHOG:0000231 arachnoid mater of between brain arachnoid mater of diencephalon arachnoid mater of interbrain arachnoid mater of mature diencephalon arachnoid mater of neuraxis of between brain arachnoid mater of neuraxis of diencephalon arachnoid mater of neuraxis of interbrain arachnoid mater of neuraxis of mature diencephalon arachnoid of between brain arachnoid of diencephalon arachnoid of interbrain arachnoid of mature diencephalon between brain arachnoid between brain arachnoid mater between brain arachnoid mater of neuraxis diencephalon arachnoid diencephalon arachnoid mater of neuraxis interbrain arachnoid interbrain arachnoid mater interbrain arachnoid mater of neuraxis mature diencephalon arachnoid mature diencephalon arachnoid mater mature diencephalon arachnoid mater of neuraxis uberon UBERON:0003558 diencephalon arachnoid mater An arachnoid mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000231 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000231 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoid mater of between brain OBOL:automatic arachnoid mater of diencephalon OBOL:automatic arachnoid mater of interbrain OBOL:automatic arachnoid mater of mature diencephalon OBOL:automatic arachnoid mater of neuraxis of between brain OBOL:automatic arachnoid mater of neuraxis of diencephalon OBOL:automatic arachnoid mater of neuraxis of interbrain OBOL:automatic arachnoid mater of neuraxis of mature diencephalon OBOL:automatic arachnoid of between brain OBOL:automatic arachnoid of diencephalon OBOL:automatic arachnoid of interbrain OBOL:automatic arachnoid of mature diencephalon OBOL:automatic between brain arachnoid OBOL:automatic between brain arachnoid mater OBOL:automatic between brain arachnoid mater of neuraxis OBOL:automatic diencephalon arachnoid OBOL:automatic diencephalon arachnoid mater of neuraxis OBOL:automatic interbrain arachnoid OBOL:automatic interbrain arachnoid mater OBOL:automatic interbrain arachnoid mater of neuraxis OBOL:automatic mature diencephalon arachnoid OBOL:automatic mature diencephalon arachnoid mater OBOL:automatic mature diencephalon arachnoid mater of neuraxis OBOL:automatic An arachnoid mater that is part of a hindbrain [Automatically generated definition]. Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17784 MA:0000988 VHOG:0000236 arachnoid mater of hindbrain arachnoid mater of neuraxis of hindbrain arachnoid of hindbrain hindbrain arachnoid hindbrain arachnoid mater of neuraxis uberon rhombencephalon arachnoid mater UBERON:0003559 hindbrain arachnoid mater An arachnoid mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000236 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000236 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoid mater of hindbrain OBOL:automatic arachnoid mater of neuraxis of hindbrain OBOL:automatic arachnoid of hindbrain OBOL:automatic hindbrain arachnoid OBOL:automatic hindbrain arachnoid mater of neuraxis OBOL:automatic rhombencephalon arachnoid mater VHOG:0000236 An arachnoid mater that is part of a spinal cord [Automatically generated definition]. The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17805 MA:0001131 VHOG:0000234 arachnoid mater of neuraxis of spinal cord arachnoid mater of spinal cord arachnoid of spinal cord spinal cord arachnoid spinal cord arachnoid mater of neuraxis uberon UBERON:0003560 spinal cord arachnoid mater An arachnoid mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000234 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000234 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoid mater of neuraxis of spinal cord OBOL:automatic arachnoid mater of spinal cord OBOL:automatic arachnoid of spinal cord OBOL:automatic spinal cord arachnoid OBOL:automatic spinal cord arachnoid mater of neuraxis OBOL:automatic A dura mater that is part of a forebrain. EMAPA:17766 EMAPA:37545 MA:0000885 dura mater of forebrain dura mater of neuraxis of forebrain forebrain dura mater of neuraxis uberon UBERON:0003561 forebrain dura mater A dura mater that is part of a forebrain. OBOL:automatic EMAPA:37545 MA:th dura mater of forebrain OBOL:automatic dura mater of neuraxis of forebrain OBOL:automatic forebrain dura mater of neuraxis OBOL:automatic A dura mater that is part of a midbrain [Automatically generated definition]. Dura mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17793 MA:0001060 VHOG:0000410 dura mater of midbrain dura mater of neuraxis of midbrain midbrain dura mater of neuraxis uberon mesencephalon dura mater UBERON:0003562 midbrain dura mater A dura mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Dura mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000410 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000410 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 dura mater of midbrain OBOL:automatic dura mater of neuraxis of midbrain OBOL:automatic midbrain dura mater of neuraxis OBOL:automatic mesencephalon dura mater VHOG:0000410 A dura mater that is part of a telencephalon [Automatically generated definition]. EMAPA:17776 MA:0000981 dura mater of neuraxis of telencephalon dura mater of telencephalon telencephalon dura mater of neuraxis uberon UBERON:0003563 telencephalon dura mater A dura mater that is part of a telencephalon [Automatically generated definition]. OBOL:automatic dura mater of neuraxis of telencephalon OBOL:automatic dura mater of telencephalon OBOL:automatic telencephalon dura mater of neuraxis OBOL:automatic A dura mater that is part of a diencephalon [Automatically generated definition]. Dura mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17766 MA:0000828 VHOG:0000258 between brain dura mater between brain dura mater of neuraxis diencephalon dura mater of neuraxis dura mater of between brain dura mater of diencephalon dura mater of interbrain dura mater of mature diencephalon dura mater of neuraxis of between brain dura mater of neuraxis of diencephalon dura mater of neuraxis of interbrain dura mater of neuraxis of mature diencephalon interbrain dura mater interbrain dura mater of neuraxis mature diencephalon dura mater mature diencephalon dura mater of neuraxis uberon UBERON:0003564 diencephalon dura mater A dura mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Dura mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000258 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000258 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 between brain dura mater OBOL:automatic between brain dura mater of neuraxis OBOL:automatic diencephalon dura mater of neuraxis OBOL:automatic dura mater of between brain OBOL:automatic dura mater of diencephalon OBOL:automatic dura mater of interbrain OBOL:automatic dura mater of mature diencephalon OBOL:automatic dura mater of neuraxis of between brain OBOL:automatic dura mater of neuraxis of diencephalon OBOL:automatic dura mater of neuraxis of interbrain OBOL:automatic dura mater of neuraxis of mature diencephalon OBOL:automatic interbrain dura mater OBOL:automatic interbrain dura mater of neuraxis OBOL:automatic mature diencephalon dura mater OBOL:automatic mature diencephalon dura mater of neuraxis OBOL:automatic A dura mater that is part of a hindbrain [Automatically generated definition]. Dura mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17785 MA:0000989 VHOG:0000409 dura mater of hindbrain dura mater of neuraxis of hindbrain hindbrain dura mater of neuraxis uberon rhombencephalon dura mater UBERON:0003565 hindbrain dura mater A dura mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Dura mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000409 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000409 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 dura mater of hindbrain OBOL:automatic dura mater of neuraxis of hindbrain OBOL:automatic hindbrain dura mater of neuraxis OBOL:automatic rhombencephalon dura mater VHOG:0000409 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 trachea. EMAPA:35876 MA:0001853 connective tissue of trachea connective tissue of windpipe uberon UBERON:0003571 trachea connective tissue A portion of connective tissue that is part of a trachea. OBOL:automatic connective tissue of trachea OBOL:automatic connective tissue of windpipe OBOL:automatic A portion of connective tissue that is part of a chest [Automatically generated definition]. EMAPA:37254 MA:0000550 anterior thoracic region connective tissue anterior thoracic region portion of connective tissue anterior thoracic region textus connectivus anterolateral part of thorax connective tissue anterolateral part of thorax portion of connective tissue anterolateral part of thorax textus connectivus chest portion of connective tissue chest textus connectivus connective tissue of anterior thoracic region connective tissue of anterolateral part of thorax connective tissue of chest connective tissue of front of thorax front of thorax connective tissue front of thorax portion of connective tissue front of thorax textus connectivus portion of connective tissue of anterior thoracic region portion of connective tissue of anterolateral part of thorax portion of connective tissue of chest portion of connective tissue of front of thorax textus connectivus of anterior thoracic region textus connectivus of anterolateral part of thorax textus connectivus of chest textus connectivus of front of thorax uberon UBERON:0003572 chest connective tissue A portion of connective tissue that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37254 MA:th anterior thoracic region connective tissue OBOL:automatic anterior thoracic region portion of connective tissue OBOL:automatic anterior thoracic region textus connectivus OBOL:automatic anterolateral part of thorax connective tissue OBOL:automatic anterolateral part of thorax portion of connective tissue OBOL:automatic anterolateral part of thorax textus connectivus OBOL:automatic chest portion of connective tissue OBOL:automatic chest textus connectivus OBOL:automatic connective tissue of anterior thoracic region OBOL:automatic connective tissue of anterolateral part of thorax OBOL:automatic connective tissue of chest OBOL:automatic connective tissue of front of thorax OBOL:automatic front of thorax connective tissue OBOL:automatic front of thorax portion of connective tissue OBOL:automatic front of thorax textus connectivus OBOL:automatic portion of connective tissue of anterior thoracic region OBOL:automatic portion of connective tissue of anterolateral part of thorax OBOL:automatic portion of connective tissue of chest OBOL:automatic portion of connective tissue of front of thorax OBOL:automatic textus connectivus of anterior thoracic region OBOL:automatic textus connectivus of anterolateral part of thorax OBOL:automatic textus connectivus of chest OBOL:automatic textus connectivus of front of thorax 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 nasopharynx [Automatically generated definition]. EMAPA:37682 MA:0001864 connective tissue of nasal part of pharynx connective tissue of nasopharynx connective tissue of rhinopharynx nasal part of pharynx connective tissue nasal part of pharynx portion of connective tissue nasal part of pharynx textus connectivus nasopharynx portion of connective tissue nasopharynx textus connectivus portion of connective tissue of nasal part of pharynx portion of connective tissue of nasopharynx portion of connective tissue of rhinopharynx rhinopharynx connective tissue rhinopharynx portion of connective tissue rhinopharynx textus connectivus textus connectivus of nasal part of pharynx textus connectivus of nasopharynx textus connectivus of rhinopharynx uberon UBERON:0003582 nasopharynx connective tissue A portion of connective tissue that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic EMAPA:37682 MA:th connective tissue of nasal part of pharynx OBOL:automatic connective tissue of nasopharynx OBOL:automatic connective tissue of rhinopharynx OBOL:automatic nasal part of pharynx connective tissue OBOL:automatic nasal part of pharynx portion of connective tissue OBOL:automatic nasal part of pharynx textus connectivus OBOL:automatic nasopharynx portion of connective tissue OBOL:automatic nasopharynx textus connectivus OBOL:automatic portion of connective tissue of nasal part of pharynx OBOL:automatic portion of connective tissue of nasopharynx OBOL:automatic portion of connective tissue of rhinopharynx OBOL:automatic rhinopharynx connective tissue OBOL:automatic rhinopharynx portion of connective tissue OBOL:automatic rhinopharynx textus connectivus OBOL:automatic textus connectivus of nasal part of pharynx OBOL:automatic textus connectivus of nasopharynx OBOL:automatic textus connectivus of rhinopharynx OBOL:automatic A portion of connective tissue that is part of a larynx [Automatically generated definition]. EMAPA:35471 MA:0001754 NCIT:C49245 UMLS:C1708651 connective tissue of larynx larynx portion of connective tissue larynx textus connectivus portion of connective tissue of larynx textus connectivus of larynx uberon laryngeal connective tissue UBERON:0003583 larynx connective tissue A portion of connective tissue that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C1708651 ncithesaurus:Laryngeal_Connective_Tissue connective tissue of larynx OBOL:automatic larynx portion of connective tissue OBOL:automatic larynx textus connectivus OBOL:automatic portion of connective tissue of larynx OBOL:automatic textus connectivus of larynx OBOL:automatic laryngeal connective tissue EMAPA:35471 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 limb [Automatically generated definition]. EMAPA:37313 MA:0000689 connective tissue of limb limb portion of connective tissue limb textus connectivus portion of connective tissue of limb textus connectivus of limb uberon UBERON:0003587 limb connective tissue A portion of connective tissue that is part of a limb [Automatically generated definition]. OBOL:automatic EMAPA:37313 MA:th connective tissue of limb OBOL:automatic limb portion of connective tissue OBOL:automatic limb textus connectivus OBOL:automatic portion of connective tissue of limb OBOL:automatic textus connectivus of limb OBOL:automatic A portion of connective tissue that is part of a forelimb [Automatically generated definition]. EMAPA:37314 MA:0000613 connective tissue of anteriormost limb connective tissue of fore limb connective tissue of forelimb connective tissue of superior member connective tissue of upper extremity wing connective tissue uberon UBERON:0003588 forelimb connective tissue A portion of connective tissue that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37314 MA:th connective tissue of anteriormost limb OBOL:automatic connective tissue of fore limb OBOL:automatic connective tissue of forelimb OBOL:automatic connective tissue of superior member OBOL:automatic connective tissue of upper extremity OBOL:automatic wing connective tissue NCBITaxon:8782 OBOL:automatic A portion of connective tissue that is part of a hindlimb [Automatically generated definition]. EMAPA:37322 MA:0000661 connective tissue of hind limb connective tissue of hindlimb connective tissue of inferior member connective tissue of lower extremity hind limb connective tissue uberon UBERON:0003589 hindlimb connective tissue A portion of connective tissue that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37322 MA:th connective tissue of hind limb OBOL:automatic connective tissue of hindlimb OBOL:automatic connective tissue of inferior member OBOL:automatic connective tissue of lower extremity OBOL:automatic hind limb connective tissue OBOL:automatic A portion of connective tissue that is part of a bronchus [Automatically generated definition]. EMAPA:32690 EMAPA:35193 MA:0001831 NCIT:C49210 UMLS:C1707052 bronchi connective tissue bronchi portion of connective tissue bronchi textus connectivus bronchial trunk connective tissue bronchial trunk portion of connective tissue bronchial trunk textus connectivus bronchus portion of connective tissue bronchus textus connectivus connective tissue of bronchi connective tissue of bronchial trunk connective tissue of bronchus portion of connective tissue of bronchi portion of connective tissue of bronchial trunk portion of connective tissue of bronchus textus connectivus of bronchi textus connectivus of bronchial trunk textus connectivus of bronchus uberon bronchial connective tissue bronchial mesenchyme UBERON:0003592 bronchus connective tissue A portion of connective tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707052 ncithesaurus:Bronchus_Connective_Tissue bronchi connective tissue OBOL:automatic bronchi portion of connective tissue OBOL:automatic bronchi textus connectivus OBOL:automatic bronchial trunk connective tissue OBOL:automatic bronchial trunk portion of connective tissue OBOL:automatic bronchial trunk textus connectivus OBOL:automatic bronchus portion of connective tissue OBOL:automatic bronchus textus connectivus OBOL:automatic connective tissue of bronchi OBOL:automatic connective tissue of bronchial trunk OBOL:automatic connective tissue of bronchus OBOL:automatic portion of connective tissue of bronchi OBOL:automatic portion of connective tissue of bronchial trunk OBOL:automatic portion of connective tissue of bronchus OBOL:automatic textus connectivus of bronchi OBOL:automatic textus connectivus of bronchial trunk OBOL:automatic textus connectivus of bronchus OBOL:automatic bronchial connective tissue EMAPA:35193 bronchial mesenchyme EMAPA:32690 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 the ring-shaped cartilaginous structures that support the trachea check whether to classify as part of splanchoncranium in mammals the rings are incomplete, in avians the rings are complete. EMAPA:18699 EMAPA:35875 FMA:7434 MA:0001857 NCIT:C49304 UMLS:C1710456 cartilage of trachea cartilage of windpipe cartilaginous ring of trachea cartilaginous trachea cartilage cartilago trachealis tracheal cartilage windpipe cartilage uberon cartilage of the trachea cartilagines tracheales ring of the trachea trachea ring tracheal ring UBERON:0003604 trachea cartilage the ring-shaped cartilaginous structures that support the trachea J:97123 MGI:smb MP:0003120 UMLS:C1710456 ncithesaurus:Trachea_Cartilage cartilage of trachea OBOL:automatic cartilage of windpipe OBOL:automatic cartilaginous ring of trachea EMAPA:18699 cartilaginous trachea cartilage OBOL:automatic cartilago trachealis FMA:7434 tracheal cartilage FMA:7434 windpipe cartilage OBOL:automatic cartilage of the trachea cartilagines tracheales ring of the trachea tracheal ring 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. 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 vascular elastic laminae 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 An elastic tissue that is part of a bronchus [Automatically generated definition]. MA:0001838 NCIT:C49211 UMLS:C1707053 bronchi elastic connective tissue bronchi elastic tissue bronchi textus connectivus elasticus bronchial trunk elastic connective tissue bronchial trunk elastic tissue bronchial trunk textus connectivus elasticus bronchus elastic connective tissue bronchus textus connectivus elasticus elastic connective tissue of bronchi elastic connective tissue of bronchial trunk elastic connective tissue of bronchus elastic tissue of bronchi elastic tissue of bronchial trunk elastic tissue of bronchus textus connectivus elasticus of bronchi textus connectivus elasticus of bronchial trunk textus connectivus elasticus of bronchus uberon UBERON:0003616 bronchus elastic tissue An elastic tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707053 ncithesaurus:Bronchus_Elastic_Tissue bronchi elastic connective tissue OBOL:automatic bronchi elastic tissue OBOL:automatic bronchi textus connectivus elasticus OBOL:automatic bronchial trunk elastic connective tissue OBOL:automatic bronchial trunk elastic tissue OBOL:automatic bronchial trunk textus connectivus elasticus OBOL:automatic bronchus elastic connective tissue OBOL:automatic bronchus textus connectivus elasticus OBOL:automatic elastic connective tissue of bronchi OBOL:automatic elastic connective tissue of bronchial trunk OBOL:automatic elastic connective tissue of bronchus OBOL:automatic elastic tissue of bronchi OBOL:automatic elastic tissue of bronchial trunk OBOL:automatic elastic tissue of bronchus OBOL:automatic textus connectivus elasticus of bronchi OBOL:automatic textus connectivus elasticus of bronchial trunk OBOL:automatic textus connectivus elasticus of bronchus OBOL:automatic An elastic tissue that is part of a trachea [Automatically generated definition]. MA:0001861 cartilaginous trachea elastic connective tissue cartilaginous trachea elastic tissue cartilaginous trachea textus connectivus elasticus elastic connective tissue of cartilaginous trachea elastic connective tissue of vertebrate trachea elastic connective tissue of windpipe elastic tissue of cartilaginous trachea elastic tissue of vertebrate trachea elastic tissue of windpipe textus connectivus elasticus of cartilaginous trachea textus connectivus elasticus of vertebrate trachea textus connectivus elasticus of windpipe vertebrate trachea elastic connective tissue vertebrate trachea elastic tissue vertebrate trachea textus connectivus elasticus windpipe elastic connective tissue windpipe elastic tissue windpipe textus connectivus elasticus uberon UBERON:0003617 trachea elastic tissue An elastic tissue that is part of a trachea [Automatically generated definition]. OBOL:automatic cartilaginous trachea elastic connective tissue OBOL:automatic cartilaginous trachea elastic tissue OBOL:automatic cartilaginous trachea textus connectivus elasticus OBOL:automatic elastic connective tissue of cartilaginous trachea OBOL:automatic elastic connective tissue of vertebrate trachea OBOL:automatic elastic connective tissue of windpipe OBOL:automatic elastic tissue of cartilaginous trachea OBOL:automatic elastic tissue of vertebrate trachea OBOL:automatic elastic tissue of windpipe OBOL:automatic textus connectivus elasticus of cartilaginous trachea OBOL:automatic textus connectivus elasticus of vertebrate trachea OBOL:automatic textus connectivus elasticus of windpipe OBOL:automatic vertebrate trachea elastic connective tissue OBOL:automatic vertebrate trachea elastic tissue OBOL:automatic vertebrate trachea textus connectivus elasticus OBOL:automatic windpipe elastic connective tissue OBOL:automatic windpipe elastic tissue OBOL:automatic windpipe textus connectivus elasticus OBOL:automatic The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. EMAPA:35138 FMA:74433 MA:0002903 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 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 An arterial blood vessel that is part of a kidney [Automatically generated definition]. EMAPA:31436 MA:0002578 uberon kidney arterial system UBERON:0003644 kidney arterial blood vessel An arterial blood vessel that is part of a kidney [Automatically generated definition]. OBOL:automatic kidney arterial system EMAPA:31436 Any joint that is part of a (free) limb. EMAPA:36501 FMA:321558 MA:0000691 galen:LimbJoint joint of limb joint of limb skeletal system skeletal limb joint uberon UBERON:0003657 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses limb joint Any joint that is part of a (free) limb. joint of limb skeletal system OBOL:automatic skeletal limb joint GO:0036023 Any muscle organ that is part of a limb [Automatically generated definition]. EMAPA:32700 MA:0000692 limb muscle organ limb skeletal muscle muscle organ of limb uberon UBERON:0003661 limb muscle prolog Any muscle organ that is part of a limb [Automatically generated definition]. OBOL:automatic limb muscle organ OBOL:accepted limb skeletal muscle OBOL:exploratory muscle organ of limb OBOL:accepted Any muscle organ that is part of a forelimb. FMA and MA class actually refer to muscles of entire pectoral complex UBERON:0005634 AAO:0000204 BTO:0000479 EMAPA:36049 FMA:37348 fore limb muscle organ forelimb muscle organ free upper limb muscle muscle of free upper limb muscle of upper limb upper limb skeletal muscle wing muscle uberon arm muscle system musculature of arm musculature of the arm UBERON:0003662 forelimb muscle prolog Any muscle organ that is part of a forelimb. OBOL:automatic FMA and MA class actually refer to muscles of entire pectoral complex FMA fore limb muscle organ OBOL:automatic forelimb muscle organ OBOL:automatic free upper limb muscle FMA:37348 muscle of free upper limb FMA:37348 muscle of upper limb FMA:9621 upper limb skeletal muscle wing muscle Geisha:syn NCBITaxon:8782 wing muscle NCBITaxon:8782 OBOL:automatic arm muscle system EHDAA2:0000141 musculature of arm musculature of the arm Any muscle organ that is part of a hindlimb [Automatically generated definition]. AAO:0000222 EFO:0001928 FMA:37368 free lower limb muscle hind limb muscle organ hindlimb muscle organ inferior member muscle organ lower extremity muscle organ lower limb skeletal muscle muscle of free lower limb muscle of posterior limb muscle organ of hind limb muscle organ of hindlimb muscle organ of inferior member muscle organ of lower extremity uberon UBERON:0003663 hindlimb muscle prolog Any muscle organ that is part of a hindlimb [Automatically generated definition]. OBOL:automatic free lower limb muscle FMA:37368 hind limb muscle organ OBOL:automatic hindlimb muscle organ OBOL:automatic inferior member muscle organ OBOL:automatic lower extremity muscle organ OBOL:automatic lower limb skeletal muscle muscle of free lower limb FMA:37368 muscle of posterior limb muscle organ of hind limb OBOL:automatic muscle organ of hindlimb OBOL:automatic muscle organ of inferior member OBOL:automatic muscle organ of lower extremity OBOL:automatic 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 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:A01.047.025 NCIT:C12664 OpenCyc:Mx4rvZR1TJwpEbGdrcN5Y29ycA UMLS:C0230168 galen:AbdominalCavity cavity of abdominal compartment cavity of compartment of abdomen space of abdominal compartment uberon cavitas abdominis UBERON:0003684 abdominal cavity 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 cavitas abdominis GAID:17 Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture. sutura suture EMAPA:35263 FMA:7493 GAID:211 MA:0001475 MESH:D003393 cranium suture suture joint of skull suture of cranium uberon UBERON:0003685 cranial suture GO Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture. FMA:71385 ISBN:3110148986 suture FMA:71385 cranium suture OBOL:automatic suture of cranium OBOL:automatic 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 EMAPA:37868 FMA:75306 GAID:228 MESH:D005539 NCIT:C12495 OpenCyc:Mx4rwOm-FpwpEbGdrcN5Y29ycA TAO:0002045 UMLS:C0016519 ZFA:0005387 uberon UBERON:0003687 Design pattern notes: check whether this fits the foramen design pattern foramen magnum 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] 2012-08-14 TAO:0002045 TAO TAO:wd EMAPA:37868 MA:th UMLS:C0016519 ncithesaurus:Foramen_Magnum The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater. epidural extradural In humans the epidural space contains lymphatics, spinal nerve roots, loose fatty tissue, small arteries, and a network of large, thin-walled blood vessels called the epidural venous plexus in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail FMA:71228 GAID:243 MESH:D004824 cavum epidurale cavum extradurale extradural space spatium epidurale spatium extradurale uberon epidural cavity UBERON:0003691 epidural space The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater. in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail FMA cavum epidurale cavum extradurale extradural space FMA:71228 spatium epidurale spatium extradurale FMA:71228 FMA:TA epidural cavity 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:A01.047.050 NCIT:C77608 UMLS:C0836916 paries abdominalis wall of abdomen wall of abdomen proper uberon abdominal wall proper layers of the abdominal wall paries abdominalis UBERON:0003697 abdominal wall 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 wall of abdomen FMA:259054 wall of abdomen proper FMA:10429 abdominal wall proper FMA:10429 layers of the abdominal wall paries abdominalis 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 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 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 A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis arterial circle EHDAA2:0000252 EHDAA:9758 EMAPA:37829 FMA:50454 GAID:486 MESH:D002941 OpenCyc:Mx4rwSrCwJwpEbGdrcN5Y29ycA arterial circle of Willis cerebral arterial circle uberon Willis circle circulus arteriosus cerebri UBERON:0003709 circle of Willis FMA-modified FMA-modified A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis arterial circle EMAPA:37829 MA:th cerebral arterial circle GAID:486 Willis circle GAID:486 circulus arteriosus cerebri 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 OpenCyc:Mx4rvz3aUJwpEbGdrcN5Y29ycA UMLS:C0006095 galen:BrachiocephalicVein brachiocephalic venous tree innominate vein uberon innomiate vein innominate trunk innominate vein innominate veins vena brachiocephalica venae anonyma UBERON:0003711 brachiocephalic vein 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. UMLS:C0006095 ncithesaurus:Innominate_Vein brachiocephalic venous tree FMA:4723 innominate vein FMA:4723 innomiate vein innominate trunk innominate vein innominate vein GAID:529 innominate veins vena brachiocephalica vena brachiocephalica venae anonyma 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 OpenCyc:Mx4rwCt0eZwpEbGdrcN5Y29ycA UMLS:C0038001 galen:SplenicVein vena splenica uberon lienal vein vena lienalis UBERON:0003713 splenic vein 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 vena lienalis 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 OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ 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 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 A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. recurrent nerve AAO:0010754 FMA:6246 GAID:804 MESH:D012009 VHOG:0001347 nervus laryngeus recurrens recurrent laryngeal nerve from vagus nerve vagus X nerve recurrent laryngeal branch uberon inferior laryngeal nerve ramus recurrens UBERON:0003716 recurrent laryngeal nerve Wikipedia A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. AAO:0010754 recurrent nerve nervus laryngeus recurrens vagus X nerve recurrent laryngeal branch VHOG:0001347 inferior laryngeal nerve GAID:804 ramus recurrens AAO:0010754 The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue. BAMS:5lg EMAPA:19168 FMA:53218 GAID:835 MA:0001102 MESH:D008036 lingual branch of trigeminal nerve trigeminal V nerve lingual branch trigeminal nerve lingual branch uberon UBERON:0003721 lingual nerve The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue. trigeminal V nerve lingual branch MA:0001102 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 OpenCyc:Mx4rwSJp_ZwpEbGdrcN5Y29ycA 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 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 UMLS:C1285089 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 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]. 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 The central part of the thoracic cavity enclosed by the left and right pleurae. mediastinal CALOHA:TS-2338 EFO:0003057 EMAPA:36001 FMA:9826 GAID:94 MA:0003075 MESH:A01.911.800.500 NCIT:C12748 OpenCyc:Mx4rv2OKJ5wpEbGdrcN5Y29ycA UMLS:C0025066 mediastinal part of chest uberon UBERON:0003728 mediastinum FMA The central part of the thoracic cavity enclosed by the left and right pleurae. UBERON:cjm UMLS:C0025066 ncithesaurus:Mediastinum mediastinal part of chest FMA:9826 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 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. the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[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 A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204] EMAPA:36141 prostate ductal progenitor prostatic bud uberon prostate gland bud prostate primordium UBERON:0003820 prostate bud A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. GO:0060513 prostate ductal progenitor prostate gland bud EMAPA:36141 A nerve that is part of a thorax [Automatically generated definition]. EMAPA:37265 MA:0000562 MESH:D013900 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 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 tissue that is part of the urethra. EMAPA:37787 MA:0002649 uberon urethral muscle layer UBERON:0003829 urethra muscle tissue Any muscle tissue that is part of the urethra. UBERON:cjm EMAPA:37787 MA:th urethral muscle layer MA:0002649 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 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 A limb joint that is part of a forelimb [Automatically generated definition]. EMAPA:19204 MA:0000614 anteriormost limb joint of limb anteriormost limb limb joint fore limb joint of limb fore limb limb joint forelimb joint of limb forelimb limb joint joint of free upper limb joint of limb of anteriormost limb joint of limb of fore limb joint of limb of forelimb joint of limb of superior member joint of limb of upper extremity limb joint of anteriormost limb limb joint of fore limb limb joint of forelimb limb joint of superior member limb joint of upper extremity superior member joint of limb superior member limb joint upper extremity joint of limb upper extremity limb joint wing joint uberon UBERON:0003839 forelimb joint A limb joint that is part of a forelimb [Automatically generated definition]. OBOL:automatic anteriormost limb joint of limb OBOL:automatic anteriormost limb limb joint OBOL:automatic fore limb joint of limb OBOL:automatic fore limb limb joint OBOL:automatic forelimb joint of limb OBOL:automatic forelimb limb joint OBOL:automatic joint of free upper limb joint of limb of anteriormost limb OBOL:automatic joint of limb of fore limb OBOL:automatic joint of limb of forelimb OBOL:automatic joint of limb of superior member OBOL:automatic joint of limb of upper extremity OBOL:automatic limb joint of anteriormost limb OBOL:automatic limb joint of fore limb OBOL:automatic limb joint of forelimb OBOL:automatic limb joint of superior member OBOL:automatic limb joint of upper extremity OBOL:automatic superior member joint of limb OBOL:automatic superior member limb joint OBOL:automatic upper extremity joint of limb OBOL:automatic upper extremity limb joint OBOL:automatic wing joint NCBITaxon:8782 OBOL:automatic A limb joint that is part of a hindlimb [Automatically generated definition]. EMAPA:32635 MA:0000662 hind limb joint of limb hind limb limb joint hindlimb joint of limb hindlimb limb joint inferior member joint of limb inferior member limb joint joint of free lower limb joint of limb of hind limb joint of limb of hindlimb joint of limb of inferior member joint of limb of lower extremity joint of lower limb limb joint of hind limb limb joint of hindlimb limb joint of inferior member limb joint of lower extremity lower extremity joint of limb lower extremity limb joint uberon UBERON:0003840 hindlimb joint A limb joint that is part of a hindlimb [Automatically generated definition]. OBOL:automatic hind limb joint of limb OBOL:automatic hind limb limb joint OBOL:automatic hindlimb joint of limb OBOL:automatic hindlimb limb joint OBOL:automatic inferior member joint of limb OBOL:automatic inferior member limb joint OBOL:automatic joint of free lower limb joint of limb of hind limb OBOL:automatic joint of limb of hindlimb OBOL:automatic joint of limb of inferior member OBOL:automatic joint of limb of lower extremity OBOL:automatic joint of lower limb limb joint of hind limb OBOL:automatic limb joint of hindlimb OBOL:automatic limb joint of inferior member OBOL:automatic limb joint of lower extremity OBOL:automatic lower extremity joint of limb OBOL:automatic lower extremity limb joint 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 cavity of neural tube lumen of neural tube neural tube neural lumen EHDAA2:0001269 neural lumen EHDAA:2889 neurocoel VHOG:0001119 An epithelium that is part of a thymus, forming a supporting framework[MP,modified]. BTO:0001836 CALOHA:TS-1040 EHDAA2:0002019 EMAPA:35864 MA:0000768 NCIT:C45713 UMLS:C1711423 VHOG:0001426 ZFA:0005779 epithelial tissue of thymus epithelial tissue of thymus gland epithelium of thymus epithelium of thymus gland thymic epithelial tissue thymic epithelium thymus epithelial tissue thymus gland epithelial tissue thymus gland epithelium uberon UBERON:0003846 thymus epithelium An epithelium that is part of a thymus, forming a supporting framework[MP,modified]. MP:0009544 UMLS:C1711423 ncithesaurus:Thymic_Epithelial_Tissue epithelial tissue of thymus OBOL:automatic epithelial tissue of thymus gland OBOL:automatic epithelium of thymus OBOL:automatic epithelium of thymus gland OBOL:automatic thymic epithelium BTO:0001836 thymus epithelial tissue OBOL:automatic thymus gland epithelial tissue OBOL:automatic thymus gland epithelium OBOL:automatic A artery that supplies a thyroid gland. Part of the external carotid which supplies blood to the thyroid gland.[AAO] relationship loss: part_of external carotid (AAO:0010218)[AAO] AAO:0010490 EHDAA2:0002029 EHDAA:7372 EMAPA:18622 MA:0002066 NCIT:C53020 UMLS:C1711424 VHOG:0001366 uberon UBERON:0003847 thyroid artery A artery that supplies a thyroid gland. OBOL:automatic Part of the external carotid which supplies blood to the thyroid gland.[AAO] 2012-06-20 AAO:0010490 AAO AAO:BJB relationship loss: part_of external carotid (AAO:0010218)[AAO] 2012-06-20 AAO:0010490 AAO UMLS:C1711424 ncithesaurus:Thyroid_Artery 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 OpenCyc:Mx4rvlWYh5wpEbGdrcN5Y29ycA VHOG:0001340 gonad vein gonada vein vein of gonad vein of gonada uberon UBERON:0003848 gonadal vein 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]. 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 mesencephalic neural crest ZFA:0000935 neural crest midbrain ZFA:0000935 A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. Cranial neural crest that is part of the telencephalon.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003574 RETIRED_EHDAA2:0001991 TAO:0000812 VHOG:0000799 ZFA:0000812 neural crest telencephalon uberon UBERON:0003850 telencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. OBOL:automatic Cranial neural crest that is part of the telencephalon.[TAO] 2012-08-14 TAO:0000812 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:0000799 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 neural crest telencephalon ZFA:0000812 A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003573 EHDAA2:0000603 EMAPA:16518 TAO:0000811 VHOG:0000798 ZFA:0000811 diencephalic neural crest future diencephalon neural crest neural crest diencephalon neural crest of future diencephalon uberon UBERON:0003851 diencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. 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:0000798 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 diencephalic neural crest ZFA:0000811 future diencephalon neural crest EHDAA2:0000603 neural crest diencephalon ZFA:0000811 neural crest of future diencephalon EMAPA:16518 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 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 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 (...) 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 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 Mesenchyme that is part of a developing forelimb [Automatically generated definition]. EMAPA:32628 VHOG:0001109 anteriormost limb mesenchyme fore limb mesenchyme mesenchyme of anteriormost limb mesenchyme of fore limb mesenchyme of forelimb mesenchyme of superior member mesenchyme of upper extremity superior member mesenchyme upper extremity mesenchyme wing mesenchyme uberon UBERON:0003859 forelimb mesenchyme Mesenchyme that is part of a developing forelimb [Automatically generated definition]. OBOL:automatic anteriormost limb mesenchyme OBOL:automatic fore limb mesenchyme OBOL:automatic mesenchyme of anteriormost limb OBOL:automatic mesenchyme of fore limb OBOL:automatic mesenchyme of forelimb OBOL:automatic mesenchyme of superior member OBOL:automatic mesenchyme of upper extremity OBOL:automatic superior member mesenchyme OBOL:automatic upper extremity mesenchyme OBOL:automatic wing mesenchyme Geisha:syn NCBITaxon:8782 wing mesenchyme NCBITaxon:8782 OBOL:automatic Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. EMAPA:32637 VHOG:0001074 hind limb mesenchyme inferior member mesenchyme lower extremity mesenchyme mesenchyme of hind limb mesenchyme of hindlimb mesenchyme of inferior member mesenchyme of lower extremity uberon UBERON:0003860 hindlimb mesenchyme Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. OBOL:automatic hind limb mesenchyme OBOL:automatic inferior member mesenchyme OBOL:automatic lower extremity mesenchyme OBOL:automatic mesenchyme of hind limb OBOL:automatic mesenchyme of hindlimb OBOL:automatic mesenchyme of inferior member OBOL:automatic mesenchyme of lower extremity 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 A mesentery that is part of a uterus [Automatically generated definition]. EMAPA:35562 FMA:19816 MA:0002931 uberon mesentery of uterus UBERON:0003885 mesometrium A mesentery that is part of a uterus [Automatically generated definition]. OBOL:automatic mesentery of uterus FMA:19816 MA:0002931 An anatomical cavity that has the potential to develop into a coelemic 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 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 UMLS:C1512940 ncithesaurus:Intraembryonic_Coelom somatic coelom Initial section of the oviduct through which the ova pass from the ovary to the uterus Homologous to appendix testis salpinges salpinx CALOHA:TS-0732 EHDAA2:0000504 EMAPA:18984 EMAPA:35660 EV:0100112 FMA:18245 GAID:365 MA:0000385 MESH:D005187 NCIT:C12403 OpenCyc:Mx4rvViVeZwpEbGdrcN5Y29ycA UMLS:C0015560 galen:FallopianTube mammalian oviduct uterine tube (sensu Mammalia) uberon fallopian tubes female paramesonephric duct paramesonephric duct of female tuba uterina UBERON:0003889 fallopian tube FMA-abduced-lr Initial section of the oviduct through which the ova pass from the ovary to the uterus MGI:smb MP:0003574 Homologous to appendix testis salpinges UMLS:C0015560 ncithesaurus:Fallopian_Tube mammalian oviduct female paramesonephric duct EHDAA2:0000504 paramesonephric duct of female EMAPA:35660 tuba uterina paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct UBERON:0005318 AAO:0010141 EHDAA2:0004048 EMAPA:27665 GAID:1309 MESH:A16.254.570 NCIT:C13260 RETIRED_EHDAA2:0001399 UMLS:C0026732 VHOG:0001199 XAO:0000330 Muellerian duct Müllerian duct ductus paramesonephricus paramesonephric duct early paramesonephric duct uberon UBERON:0003890 Mullerian duct Wikipedia paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. GO:0061205 Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] 2012-09-17 VHOG:0001199 VHOG Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] 2012-06-20 AAO:0010141 AAO AAO:RED In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] 2012-09-17 VHOG:0001199 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559 UMLS:C0026732 ncithesaurus:Mullerian_Duct paramesonephric duct EMAPA:27665 early paramesonephric duct EHDAA2:0004048 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. UMLS:C0927195 ncithesaurus:Stroma_Connective_Tissue A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]. capsular EHDAA:4739 EHDAA:9061 FMA:85272 galen:Capsule uberon UBERON:0003893 see also: protective structure surrounding some species of bacteria and fungi. Note that FMA has classes such as Articular capsule that are not subtypes of Capsule (which is undefined in FMA). GO has 'capsule' which is a fungal structure, and 'external encapsulating structure' which is restricted to cells capsule A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]. 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 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. 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 A portion of skeletal muscle tissue in the trunk. 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 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 TAO:0005261 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]. 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 The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue. The CP epithelial layer is continuous with the ependymal cell layer that lines the ventricles, but unlike the ependyma, the epithelial layer has tight gap junctions between the cells on the side facing the ventricle (apical surface). These gap junctions prevent the majority of substances from crossing the cell layer into the CSF; thus the CP acts as a blood-CSF barrier EMAPA:36608 FMA:242811 MA:0000824 NCIT:C42079 UMLS:C1516506 choroid plexus epithelial tissue epithelial tissue of chorioid plexus of cerebral hemisphere epithelial tissue of choroid plexus epithelium of choroid plexus uberon UBERON:0003911 choroid plexus epithelium The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue. UBERON:cjm UMLS:C1516506 ncithesaurus:Choroid_Plexus_Epithelium choroid plexus epithelial tissue OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic epithelial tissue of choroid plexus OBOL:automatic epithelium of choroid plexus FMA:242811 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 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 Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. check this mesenchyme of kidney uberon UBERON:0003918 kidney mesenchyme Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. GO:0072074 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 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 Wikipedia 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 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 TAO:0001390 UMLS:C1283285 ZFA:0001390 pancreatic bud pancreatic buds uberon pancreas epithelium pancreatic anlage UBERON:0003922 pancreatic epithelial bud EHDAA2 EHDAA2 zebrafish EHDAA2-inferred The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. 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 TAO:0001370 VHOG:0001428 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 EHDAA2 XAO pancreatic bud that gives rise to the accessory pancreatic duct. 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) 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 TAO:0001369 VHOG:0001429 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 EHDAA2 WP 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] 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) 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 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. Epithelium lining the lumen of the gut.[TAO] 2012-08-14 TAO:0005123 TAO ZFIN:curator 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 BGEE:ANN NCBITaxon:6073 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. 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 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. 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 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 somatic sensory system somatosensory system system for detection of somatic senses uberon UBERON:0003942 somatic sensory 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 somatosensory system NLXANAT:090818 The brain ventricles or their associated choroid plexuses TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted TODO merge into BV uberon UBERON:0003947 brain ventricle/choroid plexus The brain ventricles or their associated choroid plexuses MP:0002200 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 An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP]. add more specific classification e.g. anastomosing network - consider FMA:3726 EMAPA:18332 FMA:19834 GAID:399 MA:0003013 MESH:D012152 NCIT:C33467 UMLS:C0035278 Haller's rete uberon UBERON:0003959 rete testis Wikipedia An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP]. MP:0006416 UMLS:C0035278 ncithesaurus:Rete_Testis Haller's rete FMA:19834 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 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 valvular EHDAA2:0004046 EHDAA:1892 EHDAA:4406 FMA:67611 OpenCyc:Mx4rvqiwE5wpEbGdrcN5Y29ycA galen:Valve anatomical valve uberon UBERON:0003978 valve anatomical valve FMA:67611 One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows BAMS:CBf DHBA:12828 EMAPA:37818 FMA:321547 HBA:9406 cerebellar fissure fissurae cerebelli uberon cerebellar fissures cerebellar fissures set cerebellar sulci cerebellar sulcus set of cerebellar fissures sulcus of cerebellum UBERON:0003980 cerebellum fissure One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows MP:0009267 EMAPA:37818 MA:th fissurae cerebelli FMA:77789 FMA:TA cerebellar fissures BAMS:CBf cerebellar fissures set FMA:77789 cerebellar sulci HBA:9406 set of cerebellar fissures FMA:77789 A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]. Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO] Kardong says absent in adult tetrapods, check AAO we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally AAO:0010250 uberon UBERON:0003983 conus arteriosus A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]. MP:0009464 Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO] 2012-06-20 AAO:0010250 AAO AAO:BJB we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally ISBN:0073040584 The funnel-like expansion of the abdominal extremity of the uterine tube[MP] The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. infundibulum EMAPA:29897 FMA:18307 infundibulum of oviduct infundibulum of uterine tube infundibulum of fallopian tube uberon infundibulum tubae uterinae UBERON:0003984 uterine tube infundibulum FMA The funnel-like expansion of the abdominal extremity of the uterine tube[MP] MP:0009466 The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. infundibulum infundibulum of oviduct FMA:18307 infundibulum of uterine tube FMA:18307 infundibulum of fallopian tube FMA:18307 infundibulum tubae uterinae The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells EMAPA:37974 thymic cortico-medullary boundary thymic corticomedullary boundary thymic corticomedullary junction thymic corticomedullary zone thymus CMZ thymus cortico-medullary boundary thymus corticomedullary junction thymus corticomedullary zone uberon UBERON:0003988 thymus corticomedullary boundary The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells MP:0009543 EMAPA:37974 MA:th thymic cortico-medullary boundary MP:0009543 thymic corticomedullary boundary MP:0009543 thymic corticomedullary junction MP:0009543 thymic corticomedullary zone MP:0009543 thymus CMZ MP:0009543 thymus cortico-medullary boundary MP:0009543 thymus corticomedullary junction MP:0009543 thymus corticomedullary zone MP:0009543 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 EHDAA2_RETIRED:0003428 EHDAA:1719 EHDAA:1725 EHDAA:1731 EHDAA:1737 EMAPA:32838 FMA:295656 NCIT:C61572 UMLS:C0180383 XAO:0000220 cutis plate dermatomal mesenchyme uberon epimere mesoderm mesenchyma dermatomiale UBERON:0004016 dermatome AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. AEO:0001017 AEO:JB UMLS:C0180383 ncithesaurus:Dermatome cutis plate dermatomal mesenchyme mesenchyma dermatomiale 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 germinal neuroepithelial layer germinal neuroepithelium NCBIBook:NBK10047 original neural tube NCBIBook:NBK10047 The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects SP DHBA:10522 EMAPA:32703 PBA:294021932 cerebral cortex subplate subplate subplate zone uberon UBERON:0004035 cortical subplate The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate MP:0008440 The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects WP SP BRAINSPAN:BRAINSPAN cerebral cortex subplate EMAPA:32833 subplate zone DHBA:10522 The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone IZ EMAPA:17545 EMAPA:32712 uberon cerebral cortex mantle layer cerebral cortex mantle zone cortical mantle layer UBERON:0004040 cortical intermediate zone The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone MP:0008457 IZ BRAINSPAN:BRAINSPAN cerebral cortex mantle layer EMAPA:17545 The external masculine genital organs, including the penis and scrotum BTO:0003097 EMAPA:30977 FMA:45642 galen:MaleExternalGenitalia external male genital organ male external genitalia uberon organa genitalia masculina externa UBERON:0004053 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 external male genitalia The external masculine genital organs, including the penis and scrotum MP:0009199 external male genital organ BTO:0003097 male external genitalia FMA:45642 organa genitalia masculina externa BTO:0003097 The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands consider splitting genitalia from genital organ BTO:0003096 FMA:45655 internal male genital organ male internal genitalia uberon organa genitalia masculina interna UBERON:0004054 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 internal male genitalia The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands MP:0009205 internal male genital organ BTO:0003096 male internal genitalia FMA:45655 organa genitalia masculina interna BTO:0003096 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 ductuli biliferi bile capillary BTO:0002840 biliary ductule BTO:0002840 cholangiole BTO:0002840 terminal cholangiole 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 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 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 neural tube intermediate zone MP:0009690 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 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 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 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 UMLS:C1511061 ncithesaurus:Basal_Plate basal plate of 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 UMLS:C1517321 VHOG:0001319 embryonic frontonasal prominence uberon forebrain prominence frontonasal mass frontonasal process prominentia frontonasalis UBERON:0004066 frontonasal prominence 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 forebrain prominence MP:0009901 frontonasal mass MP:0009901 frontonasal process MP:0009901 prominentia frontonasalis The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it EHDAA2:0000916 EHDAA:4786 EMAPA:16805 FMA:295864 lateral nasal process latero-nasal process uberon lateral nasal swelling prominentia nasalis lateralis UBERON:0004067 lateral nasal prominence EHDAA2 Wikipedia The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it MP:0009902 lateral nasal process EHDAA2:0000916 latero-nasal process EMAPA:16805 lateral nasal swelling prominentia nasalis lateralis one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356]. FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. BIRNLEX:1356 BTO:0001442 EFO:0001914 EMAPA:32674 FMA:78447 HBA:9418 MA:0000818 MESH:D002552 NCIT:C12356 OpenCyc:Mx4rvmTY65wpEbGdrcN5Y29ycA UMLS:C0007799 brain ventricles cerebral ventricle region of ventricular system of brain uberon UBERON:0004086 brain ventricle one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356]. BIRNLEX:1356 FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. FMA UMLS:C0007799 ncithesaurus:Ventricle_Brain brain ventricles cerebral ventricle HP:0002118 region of ventricular system of brain FMA:78447 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 OpenCyc:Mx4rkJQ4U6gEEdudWQACs5b6Bw UMLS:C0042460 uberon caval vein venae cavae UBERON:0004087 vena cava Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. UMLS:C0042460 ncithesaurus:Vena_Cava 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 in HP covers eyelid, eyebrow. HP:0000284 content of orbital part of eye FMA:260119 eye region orbital part of face orbital content FMA:260119 orbital part of eye FMA:72951 2 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 foramen foramina uberon opening ostia ostium UBERON:0004111 anatomical conduit 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 FMA foramen EHDAA2:0003080 foramina ostia An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches. Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO] 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] EMAPA also includes a distinct pouch endoderm AAO:0011113 EFO:0003627 EHDAA:1086 EHDAA:1669 EHDAA:579 EHDAA:617 EMAPA:32752 FMA:293063 NCIT:C34252 TAO:0001106 UMLS:C0231067 VHOG:0001203 XAO:0000282 ZFA:0001106 branchial pouch visceral pouch uberon pharyngeal pouches visceral pouches UBERON:0004117 The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389] pharyngeal pouch EHDAA2 ZFA An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches. ZFA:0001106 Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO] 2012-08-14 TAO:0001106 TAO ZFIN:curator 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:0001203 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) EMAPA also includes a distinct pouch endoderm EMAPA UMLS:C0231067 ncithesaurus:Pharyngeal_Pouch branchial pouch visceral pouch pharyngeal pouches VHOG:0001203 visceral pouches VHOG:0001203 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. An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes FBbt:00025998 mesodermal derivative uberon UBERON:0004120 mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. mesodermal derivative FBbt:00025998 An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes FBbt:00025990 ectodermal deriviative uberon UBERON:0004121 ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. 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 OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g 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 UMLS:C0042066 ncithesaurus:Genitourinary_System Urogenitalsystem BTO:0003091 genito-urinary system FMA:280610 urogenital tract BTO:0003091 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 TAO:0000050 UMLS:C0231106 VHOG:0000165 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 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 (...) 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 UMLS:C0231106 ncithesaurus:Optic_Vesicle eye vesicle XAO:0000228 ocular vesicle VHOG:0000165 optic vesicles ZFA:0000050 A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo. BIRNLEX:880 EMAPA:35212 FMA:83141 MA:0000201 NCIT:C49137 UMLS:C1707522 cell layer of cerebellar cortex cytoarchitectural part of the cerebellar cortex gray matter layer of cerebellum layer of cerebellar cortex layer of cerebellum uberon UBERON:0004130 cerebellar layer A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo. ncithesaurus:Cortical_Cell_Layer_of_the_Cerebellum UMLS:C1707522 ncithesaurus:Cortical_Cell_Layer_of_the_Cerebellum cytoarchitectural part of the cerebellar cortex BIRNLEX:880 gray matter layer of cerebellum FMA:83141 . salivary nucleus uberon UBERON:0004133 salivatory nucleus . 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) 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 BGEE:ann 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 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 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 arterial (outflow) pole Vein of heart that drains the myocardium EHDAA2:0004507 EMAPA:37137 FMA:12846 NCIT:C12878 NCIT:C12882 UMLS:C0226654 UMLS:C0226737 ZFA:0005814 galen:CoronaryVein cardiac vein coronary vein heart vein vein of heart uberon coronary vein UBERON:0004148 cardiac vein FMA Vein of heart that drains the myocardium 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 A cardiac chamber surrounds an enclosed cavity within the heart FMA:7095 OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw 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 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 UMLS:C0231004 VHOG:0000019 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 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 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 in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2 UMLS:C0231004 ncithesaurus:Septum_Transversum transverse septum 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 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 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]. 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 The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland TODO - check also FMA Stroma of glandular part of prostate UBERON:0005084 EMAPA:35714 FMA:45719 MA:0002912 NCIT:C13104 UMLS:C1521760 prostate stroma prostatic stroma stroma of prostate stroma of prostate gland stroma of glandular part of prostate uberon UBERON:0004184 prostate gland stroma The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland GO:0060741 UMLS:C1521760 ncithesaurus:Prostatic_Stroma prostate stroma OBOL:automatic prostatic stroma FMA:45719 stroma of prostate OBOL:automatic stroma of prostate gland OBOL:automatic stroma of glandular part of prostate FMA:74349 OBOL:automatic 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 Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) UBERON:0002449 UBERON:0005098 pyramid BTO:0003926 FMA:258870 MA:0001654 NCIT:C12886 NCIT:C33436 UMLS:C0227629 UMLS:C1514613 Malpighian pyramid renal pyramid uberon Malphigian pyramid Malpighian pyramid medullary pyramid pyramid of Malphigi pyramid of Malpighi pyramides renales pyramis renalis renal medullary region UBERON:0004200 kidney pyramid Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. GO:0072056 not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) FMA pyramid GO:0072056 UMLS:C0227629 ncithesaurus:Renal_Pyramid UMLS:C1514613 ncithesaurus:Pyramid_of_Malpighi Malpighian pyramid renal pyramid Malphigian pyramid BTO:0003926 pyramid of Malphigi ncithesaurus:Pyramid_of_Malpighi pyramid of Malpighi UBERON:cjm pyramides renales pyramis renalis BTO:0003926 renal medullary region FMA:258870 The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex UBERON:0005267 BTO:0002643 EMAPA:28130 MA:0002600 kidney cortex collecting duct uberon renal cortex collecting duct UBERON:0004203 cortical collecting duct The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex GO:0072059 kidney cortex collecting duct MA:0002600 renal cortex collecting duct MA:0002600 Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron mesenchyme of nephron nephron mesenchyme uberon UBERON:0004208 The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] nephrogenic mesenchyme Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron GO:0072076 mesenchyme of nephron OBOL:automatic nephron mesenchyme OBOL:automatic The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap stage I nephron uberon UBERON:0004209 renal vesicle EHDAA2 The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. GO:0072077 stage I nephron ZFA:0005586 The nephron epithelium is a tissue that covers the surface of a nephron epithelial tissue of nephron epithelium of nephron nephron epithelial tissue uberon UBERON:0004211 nephron epithelium The nephron epithelium is a tissue that covers the surface of a nephron GO:0072088 epithelial tissue of nephron OBOL:automatic epithelium of nephron OBOL:automatic nephron epithelial tissue OBOL:automatic 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 urethra [Automatically generated definition]. EMAPA:36630 FMA:76909 MA:0001691 muscle layer of urethra muscular coat of urethra muscular layer of urethra smooth muscle of urethra smooth muscle tissue of urethra tunica muscularis urethrae urethra smooth muscle tissue uberon urethral smooth muscle UBERON:0004219 urethra smooth muscle layer A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. OBOL:automatic muscle layer of urethra FMA:76909 muscular coat of urethra FMA:76909 muscular layer of urethra FMA:76909 smooth muscle of urethra OBOL:automatic smooth muscle tissue of urethra OBOL:automatic tunica muscularis urethrae FMA:TA urethra smooth muscle tissue OBOL:automatic urethral smooth muscle MA:0001691 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 vagina [Automatically generated definition]. BTO:0004999 EMAPA:30997 MA:0001733 involuntary muscle of vagina non-striated muscle of vagina smooth muscle of vagina smooth muscle tissue of vagina vagina involuntary muscle vagina non-striated muscle vagina smooth muscle tissue vaginal smooth muscle uberon vagina smooth muscle UBERON:0004223 vagina smooth muscle A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition]. OBOL:automatic involuntary muscle of vagina OBOL:automatic non-striated muscle of vagina OBOL:automatic smooth muscle of vagina OBOL:automatic smooth muscle tissue of vagina OBOL:automatic vagina involuntary muscle OBOL:automatic vagina non-striated muscle OBOL:automatic vagina smooth muscle tissue OBOL:automatic vaginal smooth muscle BTO:0004999 vagina smooth muscle BTO:0004999 A muscular coat that is part of a vas deferens [Automatically generated definition]. TODO - check MA and FMA classes mean the same thing EMAPA:29270 FMA:19239 MA:0001750 muscle layer of deferent duct muscle layer of ductus deferens muscle layer of vas deferens muscular coat of ductus deferens muscular layer of ductus deferens muscularis of vas deferens tunica muscularis (ductus deferens) tunica muscularis ductus deferentis uberon UBERON:0004224 muscular coat of vas deferens A muscular coat that is part of a vas deferens [Automatically generated definition]. OBOL:automatic muscle layer of deferent duct FMA:19239 muscle layer of ductus deferens FMA:19239 muscle layer of vas deferens FMA:19239 muscular coat of ductus deferens FMA:19239 muscular layer of ductus deferens FMA:19239 muscularis of vas deferens FMA:19239 tunica muscularis (ductus deferens) FMA:19239 tunica muscularis ductus deferentis FMA:19239 FMA:TA 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 the smooth muscle tissue surrounding the urothelium of the kidney pelvis EMAPA:28120 FMA:262022 MA:0002631 kidney pelvis smooth muscle renal pelvis smooth muscle smooth muscle tissue of renal pelvis uberon pelvic smooth muscle UBERON:0004227 kidney pelvis smooth muscle the smooth muscle tissue surrounding the urothelium of the kidney pelvis MGI:csmith MP:0011335 kidney pelvis smooth muscle EMAPA:28120 renal pelvis smooth muscle EMAPA:28120 smooth muscle tissue of renal pelvis FMA:262022 pelvic smooth muscle EMAPA:28120 A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]. BTO:0001849 CALOHA:TS-1087 EMAPA:37791 MA:0001697 bladder involuntary muscle bladder non-striated muscle bladder smooth muscle bladder smooth muscle tissue involuntary muscle of bladder involuntary muscle of urinary bladder non-striated muscle of bladder non-striated muscle of urinary bladder smooth muscle of bladder smooth muscle of urinary bladder smooth muscle tissue of bladder smooth muscle tissue of urinary bladder urinary bladder involuntary muscle urinary bladder muscle urinary bladder non-striated muscle urinary bladder smooth muscle tissue uberon smooth muscle layer of bladder UBERON:0004228 urinary bladder smooth muscle A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic EMAPA:37791 MA:th bladder involuntary muscle OBOL:automatic bladder non-striated muscle OBOL:automatic bladder smooth muscle OBOL:automatic bladder smooth muscle tissue OBOL:automatic involuntary muscle of bladder OBOL:automatic involuntary muscle of urinary bladder OBOL:automatic non-striated muscle of bladder OBOL:automatic non-striated muscle of urinary bladder OBOL:automatic smooth muscle of bladder OBOL:automatic smooth muscle of urinary bladder OBOL:automatic smooth muscle tissue of bladder OBOL:automatic smooth muscle tissue of urinary bladder OBOL:automatic urinary bladder involuntary muscle OBOL:automatic urinary bladder muscle MA:0001697 urinary bladder non-striated muscle OBOL:automatic urinary bladder smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]. EMAPA:30123 FMA:67990 MA:0001699 bladder neck involuntary muscle bladder neck non-striated muscle bladder neck smooth muscle bladder neck smooth muscle tissue involuntary muscle of bladder neck involuntary muscle of neck of bladder involuntary muscle of neck of urinary bladder involuntary muscle of urinary bladder neck involuntary muscle of vesical neck neck of bladder involuntary muscle neck of bladder non-striated muscle neck of bladder smooth muscle neck of bladder smooth muscle tissue neck of urinary bladder involuntary muscle neck of urinary bladder non-striated muscle neck of urinary bladder smooth muscle neck of urinary bladder smooth muscle tissue non-striated muscle of bladder neck non-striated muscle of neck of bladder non-striated muscle of neck of urinary bladder non-striated muscle of urinary bladder neck non-striated muscle of vesical neck smooth muscle of bladder neck smooth muscle of neck of bladder smooth muscle of neck of urinary bladder smooth muscle of urinary bladder neck smooth muscle of vesical neck smooth muscle tissue of bladder neck smooth muscle tissue of neck of bladder smooth muscle tissue of neck of urinary bladder smooth muscle tissue of urinary bladder neck smooth muscle tissue of vesical neck trigonal muscle trigonal muscle of urinary bladder urinary bladder neck involuntary muscle urinary bladder neck muscle urinary bladder neck non-striated muscle urinary bladder neck smooth muscle tissue vesical neck involuntary muscle vesical neck non-striated muscle vesical neck smooth muscle vesical neck smooth muscle tissue uberon UBERON:0004230 urinary bladder neck smooth muscle A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck involuntary muscle OBOL:automatic bladder neck non-striated muscle OBOL:automatic bladder neck smooth muscle OBOL:automatic bladder neck smooth muscle tissue OBOL:automatic involuntary muscle of bladder neck OBOL:automatic involuntary muscle of neck of bladder OBOL:automatic involuntary muscle of neck of urinary bladder OBOL:automatic involuntary muscle of urinary bladder neck OBOL:automatic involuntary muscle of vesical neck OBOL:automatic neck of bladder involuntary muscle OBOL:automatic neck of bladder non-striated muscle OBOL:automatic neck of bladder smooth muscle OBOL:automatic neck of bladder smooth muscle tissue OBOL:automatic neck of urinary bladder involuntary muscle OBOL:automatic neck of urinary bladder non-striated muscle OBOL:automatic neck of urinary bladder smooth muscle OBOL:automatic neck of urinary bladder smooth muscle tissue OBOL:automatic non-striated muscle of bladder neck OBOL:automatic non-striated muscle of neck of bladder OBOL:automatic non-striated muscle of neck of urinary bladder OBOL:automatic non-striated muscle of urinary bladder neck OBOL:automatic non-striated muscle of vesical neck OBOL:automatic smooth muscle of bladder neck OBOL:automatic smooth muscle of neck of bladder OBOL:automatic smooth muscle of neck of urinary bladder OBOL:automatic smooth muscle of urinary bladder neck OBOL:automatic smooth muscle of vesical neck OBOL:automatic smooth muscle tissue of bladder neck OBOL:automatic smooth muscle tissue of neck of bladder OBOL:automatic smooth muscle tissue of neck of urinary bladder OBOL:automatic smooth muscle tissue of urinary bladder neck OBOL:automatic smooth muscle tissue of vesical neck OBOL:automatic trigonal muscle FMA:67990 trigonal muscle of urinary bladder FMA:67990 urinary bladder neck involuntary muscle OBOL:automatic urinary bladder neck muscle MA:0001699 urinary bladder neck non-striated muscle OBOL:automatic urinary bladder neck smooth muscle tissue OBOL:automatic vesical neck involuntary muscle OBOL:automatic vesical neck non-striated muscle OBOL:automatic vesical neck smooth muscle OBOL:automatic vesical neck smooth muscle tissue 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 lymphatic vessel [Automatically generated definition]. EMAPA:36313 FMA:262026 MA:0000751 NCIT:C49260 UMLS:C1708791 involuntary muscle of lymph vessel involuntary muscle of lymphatic vessel lymph vessel involuntary muscle lymph vessel non-striated muscle lymph vessel smooth muscle lymph vessel smooth muscle tissue lymphatic vessel involuntary muscle lymphatic vessel non-striated muscle lymphatic vessel smooth muscle tissue non-striated muscle of lymph vessel non-striated muscle of lymphatic vessel smooth muscle of lymph vessel smooth muscle of lymphatic vessel smooth muscle tissue of lymph vessel smooth muscle tissue of lymphatic vessel uberon UBERON:0004232 lymphatic vessel smooth muscle A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition]. OBOL:automatic UMLS:C1708791 ncithesaurus:Lymphatic_Vessel_Smooth_Muscle_Tissue involuntary muscle of lymph vessel OBOL:automatic involuntary muscle of lymphatic vessel OBOL:automatic lymph vessel involuntary muscle OBOL:automatic lymph vessel non-striated muscle OBOL:automatic lymph vessel smooth muscle OBOL:automatic lymph vessel smooth muscle tissue OBOL:automatic lymphatic vessel involuntary muscle OBOL:automatic lymphatic vessel non-striated muscle OBOL:automatic lymphatic vessel smooth muscle tissue OBOL:automatic non-striated muscle of lymph vessel OBOL:automatic non-striated muscle of lymphatic vessel OBOL:automatic smooth muscle of lymph vessel OBOL:automatic smooth muscle of lymphatic vessel OBOL:automatic smooth muscle tissue of lymph vessel OBOL:automatic smooth muscle tissue of lymphatic vessel 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 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 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. 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 tissue gallbladder involuntary muscle gallbladder non-striated muscle gallbladder smooth 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 gall bladder 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 tissue OBOL:automatic gallbladder involuntary muscle OBOL:automatic gallbladder non-striated muscle OBOL:automatic gallbladder smooth muscle OBOL:automatic gallbladder smooth muscle tissue 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 bronchus [Automatically generated definition]. BTO:0004401 EMAPA:35195 MA:0001840 NCIT:C49213 UMLS:C1707055 bronchi involuntary muscle bronchi non-striated muscle bronchi smooth muscle bronchi smooth muscle tissue bronchial trunk involuntary muscle bronchial trunk non-striated muscle bronchial trunk smooth muscle bronchial trunk smooth muscle tissue bronchus involuntary muscle bronchus non-striated muscle bronchus smooth muscle tissue involuntary muscle of bronchi involuntary muscle of bronchial trunk involuntary muscle of bronchus non-striated muscle of bronchi non-striated muscle of bronchial trunk non-striated muscle of bronchus smooth muscle of bronchi smooth muscle of bronchial trunk smooth muscle of bronchus smooth muscle tissue of bronchi smooth muscle tissue of bronchial trunk smooth muscle tissue of bronchus uberon bronchial smooth muscle UBERON:0004242 bronchus smooth muscle A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707055 ncithesaurus:Bronchus_Smooth_Muscle_Tissue bronchi involuntary muscle OBOL:automatic bronchi non-striated muscle OBOL:automatic bronchi smooth muscle OBOL:automatic bronchi smooth muscle tissue OBOL:automatic bronchial trunk involuntary muscle OBOL:automatic bronchial trunk non-striated muscle OBOL:automatic bronchial trunk smooth muscle OBOL:automatic bronchial trunk smooth muscle tissue OBOL:automatic bronchus involuntary muscle OBOL:automatic bronchus non-striated muscle OBOL:automatic bronchus smooth muscle tissue OBOL:automatic involuntary muscle of bronchi OBOL:automatic involuntary muscle of bronchial trunk OBOL:automatic involuntary muscle of bronchus OBOL:automatic non-striated muscle of bronchi OBOL:automatic non-striated muscle of bronchial trunk OBOL:automatic non-striated muscle of bronchus OBOL:automatic smooth muscle of bronchi OBOL:automatic smooth muscle of bronchial trunk OBOL:automatic smooth muscle of bronchus OBOL:automatic smooth muscle tissue of bronchi OBOL:automatic smooth muscle tissue of bronchial trunk OBOL:automatic smooth muscle tissue of bronchus OBOL:automatic bronchial smooth muscle EMAPA:35195 A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition]. BTO:0003159 EMAPA:35713 FMA:74245 MA:0001741 involuntary muscle of prostate involuntary muscle of prostate gland muscular tissue of prostate non-striated muscle of prostate non-striated muscle of prostate gland prostate gland involuntary muscle prostate gland non-striated muscle prostate gland smooth muscle tissue prostate involuntary muscle prostate non-striated muscle prostate smooth muscle prostate smooth muscle tissue smooth muscle of prostate smooth muscle of prostate gland smooth muscle tissue of prostate smooth muscle tissue of prostate gland substantia muscularis prostatae uberon UBERON:0004243 prostate gland smooth muscle A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition]. OBOL:automatic involuntary muscle of prostate OBOL:automatic involuntary muscle of prostate gland OBOL:automatic muscular tissue of prostate FMA:74245 non-striated muscle of prostate OBOL:automatic non-striated muscle of prostate gland OBOL:automatic prostate gland involuntary muscle OBOL:automatic prostate gland non-striated muscle OBOL:automatic prostate gland smooth muscle tissue OBOL:automatic prostate involuntary muscle OBOL:automatic prostate non-striated muscle OBOL:automatic prostate smooth muscle OBOL:automatic prostate smooth muscle tissue OBOL:automatic smooth muscle of prostate OBOL:automatic smooth muscle of prostate gland OBOL:automatic smooth muscle tissue of prostate OBOL:automatic smooth muscle tissue of prostate gland OBOL:automatic substantia muscularis prostatae FMA:74245 FMA:TA A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]. EMAPA:29046 MA:0001721 fallopian tube involuntary muscle fallopian tube non-striated muscle fallopian tube smooth muscle fallopian tube smooth muscle tissue involuntary muscle of fallopian tube non-striated muscle of fallopian tube smooth muscle of fallopian tube smooth muscle tissue of fallopian tube uberon UBERON:0004245 oviduct smooth muscle A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]. OBOL:automatic fallopian tube involuntary muscle OBOL:automatic fallopian tube non-striated muscle OBOL:automatic fallopian tube smooth muscle OBOL:automatic fallopian tube smooth muscle tissue OBOL:automatic involuntary muscle of fallopian tube OBOL:automatic non-striated muscle of fallopian tube OBOL:automatic smooth muscle of fallopian tube OBOL:automatic smooth muscle tissue of fallopian tube OBOL:automatic 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. EMAPA:37248 MA:th back bone MA:0000494 bone of back OBOL:automatic dorsal region bone 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) 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 cranial suture that is part of a cartilaginous joint [Automatically generated definition]. EMAPA:37463 MA:0001498 articulatio cartilaginea cranial suture articulatio cartilaginea cranial sutures articulatio cartilaginea cranial sutures set articulatio cartilaginea cranium suture articulatio cartilaginea suture of cranium cartilaginous joint cranial suture cartilaginous joint cranial sutures cartilaginous joint cranial sutures set cartilaginous joint cranium suture cartilaginous joint suture of cranium cranial suture of articulatio cartilaginea cranial suture of cartilaginous joint cranial sutures of articulatio cartilaginea cranial sutures of cartilaginous joint cranial sutures set of articulatio cartilaginea cranial sutures set of cartilaginous joint cranium suture of articulatio cartilaginea cranium suture of cartilaginous joint suture of cranium of articulatio cartilaginea suture of cranium of cartilaginous joint uberon UBERON:0004273 cartilaginous joint suture A cranial suture that is part of a cartilaginous joint [Automatically generated definition]. OBOL:automatic EMAPA:37463 MA:th articulatio cartilaginea cranial suture OBOL:automatic articulatio cartilaginea cranial sutures OBOL:automatic articulatio cartilaginea cranial sutures set OBOL:automatic articulatio cartilaginea cranium suture OBOL:automatic articulatio cartilaginea suture of cranium OBOL:automatic cartilaginous joint cranial suture OBOL:automatic cartilaginous joint cranial sutures OBOL:automatic cartilaginous joint cranial sutures set OBOL:automatic cartilaginous joint cranium suture OBOL:automatic cartilaginous joint suture of cranium OBOL:automatic cranial suture of articulatio cartilaginea OBOL:automatic cranial suture of cartilaginous joint OBOL:automatic cranial sutures of articulatio cartilaginea OBOL:automatic cranial sutures of cartilaginous joint OBOL:automatic cranial sutures set of articulatio cartilaginea OBOL:automatic cranial sutures set of cartilaginous joint OBOL:automatic cranium suture of articulatio cartilaginea OBOL:automatic cranium suture of cartilaginous joint OBOL:automatic suture of cranium of articulatio cartilaginea OBOL:automatic suture of cranium of cartilaginous joint OBOL:automatic A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition]. EHDAA2:0004450 FMA:242815 MA:0000962 NCIT:C49248 UMLS:C1711323 chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle chorioid plexus of cerebral hemisphere epithelium of lateral ventricle choroid plexus epithelial tissue of lateral ventricle choroid plexus epithelium of lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle epithelial tissue of choroid plexus of lateral ventricle epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle epithelium of choroid plexus of lateral ventricle lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue lateral ventricle chorioid plexus of cerebral hemisphere epithelium lateral ventricle choroid plexus epithelial tissue lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere lateral ventricle epithelial tissue of choroid plexus lateral ventricle epithelium of chorioid plexus of cerebral hemisphere lateral ventricle epithelium of choroid plexus uberon UBERON:0004274 lateral ventricle choroid plexus epithelium A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition]. OBOL:automatic UMLS:C1711323 ncithesaurus:Choroid_Plexus_Epithelium_of_the_Lateral_Ventricle chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle OBOL:automatic chorioid plexus of cerebral hemisphere epithelium of lateral ventricle OBOL:automatic choroid plexus epithelial tissue of lateral ventricle OBOL:automatic choroid plexus epithelium of lateral ventricle OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic epithelial tissue of choroid plexus of lateral ventricle OBOL:automatic epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic epithelium of choroid plexus of lateral ventricle OBOL:automatic lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue OBOL:automatic lateral ventricle chorioid plexus of cerebral hemisphere epithelium OBOL:automatic lateral ventricle choroid plexus epithelial tissue OBOL:automatic lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic lateral ventricle epithelial tissue of choroid plexus OBOL:automatic lateral ventricle epithelium of chorioid plexus of cerebral hemisphere OBOL:automatic lateral ventricle epithelium of choroid plexus OBOL:automatic A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition]. FMA:242823 MA:0000984 NCIT:C49230 UMLS:C1707392 chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle chorioid plexus of cerebral hemisphere epithelium of fourth ventricle choroid plexus epithelial tissue of fourth ventricle choroid plexus epithelium of fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle epithelial tissue of choroid plexus of fourth ventricle epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle epithelium of choroid plexus of fourth ventricle fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue fourth ventricle chorioid plexus of cerebral hemisphere epithelium fourth ventricle choroid plexus epithelial tissue fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere fourth ventricle epithelial tissue of choroid plexus fourth ventricle epithelium of chorioid plexus of cerebral hemisphere fourth ventricle epithelium of choroid plexus uberon UBERON:0004276 fourth ventricle choroid plexus epithelium A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition]. OBOL:automatic UMLS:C1707392 ncithesaurus:Choroid_Plexus_Epithelium_of_the_Fourth_Ventricle chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle OBOL:automatic chorioid plexus of cerebral hemisphere epithelium of fourth ventricle OBOL:automatic choroid plexus epithelial tissue of fourth ventricle OBOL:automatic choroid plexus epithelium of fourth ventricle OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic epithelial tissue of choroid plexus of fourth ventricle OBOL:automatic epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic epithelium of choroid plexus of fourth ventricle OBOL:automatic fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue OBOL:automatic fourth ventricle chorioid plexus of cerebral hemisphere epithelium OBOL:automatic fourth ventricle choroid plexus epithelial tissue OBOL:automatic fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic fourth ventricle epithelial tissue of choroid plexus OBOL:automatic fourth ventricle epithelium of chorioid plexus of cerebral hemisphere OBOL:automatic fourth ventricle epithelium of choroid plexus OBOL:automatic A muscle that is part of the eye region. AAO:0000156 EMAPA:35335 MA:0000271 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA 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 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA VSAO:0000026 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]. 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. 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) 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 A nerve that is part of a parasympathetic nervous system [Automatically generated definition]. EHDAA2:0001401 EMAPA:17271 MA:0000224 VHOG:0000641 nerve of parasympathetic nervous system uberon UBERON:0004293 parasympathetic nerve NCBIBook:NBK10065 NCBIBook:NBK10065 A nerve that is part of a parasympathetic nervous system [Automatically generated definition]. OBOL:automatic nerve of parasympathetic nervous system OBOL:automatic A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. EMAPA:37582 MA:0001826 smooth muscle of lymph vessel of respiratory system uberon UBERON:0004296 respiratory system lymphatic vessel smooth muscle A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37582 MA:th smooth muscle of lymph vessel of respiratory system OBOL:automatic 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 A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]. A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG] Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] allantoic a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)] part_of embryo in EHDAA2 - note differences in humans BTO:0000474 EHDAA2:0001504 EMAPA:16107 EMAPA_RETIRED:16084 MESH:A16.254.403.147 NCIT:C34101 RETIRED_EHDAA2:0000114 UMLS:C0002084 VHOG:0000738 uberon allantoic bud UBERON:0004340 allantois EHDAA2-modified Hymans hindgut diverticulum endoderm ISBN:0073040584 ISBN:0073040584 A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]. VHOG:0000738 A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG] 2012-09-17 VHOG:0000738 VHOG 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:0000738 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 part_of embryo in EHDAA2 - note differences in humans EHDAA2 UMLS:C0002084 ncithesaurus:Allantois allantoic bud EMAPA:16107 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP] (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 EHDAA2:0001525 EHDAA:185 EMAPA:16072 FMA:293110 NCIT:C28402 UMLS:C0033153 VHOG:0001202 primitive streak - blastopore - germ ring uberon UBERON:0004341 primitive streak EHDAA2 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP] MP:0002231 (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001202 VHOG PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139 VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 VHOG UMLS:C0033153 ncithesaurus:Primitive_Streak primitive streak - blastopore - germ ring VHOG:0001202 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 (...) 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 BTO has this has part of the trophoblast BTO An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. Early outgrowth of presumptive limb.[AAO] AAO:0010375 BTO:0001640 EMAPA:35944 FMA:296780 GAID:1307 MESH:A16.254.462 NCIT:C34203 UMLS:C0282505 XAO:0003161 limb buds limbbud uberon gemmae membrorum UBERON:0004347 developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm limb bud ISBN:9780878932504 An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. ISBN:9780878932504 MP:0005650 Early outgrowth of presumptive limb.[AAO] 2012-06-20 AAO:0010375 AAO AAO:EJS UMLS:C0282505 ncithesaurus:Limb_Bud limb buds limbbud GO:0060174 gemmae membrorum 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 XAO:0004121 ZFA:0001702 apical epidermal ridge uberon AER crista ectodermalis apicalis UBERON:0004356 apical ectodermal ridge 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 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 UMLS:C1516037 ncithesaurus:Apical_Ectodermal_Ridge apical epidermal ridge XAO:0004121 AER MP:0001676 crista ectodermalis apicalis 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 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) 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 TAO:0001595 UMLS:C1517197 VHOG:0000296 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 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] 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) 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 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 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 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 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 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 aortic arch artery EMAPA:16684 arteriae arcuum pharyngeorum branchial aortic arches ZFA:0005004 ZFIN:ZDB-PUB-080512-6 pharyngeal arch arteries pharyngeal arch artery VHOG:0000122 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. 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 TAO:0002157 UMLS:C0011665 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 Cline et al lexical A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. MP:0004285 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 ORCiD:0000-0001-9114-8737 ZFIN:ZDB-PUB-061010-3 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 TAO:0002155 UMLS:C0229127 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 anterior limiting membrane ZFA:0001684 vascular network that is connected to the yolk sac. uberon omphalomesenteric system vitelline bloos vessel system vitelline system UBERON:0004374 vitelline vasculature vascular network that is connected to the yolk sac. omphalomesenteric system vitelline bloos vessel system vitelline system 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 The collection of all skeletal elements in an individual limb. Skeletal subdivision that is part of the limb.[VSAO] EHDAA2 considers hip and shoulder joints part of limb skeleton. EHDAA2:0002221 EMAPA:32702 VSAO:0000300 free limb skeleton limb skeleton set of bones of limb uberon UBERON:0004381 skeleton of limb The collection of all skeletal elements in an individual limb. Skeletal subdivision that is part of the limb.[VSAO] 2012-08-14 VSAO:0000300 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 EHDAA2 considers hip and shoulder joints part of limb skeleton. EHDAA2 free limb skeleton VSAO:0000300 limb skeleton EHDAA2:0002221 One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain. Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO] relationship loss: part_of internal carotid (AAO:0010219)[AAO] in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required AAO:0010493 BTO:0005205 CALOHA:TS-0126 EHDAA2:0000233 EHDAA:5294 EMAPA:18613 GAID:484 MA:0002562 MESH:D002536 NCIT:C12691 UMLS:C0007770 XAO:0000367 uberon UBERON:0004449 cerebral artery One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain. Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO] 2012-06-20 AAO:0010493 AAO AAO:BJB relationship loss: part_of internal carotid (AAO:0010219)[AAO] 2012-06-20 AAO:0010493 AAO in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required AAO UMLS:C0007770 ncithesaurus:Cerebral_Artery 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. 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. 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 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. 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 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 The collection of muscles that are part of the larynx. currently defined by location rather than attachment FMA:264611 FMA:46616 MESH:D007821 laryngeal muscles laryngeal muscles set muscle group of larynx set of laryngeal muscles set of muscles of larynx uberon UBERON:0004478 musculature of larynx The collection of muscles that are part of the larynx. laryngeal muscles FMA:46616 laryngeal muscles set FMA:46616 muscle group of larynx FMA:46616 set of laryngeal muscles FMA:46616 set of muscles of larynx FMA:264611 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 Any collection of muscles that is part of a limb [Automatically generated definition]. currently defined by location rather than attachment UBERON:0005635 EHDAA2:0000995 EMAPA:32700 FMA:50188 limb muscle system limb musculature muscle group of limb set of muscles of limb uberon UBERON:0004480 musculature of limb Any collection of muscles that is part of a limb [Automatically generated definition]. OBOL:automatic limb muscle system EHDAA2:0000995 limb musculature FMA:50188 muscle group of limb FMA:50188 set of muscles of limb FMA:50188 Any collection of muscles that is part of a forelimb [Automatically generated definition]. currently defined by location rather than attachment FMA:50396 free upper limb musculature muscle group of free upper limb musculature of free upper limb set of muscles of free upper limb uberon UBERON:0004481 musculature of upper limb Any collection of muscles that is part of a forelimb [Automatically generated definition]. OBOL:automatic free upper limb musculature FMA:50396 muscle group of free upper limb FMA:50396 musculature of free upper limb FMA:50396 set of muscles of free upper limb FMA:50396 Any collection of muscles that is part of a hindlimb [Automatically generated definition]. currently defined by location rather than attachment FMA:50399 free lower limb musculature muscle group of free lower limb musculature of free lower limb set of muscles of free lower limb uberon UBERON:0004482 musculature of lower limb Any collection of muscles that is part of a hindlimb [Automatically generated definition]. OBOL:automatic free lower limb musculature FMA:50399 muscle group of free lower limb FMA:50399 musculature of free lower limb FMA:50399 set of muscles of free lower limb FMA:50399 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 cardiac septum heart muscle cardiac septum muscle cardiac septum myocardium 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 portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition]. FMA:261045 FMA:261081 smooth muscle tissue of lobular bronchiole uberon UBERON:0004515 smooth muscle tissue of bronchiole A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition]. OBOL:automatic smooth muscle tissue of lobular bronchiole FMA:261081 A portion of smooth muscle tissue that is part of a terminal bronchiole [Automatically generated definition]. FMA:261051 uberon UBERON:0004516 smooth muscle tissue of terminal bronchiole A portion of smooth muscle tissue that is part of a terminal bronchiole [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. vertebral column muscle FMA:22594 A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition]. FMA:45716 uberon UBERON:0004520 striated muscle tissue of prostate A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition]. OBOL:automatic 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 projection or outgrowth of tissue from a larger body or organ. should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs) Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO] anatomical process process AAO:0010278 FMA:67601 HAO:0000822 NCIT:C61549 TAO:0001834 VSAO:0000180 XAO:0004020 galen:Ridge processus projection flange flanges lamella lamellae lamina laminae organ process papilla process of organ processes projection projections ridge ridges shelf shelves uberon anatomical protrusion protrusion spine UBERON:0004529 anatomical projection A projection or outgrowth of tissue from a larger body or organ. Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO] 2012-06-20 AAO:0010278 AAO AAO:BJB Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO] 2012-08-14 TAO:0001834 TAO TAO:wd Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO] 2012-08-14 VSAO:0000180 VSAO TAO:curator process VSAO:0000180 processus FMA:67601 FMA:TA flange VSAO:0000180 flanges VSAO:0000180 lamella VSAO:0000180 lamellae VSAO:0000180 lamina VSAO:0000180 laminae VSAO:0000180 processes VSAO:0000180 projection VSAO:0000180 projections VSAO:0000180 ridge VSAO:0000180 ridges VSAO:0000180 shelf VSAO:0000180 shelves VSAO:0000180 Anatomical projection that is composed of bone tissue. FMA:75433 ZFA:0001637 bone process projection of bone uberon bony projections UBERON:0004530 bony projection Anatomical projection that is composed of bone tissue. VSAO:wd bone process FMA:75433 bony projections ZFA:0001637 A testis that is in the left side of the genitalia [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37370 FMA:7212 MA:0001746 NCIT:C49323 UMLS:C0227998 left testicle uberon UBERON:0004533 left testis A testis that is in the left side of the genitalia [Automatically generated definition]. OBOL:automatic EMAPA:37370 MA:th UMLS:C0227998 ncithesaurus:Left_Testis left testicle MA:0001746 A testis that is in the right side of the genitalia [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37371 FMA:7211 MA:0001747 NCIT:C49326 OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA UMLS:C0227997 right testicle uberon UBERON:0004534 right testis A testis that is in the right side of the genitalia [Automatically generated definition]. OBOL:automatic EMAPA:37371 MA:th UMLS:C0227997 ncithesaurus:Right_Testis right testicle MA:0001747 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 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA 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 UMLS:C0007226 ncithesaurus:Cardiovascular_System CV system BTO:0000088 Herz und Gefaesssystem BTO:0000088 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep. consider merging with parent A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] FMA:63815 TAO:0005105 ZFA:0005105 lymphatic trunks and ducts lymphatic vasculature lymphatic vessel network lymphatic vessels set set of lymphatic vessels trunci et ductus lymphatici uberon lymph vessels UBERON:0004536 lymph vasculature A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep. ZFA:0005105 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] 2012-08-14 TAO:0005105 TAO ZFIN:curator lymphatic trunks and ducts FMA:63815 lymphatic vessels set FMA:63815 trunci et ductus lymphatici FMA:63815 FMA:TA lymph vessels ZFA:0005105 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 A vascular network consisting of blood vessels. blood vessels TAO:0001079 A kidney that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:36589 FMA:7205 MA:0001655 NCIT:C34006 UMLS:C0227614 uberon UBERON:0004538 left kidney A kidney that is part of a left side of organism [Automatically generated definition]. OBOL:automatic UMLS:C0227614 ncithesaurus:Left_Kidney A kidney that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:36590 FMA:7204 MA:0001683 NCIT:C34005 UMLS:C0227613 uberon UBERON:0004539 right kidney A kidney that is part of a right side of organism [Automatically generated definition]. OBOL:automatic UMLS:C0227613 ncithesaurus:Right_Kidney the layer of secretory cells which lines the epididymis BTO:0005768 CALOHA:TS-2063 EMAPA:30445 FMA:19153 MA:0002825 epididymis epithelium epithelium of epididymis uberon UBERON:0004544 epididymis epithelium the layer of secretory cells which lines the epididymis MGI:csmith MP:0004933 epididymis epithelium FMA:19153 epithelium of epididymis FMA:19153 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 left eyeball left orbital part of face left orbital region uberon UBERON:0004548 left eye 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 right eyeball right orbital part of face right orbital region uberon UBERON:0004549 right eye 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 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. 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 VHOG:0000273 uberon UBERON:0004572 arterial system MA 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] 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) 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 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. 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 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 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] 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) 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 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. 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) 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 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. 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 UMLS:C1706972 ncithesaurus:Blood_Vessel_Endothelium the connective tissue that surrounds the spleen EMAPA:35802 FMA:15849 MA:0000753 NCIT:C33598 UMLS:C0229681 Malpighian capsule capsula splenica capsule of spleen fibroelastic coat of spleen fibrous capsule of spleen splenic capsule tunica fibrosa (splen)(lien) tunica fibrosa splenica uberon UBERON:0004641 spleen capsule the connective tissue that surrounds the spleen MGI:cwg MP:0002227 UMLS:C0229681 ncithesaurus:Splenic_Capsule Malpighian capsule FMA:15849 capsula splenica FMA:15849 FMA:TA capsule of spleen FMA:15849 fibroelastic coat of spleen FMA:15849 fibrous capsule of spleen FMA:15849 splenic capsule FMA:15849 tunica fibrosa (splen)(lien) FMA:15849 tunica fibrosa splenica FMA:15849 FMA:TA 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 UMLS:C0227518 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 lobuli hepatis 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. 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 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 A muscular coat that is part of a seminal vesicle [Automatically generated definition]. EMAPA:29773 FMA:19404 MA:0002913 muscle layer of seminal vesicle muscular coat of seminal gland muscular layer of seminal gland tunica muscularis (vesicula seminalis) tunica muscularis glandulae vesiculosae uberon UBERON:0004665 muscular coat of seminal vesicle A muscular coat that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic muscle layer of seminal vesicle FMA:19404 muscular coat of seminal gland FMA:19404 muscular layer of seminal gland FMA:19404 tunica muscularis (vesicula seminalis) FMA:19404 tunica muscularis glandulae vesiculosae FMA:19404 FMA:TA 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 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 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 The muscular septum is the lower part of the ventricular septum[GO] GO:0003150 muscular septum GO:0003150 cardiac ventricular muscular septum 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 One of: the 4th ventricle median or lateral apertures. FMA:242766 MA:0002945 aperture of 4th ventricle aperture of fourth ventricle uberon UBERON:0004668 fourth ventricle aperture One of: the 4th ventricle median or lateral apertures. aperture of fourth ventricle FMA:242766 The sensory system for the sense of balance. The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system]. FMA and NIF have no part information for this class. This is a GAT in FMA BTO:0003381 EMAPA:37986 FMA:7193 NLXANAT:090819 vestibular organ system vestibular system equilibrioception system vestibulomotor system uberon UBERON:0004681 vestibular system The sensory system for the sense of balance. NLXANAT:090819 The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system]. FMA and NIF have no part information for this class. This is a GAT in FMA FMA EMAPA:37986 MA:th vestibular organ system FMA:7193 vestibular system NLXANAT:090819 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:A08.186.211.132.659.632 NCIT:C97335 NLXANAT:20090205 TAO:0001429 UMLS:C0034671 ZFA:0001429 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 GO Wikipedia The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. NLXANAT:20090205 UMLS:C0034671 ncithesaurus:Raphe_Nuclei nuclei raphes FMA:84017 FMA:TA raphe nuclei FMA:84017 raphe nuclei NLXANAT:20090205 raphe nuclei set FMA:84017 nuclei raphes raphe cluster 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 costocervical trunk trunk of costocervical artery uberon truncus costocervicalis UBERON:0004688 costo-cervical trunk 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 MA:th costocervical trunk FMA:10636 trunk of costocervical artery FMA:10636 truncus costocervicalis 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) 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 UMLS:C1284055 primitive right ventricle endocardium uberon UBERON:0004706 bulbus cordis 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 JB:def A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities. Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001) DrerDO:0000052 EFO:0001310 OGES:000006 ZFS:0000050 phylotypic stage uberon pharyngula UBERON:0004707 pharyngula stage A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities. 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 girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage 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 pelvic appendage VSAO:0000126 pelvic limb/fin 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) anterior limb/fin anterior paired appendage VSAO:0000148 forelimb - pectoral fin VHOG:0001753 forelimb or pectoral fin forelimb/pectoral fin pectoral limb/fin 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 UMLS:C0022427 uberon jugular vena jugularis UBERON:0004711 jugular vein The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. 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 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 UMLS:C1516779 ncithesaurus:Conceptus 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] Melissa Haendel 2009-06-18T09:00:04Z NLX:147842 TAO:0001328 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). A metameric segment of the central nervous system.[ZFA] 2012-08-14 TAO:0001328 TAO ZFIN:curator neural tube metameric segment 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) FBbt:00005140 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 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:A16.254.412 MIAA:0000179 NCIT:C34057 NCIT:C34058 UMLS:C0017199 UMLS:C1284022 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. We explicitly merge the NCITA terms here NCIT UMLS:C0017199 ncithesaurus:Gastrula UMLS:C1284022 ncithesaurus:Trilaminar_Embryonic_Disc gastrula embryo BILA:0000060 blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition]. VHOG:0000983 collecting duct of metanephros uberon metanephric collecting tubule UBERON:0004737 metanephric collecting duct true Wikipedia-abduced A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition]. OBOL:automatic metanephric collecting tubule VHOG:0000983 The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO] Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO] The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG] relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO] Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG] In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular. AAO:0000124 EFO:0003508 TAO:0000191 VHOG:0001022 ZFA:0000191 dentaries dentary bone uberon dentale os dentale sur-angulaire UBERON:0004742 dentary ZFA mandibular series ISBN:0073040584 ZFA EHDAA2 EHDAA2-modified The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. VHOG:0001022 Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO] 2012-08-14 TAO:0000191 TAO TAO:GA_TG Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO] 2012-06-20 AAO:0000124 AAO AAO:LAP The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG] 2012-09-17 VHOG:0001022 VHOG relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO] 2012-08-14 TAO:0000191 TAO Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG] 2012-09-17 VHOG:0001022 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248 dentaries TAO:0000191 dentary bone ZFA:0000191 dentale AAO:0000124 os dentale AAO:0000124 sur-angulaire AAO:0000124 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 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 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 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. 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 UMLS:C0162322 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 UMLS:C0162322 ncithesaurus:Anal_Gland gland of anal canal OBOL:automatic anal sac 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 UMLS:C1516496 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]. 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 neurocranium 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. 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 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 Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 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 submucosa that is part of a larynx [Automatically generated definition]. EMAPA:35474 FMA:321584 MA:0002728 submucosa of larynx uberon laryngeal submucosa UBERON:0004778 larynx submucosa A submucosa that is part of a larynx [Automatically generated definition]. OBOL:automatic submucosa of larynx OBOL:automatic laryngeal submucosa EMAPA:35474 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 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 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 mucosa gallbladder lamina propria 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 gall bladder lamina propria true A lamina propria that is part of a gallbladder [Automatically generated definition]. OBOL:automatic UMLS:C1708175 ncithesaurus:Gallbladder_Lamina_Propria gall bladder lamina propria mucosa OBOL:automatic gallbladder lamina propria OBOL:automatic gallbladder 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 gall bladder serous membrane gallbladder serosa 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 gall bladder serosa A serous membrane that is part of a gallbladder [Automatically generated definition]. OBOL:automatic gall bladder serous membrane OBOL:automatic gallbladder 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 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 BTO-modified A mucosa that is part of a gastrointestinal system. OBOL:automatic digestive tract mucosa gut mucosa BTO:0000546 gut mucuous membrane mucosa of gut A mucous gland that is part of a larynx [Automatically generated definition]. EMAPA:37631 MA:0001767 mucous gland of larynx uberon UBERON:0004789 larynx mucous gland A mucous gland that is part of a larynx [Automatically generated definition]. OBOL:automatic EMAPA:37631 MA:th mucous gland of larynx OBOL:automatic 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. 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 A bodily secretion that is produced by the prostate gland. Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline. A secretion of the prostate this is slightly alkaline fluid, milky or white in appearance. Usually constitutes 20-30% of the volume of the semen along with spermatozoa and seminal vesicle fluid [Wikipedia:Prostate#Secretions] UBERON:0010142 EMAPA:36545 FMA:66884 MA:0002525 NCIT:C52553 UMLS:C1709733 prostate secretion prostatic fluid secretion of prostate secretion of prostate gland uberon prostate fluid UBERON:0004796 prostate gland secretion FMA A bodily secretion that is produced by the prostate gland. UMLS:C1709733 ncithesaurus:Prostate_Gland_Secretion prostate secretion OBOL:automatic prostatic fluid FMA:66884 secretion of prostate OBOL:automatic secretion of prostate gland OBOL:automatic prostate fluid BTO:0001232 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 Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. An epithelium that is part of a uterine cervix [Automatically generated definition]. The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium BTO:0000241 CALOHA:TS-0137 EFO:0001913 EMAPA:29929 MA:0001724 NCIT:C49218 UMLS:C1711358 cervical canal epithelial tissue cervical canal epithelium cervical epithelium cervix epithelial tissue epithelium of cervix uberon UBERON:0004801 cervix epithelium An epithelium that is part of a uterine cervix [Automatically generated definition]. OBOL:automatic The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium UMLS:C1711358 ncithesaurus:Cervix_Epithelium cervical canal epithelial tissue OBOL:automatic cervical canal epithelium OBOL:automatic cervical epithelium BTO:0000241 cervix epithelial tissue OBOL:automatic epithelium of cervix OBOL:automatic 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 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 penis [Automatically generated definition]. EHDAA2:0004039 EMAPA:35674 MA:0001742 epithelial tissue of penis epithelium of penis penis epithelial tissue uberon UBERON:0004803 penis epithelium An epithelium that is part of a penis [Automatically generated definition]. OBOL:automatic epithelial tissue of penis OBOL:automatic epithelium of penis OBOL:automatic penis epithelial tissue OBOL:automatic An epithelium that is part of a oviduct [Automatically generated definition]. in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label BTO:0002402 CALOHA:TS-1316 EMAPA:29043 MA:0001718 epithelial tissue of oviduct epithelium of fallopian tube epithelium of oviduct epithelium of uterine tube oviduct epithelial tissue uberon columnar epithelium of the fallopian tube columnar epithelium of the oviduct fallopian tube epithelium UBERON:0004804 oviduct epithelium An epithelium that is part of a oviduct [Automatically generated definition]. OBOL:automatic in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA epithelial tissue of oviduct OBOL:automatic epithelium of fallopian tube OBOL:automatic epithelium of oviduct OBOL:automatic epithelium of uterine tube FMA:62016 oviduct epithelial tissue OBOL:automatic columnar epithelium of the fallopian tube BTO:0002402 columnar epithelium of the oviduct BTO:0002402 fallopian tube epithelium BTO:0002402 An epithelium that is part of a seminal vesicle [Automatically generated definition]. CALOHA:TS-2069 EMAPA:29771 MA:0001745 NCIT:C49295 UMLS:C1710049 epithelial tissue of seminal gland epithelial tissue of seminal vesicle epithelium of seminal gland epithelium of seminal vesicle seminal gland epithelial tissue seminal gland epithelium seminal vesicle epithelial tissue uberon UBERON:0004805 seminal vesicle epithelium An epithelium that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic UMLS:C1710049 ncithesaurus:Seminal_Vesicle_Epithelium epithelial tissue of seminal gland OBOL:automatic epithelial tissue of seminal vesicle OBOL:automatic epithelium of seminal gland OBOL:automatic epithelium of seminal vesicle OBOL:automatic seminal gland epithelial tissue OBOL:automatic seminal gland epithelium OBOL:automatic seminal vesicle epithelial tissue OBOL:automatic An epithelium that is part of a vas deferens [Automatically generated definition]. EMAPA:29274 FMA:225317 MA:0001749 NCIT:C49315 UMLS:C1710617 deferent duct epithelial tissue deferent duct epithelium ductus deferens epithelial tissue ductus deferens epithelium epithelial tissue of deferent duct epithelial tissue of ductus deferens epithelial tissue of sperm duct epithelial tissue of vas deferen epithelial tissue of vas deferens epithelium of deferent duct epithelium of ductus deferens epithelium of sperm duct epithelium of vas deferen epithelium of vas deferens sperm duct epithelial tissue sperm duct epithelium vas deferen epithelial tissue vas deferen epithelium vas deferens epithelial tissue uberon UBERON:0004806 vas deferens epithelium An epithelium that is part of a vas deferens [Automatically generated definition]. OBOL:automatic UMLS:C1710617 ncithesaurus:Vas_Deferens_Epithelium deferent duct epithelial tissue OBOL:automatic deferent duct epithelium OBOL:automatic ductus deferens epithelial tissue OBOL:automatic ductus deferens epithelium OBOL:automatic epithelial tissue of deferent duct OBOL:automatic epithelial tissue of ductus deferens OBOL:automatic epithelial tissue of sperm duct OBOL:automatic epithelial tissue of vas deferen OBOL:automatic epithelial tissue of vas deferens OBOL:automatic epithelium of deferent duct OBOL:automatic epithelium of ductus deferens OBOL:automatic epithelium of sperm duct OBOL:automatic epithelium of vas deferen OBOL:automatic epithelium of vas deferens OBOL:automatic sperm duct epithelial tissue OBOL:automatic sperm duct epithelium OBOL:automatic vas deferen epithelial tissue OBOL:automatic vas deferen epithelium OBOL:automatic vas deferens epithelial tissue OBOL:automatic 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 salivary gland [Automatically generated definition]. BTO:0004421 CALOHA:TS-2067 EMAPA:32816 MA:0001587 epithelial tissue of salivary gland epithelium of salivary gland salivary gland epithelial tissue uberon UBERON:0004809 salivary gland epithelium An epithelium that is part of a salivary gland [Automatically generated definition]. OBOL:automatic epithelial tissue of salivary gland OBOL:automatic epithelium of salivary gland OBOL:automatic salivary gland epithelial tissue OBOL:automatic the cellular avascular layer of the renal tubule luminar surfaces See https://github.com/obophenotype/uberon/issues/1305 BTO:0005239 EMAPA:36524 MA:0001681 NCIT:C49276 UMLS:C1709902 kidney tubule epithelium uberon UBERON:0004810 nephron tubule epithelium the cellular avascular layer of the renal tubule luminar surfaces MGI:csmith MP:0009640 UMLS:C1709902 ncithesaurus:Renal_Tubule_Epithelium kidney tubule epithelium MA:0001681 An epithelium that is part of an endometrium [Automatically generated definition]. In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) EMAPA:35307 MA:0002731 endometrium epithelial tissue epithelial tissue of endometrium epithelium of endometrium epithelium of tunica mucosa of endometrium uberon uterine epithelium UBERON:0004811 endometrium epithelium An epithelium that is part of an endometrium [Automatically generated definition]. OBOL:automatic In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) endometrium epithelial tissue OBOL:automatic epithelial tissue of endometrium OBOL:automatic epithelium of endometrium OBOL:automatic epithelium of tunica mucosa of endometrium OBOL:automatic uterine epithelium the stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule BTO:0001811 CALOHA:TS-0920 EHDAA:8148 EMAPA:35761 FMA:19885 GAID:401 MA:0001748 MESH:D012670 NCIT:C49296 RETIRED_EHDAA2:0002009 UMLS:C0036629 VHOG:0000631 epithelial tissue of seminiferous tubule epithelial tissue of seminiferous tubule of testis epithelium of seminiferous tubule epithelium of seminiferous tubule of testis germinal epithelium (male) male germinal epithelium seminiferous epithelium seminiferous tubule epithelial tissue testis germinal epithelium wall of seminiferous tubule uberon UBERON:0004813 seminiferous tubule epithelium the stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule MGI:csmith MP:0011750 UMLS:C0036629 ncithesaurus:Seminiferous_Epithelium epithelial tissue of seminiferous tubule OBOL:automatic epithelial tissue of seminiferous tubule of testis OBOL:automatic epithelium of seminiferous tubule OBOL:automatic epithelium of seminiferous tubule of testis OBOL:automatic germinal epithelium (male) male germinal epithelium seminiferous epithelium BTO:0001811 seminiferous tubule epithelial tissue OBOL:automatic testis germinal epithelium VHOG:0000631 wall of seminiferous tubule An epithelium that is part of a upper respiratory tract [Automatically generated definition]. EMAPA:35894 MA:0001912 epithelial tissue of upper respiratory tract epithelium of upper respiratory tract upper respiratory tract epithelial tissue uberon UBERON:0004814 upper respiratory tract epithelium An epithelium that is part of a upper respiratory tract [Automatically generated definition]. OBOL:automatic epithelial tissue of upper respiratory tract OBOL:automatic epithelium of upper respiratory tract OBOL:automatic upper respiratory tract 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 An epithelium that is part of a larynx [Automatically generated definition]. composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0] EHDAA2:0004065 EMAPA:35472 MA:0001765 NCIT:C49247 UMLS:C0751258 epithelial tissue of larynx epithelium of larynx laryngeal epithelium larynx epithelial tissue uberon UBERON:0004816 larynx epithelium An epithelium that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C0751258 ncithesaurus:Laryngeal_Epithelium epithelial tissue of larynx OBOL:automatic epithelium of larynx OBOL:automatic laryngeal epithelium OBOL:automatic larynx epithelial tissue OBOL:automatic An epithelium that is part of a lacrimal gland [Automatically generated definition]. EMAPA:36515 MA:0001297 epithelial tissue of lacrimal gland epithelium of lacrimal gland lacrimal gland epithelial tissue uberon UBERON:0004817 lacrimal gland epithelium An epithelium that is part of a lacrimal gland [Automatically generated definition]. OBOL:automatic epithelial tissue of lacrimal gland OBOL:automatic epithelium of lacrimal gland OBOL:automatic lacrimal gland epithelial tissue OBOL:automatic the cellular avascular layer of the kidney luminar surfaces BTO:0000059 CALOHA:TS-0505 EMAPA:35457 MA:0002846 epithelial tissue of kidney epithelium of kidney kidney epithelial tissue uberon renal epithelium UBERON:0004819 kidney epithelium the cellular avascular layer of the kidney luminar surfaces MGI:csmith MP:0004967 epithelial tissue of kidney OBOL:automatic epithelium of kidney OBOL:automatic kidney epithelial tissue OBOL:automatic renal epithelium EMAPA:35457 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. 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 medulla that is part of a thyroid [Automatically generated definition]. EMAPA:37768 MA:0000132 medulla of thyroid medulla of thyroid follicle medulla of thyroid gland medulla of thyroid gland follicle thyroid follicle medulla thyroid gland follicle medulla thyroid medulla uberon UBERON:0004827 thyroid gland medulla A medulla that is part of a thyroid [Automatically generated definition]. OBOL:automatic EMAPA:37768 MA:th medulla of thyroid OBOL:automatic medulla of thyroid follicle OBOL:automatic medulla of thyroid gland OBOL:automatic medulla of thyroid gland follicle OBOL:automatic thyroid follicle medulla OBOL:automatic thyroid gland follicle medulla OBOL:automatic thyroid medulla OBOL:automatic A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. EMAPA:37788 MA:0001690 skeletal muscle of urethra skeletal muscle tissue of urethra urethra skeletal muscle tissue uberon urethra skeletal muscle urethral skeletal muscle UBERON:0004829 urethra skeletal muscle tissue A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. OBOL:automatic EMAPA:37788 MA:th skeletal muscle of urethra OBOL:automatic skeletal muscle tissue of urethra OBOL:automatic urethra skeletal muscle tissue OBOL:automatic urethra skeletal muscle MA:0001690 urethral skeletal muscle MA:0001690 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. EMAPA:37598 MA:th A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition]. EMAPA:30747 MA:0001736 epididymis involuntary muscle epididymis non-striated muscle epididymis smooth muscle tissue involuntary muscle of epididymis non-striated muscle of epididymis smooth muscle of epididymis smooth muscle tissue of epididymis uberon UBERON:0004835 epididymis smooth muscle A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition]. OBOL:automatic epididymis involuntary muscle OBOL:automatic epididymis non-striated muscle OBOL:automatic epididymis smooth muscle tissue OBOL:automatic involuntary muscle of epididymis OBOL:automatic non-striated muscle of epididymis OBOL:automatic smooth muscle of epididymis OBOL:automatic smooth muscle tissue of epididymis OBOL:automatic 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 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 An endothelium that is part of a lymph node [Automatically generated definition]. EMAPA:35526 MA:0000741 endothelium of lymph node uberon UBERON:0004850 lymph node endothelium An endothelium that is part of a lymph node [Automatically generated definition]. OBOL:automatic endothelium of lymph node 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. 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 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. eye-associated gland 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 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 Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]. check BILA AAO:0011100 BILA:0000047 FMA:295570 XAO:0000271 outer layer of lateral plate mesoderm uberon parietal mesoderm somatic mesoderm UBERON:0004871 somatic layer of lateral plate mesoderm Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]. parietal mesoderm ISBN:9780878932504 somatic mesoderm BILA:0000047 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 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]. We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors BILA visceral mesoderm BILA:0000044 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 uberon ventral splanchnic mesoderm UBERON:0004873 splanchnopleure 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]. UMLS:C1519472 ncithesaurus:Splanchnopleure ventral splanchnic mesoderm 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 uberon UBERON:0004874 somatopleure 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]. UMLS:C1519423 ncithesaurus:Somatopleure A portion of the urogenital ridge which is the source of much of the urinary system[WP]. FMA:72168 NCIT:C34219 UMLS:C1283944 uberon chorda nephrogenica UBERON:0004875 part_of or develops_from urogenital ridge? nephrogenic cord A portion of the urogenital ridge which is the source of much of the urinary system[WP]. UMLS:C1283944 ncithesaurus:Nephrogenic_Cord chorda nephrogenica One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] EHDAA2:0004022 EMAPA:30888 FMA:321919 urethral fold urogenital fold uberon urogenital ridge UBERON:0004876 urogenital fold EHDAA2 Wikipedia EHDAA2 One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. MP:0011835 MP:anna urethral fold EMAPA:30888 urogenital fold EHDAA2:0004022 MP:0011835 urogenital ridge MP:0011835 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 Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 axial chorda mesoderm ZFA:0000091 dorsal mesoderm 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 The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra we follow EHDAA2 in dividing the UGS into epithelium and lumen EHDAA2:0004061 EMAPA:31509 UGE epithelium of urogenital sinus uberon UBERON:0004902 urogenital sinus epithelium The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra we follow EHDAA2 in dividing the UGS into epithelium and lumen EHDAA2 UGE epithelium of urogenital sinus OBOL:automatic 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 optic nerve BTO:0000966 Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint uberon UBERON:0004905 articulation Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. 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 UMLS:C0226875 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]. 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 UMLS:C0226874 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. 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 FBbt:00004859 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 a testis. 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:0001364 EMAPA:17973 FBbt:00004955 testis epithelium testis sheath uberon UBERON:0004910 epithelium of male gonad An epithelium surrounding a testis. OBOL:automatic testis epithelium OBOL:automatic testis sheath FBbt:00004955 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 FBbt:00004896 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 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:A03.159.183.079.300.900 NCIT:C13011 TAO:0005167 UMLS:C0042425 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 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] 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 ampulla hepatopancreatica 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 papilla duodenalis papilla of duodenum uberon papilla duodeni UBERON:0004914 duodenal papilla 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. papilla duodeni 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:A03.159.183.079.300.900.600 NCIT:C13065 UMLS:C0028872 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 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]. 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 sphincter muscle surrounding the urethra. EMAPA:37789 MA:0002650 sphincter muscle of urethra sphincter of urethra sphincter urethrae urethral sphincter muscle uberon UBERON:0004917 urethral sphincter A sphincter muscle surrounding the urethra. EMAPA:37789 MA:th 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 intestinal tract segment of intestinal tract subdivision of alimentary system UBERON:0004921 subdivision of digestive tract A proximal-distal subdivision of the digestive tract. alimentary system subdivision FMA:71131 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. The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 FMA:75144 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 hypopharynx [Automatically generated definition]. FMA:55072 hypopharynx submucosa laryngeal pharynx submucosa laryngopharynx submucosa submucosa of hypopharynx submucosa of laryngeal pharynx tela submucosa (pars laryngea pharyngis) uberon UBERON:0004925 submucosa of laryngopharynx A submucosa that is part of a hypopharynx [Automatically generated definition]. OBOL:automatic hypopharynx submucosa OBOL:automatic laryngeal pharynx submucosa OBOL:automatic laryngopharynx submucosa OBOL:automatic submucosa of hypopharynx OBOL:automatic submucosa of laryngeal pharynx OBOL:automatic tela submucosa (pars laryngea pharyngis) FMA:55072 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 cecum [Automatically generated definition]. FMA:14999 caecum submucosa cecum submucosa intestinum crassum caecum submucosa submucosa of caecum submucosa of intestinum crassum caecum uberon UBERON:0004927 submucosa of cecum A submucosa that is part of a cecum [Automatically generated definition]. OBOL:automatic caecum submucosa OBOL:automatic cecum submucosa OBOL:automatic intestinum crassum caecum submucosa OBOL:automatic submucosa of caecum OBOL:automatic submucosa of intestinum crassum caecum OBOL:automatic A submucosa that is part of an appendix [Automatically generated definition]. FMA:14992 appendiceal submucosa appendix submucosa caecal appendix submucosa submucosa of caecal appendix submucosa of vermiform appendix submucosa of vermix vermiform appendix submucosa vermix submucosa uberon UBERON:0004928 submucosa of appendix A submucosa that is part of an appendix [Automatically generated definition]. OBOL:automatic appendiceal submucosa FMA:14992 appendix submucosa OBOL:automatic caecal appendix submucosa OBOL:automatic submucosa of caecal appendix OBOL:automatic submucosa of vermiform appendix OBOL:automatic submucosa of vermix OBOL:automatic vermiform appendix submucosa OBOL:automatic vermix submucosa OBOL:automatic A submucosa that is part of an ascending colon [Automatically generated definition]. FMA:15006 ascending colon submucosa uberon UBERON:0004929 submucosa of ascending colon A submucosa that is part of an ascending colon [Automatically generated definition]. OBOL:automatic ascending colon submucosa OBOL:automatic A submucosa that is part of a transverse colon [Automatically generated definition]. FMA:15013 transverse colon submucosa uberon UBERON:0004930 submucosa of transverse colon A submucosa that is part of a transverse colon [Automatically generated definition]. OBOL:automatic transverse colon submucosa OBOL:automatic A submucosa that is part of a descending colon [Automatically generated definition]. FMA:15020 descending colon submucosa uberon UBERON:0004931 submucosa of descending colon A submucosa that is part of a descending colon [Automatically generated definition]. OBOL:automatic descending colon submucosa OBOL:automatic 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 pylorus submucosa 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 The submucous layer of the wall of the urinary bladder. BTO:0002117 EMAPA:32275 FMA:15929 bladder submucosa submucosa of bladder tela submucosa (vesica urinaria) tela submucosa vesicae tela submucosa vesicae urinariae urinary bladder submucosa uberon submucous layer of urinary bladder UBERON:0004943 submucosa of urinary bladder The submucous layer of the wall of the urinary bladder. BTO:0002117 bladder submucosa OBOL:automatic submucosa of bladder OBOL:automatic tela submucosa (vesica urinaria) FMA:15929 FMA:TA tela submucosa vesicae FMA:15929 FMA:TA tela submucosa vesicae urinariae BTO:0002117 urinary bladder submucosa OBOL:automatic submucous layer of urinary bladder BTO:0002117 A submucosa that is part of a neck of urinary bladder [Automatically generated definition]. EMAPA:32276 FMA:17851 bladder neck submucosa neck of bladder submucosa neck of urinary bladder submucosa submucosa of bladder neck submucosa of neck of bladder submucosa of urinary bladder neck submucosa of vesical neck urinary bladder neck submucosa vesical neck submucosa uberon UBERON:0004945 submucosa of neck of urinary bladder A submucosa that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck submucosa OBOL:automatic neck of bladder submucosa OBOL:automatic neck of urinary bladder submucosa OBOL:automatic submucosa of bladder neck OBOL:automatic submucosa of neck of bladder OBOL:automatic submucosa of urinary bladder neck OBOL:automatic submucosa of vesical neck OBOL:automatic urinary bladder neck submucosa OBOL:automatic vesical neck submucosa OBOL:automatic A submucosa that is part of a bronchiole [Automatically generated definition]. FMA:62775 bronchiole submucosa lobular bronchiole submucosa submucosa of lobular bronchiole uberon UBERON:0004952 submucosa of bronchiole A submucosa that is part of a bronchiole [Automatically generated definition]. OBOL:automatic bronchiole submucosa OBOL:automatic lobular bronchiole submucosa OBOL:automatic submucosa of lobular bronchiole OBOL:automatic A mucosa that is part of a ureter [Automatically generated definition]. FMA:15894 galen:MucousMembraneOfUreter mucosa of organ of ureter mucosal layer of ureter mucous membrane of ureter organ mucosa of ureter tunica mucosa (ureter) tunica mucosa ureteris ureter mucosa ureter mucosa of organ ureter mucous membrane ureter organ mucosa ureteral mucosa ureteric mucosa uberon UBERON:0004980 mucosa of ureter A mucosa that is part of a ureter [Automatically generated definition]. OBOL:automatic mucosa of organ of ureter OBOL:automatic mucosal layer of ureter FMA:15894 mucous membrane of ureter OBOL:automatic organ mucosa of ureter OBOL:automatic tunica mucosa (ureter) FMA:15894 tunica mucosa ureteris FMA:15894 FMA:TA ureter mucosa OBOL:automatic ureter mucosa of organ OBOL:automatic ureter mucous membrane OBOL:automatic ureter organ mucosa OBOL:automatic ureteral mucosa FMA:15894 ureteric mucosa FMA:15894 A mucosa that is part of a vagina [Automatically generated definition]. BTO:0005676 FMA:19975 mucosa of organ of vagina mucous membrane of vagina organ mucosa of vagina tunica mucosa vaginae vagina mucosa vagina mucosa of organ vagina mucous membrane vagina organ mucosa vaginal mucosa uberon UBERON:0004983 mucosa of vagina A mucosa that is part of a vagina [Automatically generated definition]. OBOL:automatic mucosa of organ of vagina OBOL:automatic mucous membrane of vagina OBOL:automatic organ mucosa of vagina OBOL:automatic tunica mucosa vaginae FMA:19975 FMA:TA vagina mucosa OBOL:automatic vagina mucosa of organ OBOL:automatic vagina mucous membrane OBOL:automatic vagina organ mucosa OBOL:automatic vaginal mucosa FMA:19975 A mucosa that is part of a seminal vesicle [Automatically generated definition]. FMA:19405 mucosa of organ of seminal gland mucosa of organ of seminal vesicle mucosa of seminal gland mucous membrane of seminal gland mucous membrane of seminal vesicle organ mucosa of seminal gland organ mucosa of seminal vesicle seminal gland mucosa seminal gland mucosa of organ seminal gland mucous membrane seminal gland organ mucosa seminal vesicle mucosa seminal vesicle mucosa of organ seminal vesicle mucous membrane seminal vesicle organ mucosa tunica mucosa glandulae vesiculosae uberon UBERON:0004984 mucosa of seminal vesicle A mucosa that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic mucosa of organ of seminal gland OBOL:automatic mucosa of organ of seminal vesicle OBOL:automatic mucosa of seminal gland OBOL:automatic mucous membrane of seminal gland OBOL:automatic mucous membrane of seminal vesicle OBOL:automatic organ mucosa of seminal gland OBOL:automatic organ mucosa of seminal vesicle OBOL:automatic seminal gland mucosa OBOL:automatic seminal gland mucosa of organ OBOL:automatic seminal gland mucous membrane OBOL:automatic seminal gland organ mucosa OBOL:automatic seminal vesicle mucosa OBOL:automatic seminal vesicle mucosa of organ OBOL:automatic seminal vesicle mucous membrane OBOL:automatic seminal vesicle organ mucosa OBOL:automatic tunica mucosa glandulae vesiculosae FMA:19405 FMA:TA A mucosa that is part of a ejaculatory duct [Automatically generated definition]. FMA:19373 ejaculatory duct mucosa ejaculatory duct mucosa of organ ejaculatory duct mucous membrane ejaculatory duct organ mucosa ejaculatory ductal mucosa mucosa of organ of ejaculatory duct mucous membrane of ejaculatory duct organ mucosa of ejaculatory duct uberon UBERON:0004985 mucosa of ejaculatory duct A mucosa that is part of a ejaculatory duct [Automatically generated definition]. OBOL:automatic ejaculatory duct mucosa OBOL:automatic ejaculatory duct mucosa of organ OBOL:automatic ejaculatory duct mucous membrane OBOL:automatic ejaculatory duct organ mucosa OBOL:automatic ejaculatory ductal mucosa FMA:19373 mucosa of organ of ejaculatory duct OBOL:automatic mucous membrane of ejaculatory duct OBOL:automatic organ mucosa of ejaculatory duct OBOL:automatic A mucosa that is part of a vas deferens [Automatically generated definition]. FMA:19240 deferent duct mucosa deferent duct mucosa of organ deferent duct mucous membrane deferent duct organ mucosa deferent ductal mucosa ductus deferens mucosa ductus deferens mucosa of organ ductus deferens mucous membrane ductus deferens organ mucosa mucosa of ductus deferens mucosa of organ of deferent duct mucosa of organ of ductus deferens mucosa of organ of sperm duct mucosa of organ of vas deferen mucosa of organ of vas deferens mucosa of sperm duct mucosa of vas deferen mucosa of vas deferens mucous membrane of deferent duct mucous membrane of ductus deferens mucous membrane of sperm duct mucous membrane of vas deferen mucous membrane of vas deferens organ mucosa of deferent duct organ mucosa of ductus deferens organ mucosa of sperm duct organ mucosa of vas deferen organ mucosa of vas deferens sperm duct mucosa sperm duct mucosa of organ sperm duct mucous membrane sperm duct organ mucosa tunica mucosa (ductus deferens) tunica mucosa ductus deferentis vas deferen mucosa vas deferen mucosa of organ vas deferen mucous membrane vas deferen organ mucosa vas deferens mucosa vas deferens mucosa of organ vas deferens mucous membrane vas deferens organ mucosa uberon UBERON:0004986 mucosa of deferent duct A mucosa that is part of a vas deferens [Automatically generated definition]. OBOL:automatic deferent duct mucosa OBOL:automatic deferent duct mucosa of organ OBOL:automatic deferent duct mucous membrane OBOL:automatic deferent duct organ mucosa OBOL:automatic deferent ductal mucosa FMA:19240 ductus deferens mucosa OBOL:automatic ductus deferens mucosa of organ OBOL:automatic ductus deferens mucous membrane OBOL:automatic ductus deferens organ mucosa OBOL:automatic mucosa of ductus deferens OBOL:automatic mucosa of organ of deferent duct OBOL:automatic mucosa of organ of ductus deferens OBOL:automatic mucosa of organ of sperm duct OBOL:automatic mucosa of organ of vas deferen OBOL:automatic mucosa of organ of vas deferens OBOL:automatic mucosa of sperm duct OBOL:automatic mucosa of vas deferen OBOL:automatic mucosa of vas deferens OBOL:automatic mucous membrane of deferent duct OBOL:automatic mucous membrane of ductus deferens OBOL:automatic mucous membrane of sperm duct OBOL:automatic mucous membrane of vas deferen OBOL:automatic mucous membrane of vas deferens OBOL:automatic organ mucosa of deferent duct OBOL:automatic organ mucosa of ductus deferens OBOL:automatic organ mucosa of sperm duct OBOL:automatic organ mucosa of vas deferen OBOL:automatic organ mucosa of vas deferens OBOL:automatic sperm duct mucosa OBOL:automatic sperm duct mucosa of organ OBOL:automatic sperm duct mucous membrane OBOL:automatic sperm duct organ mucosa OBOL:automatic tunica mucosa (ductus deferens) FMA:19240 tunica mucosa ductus deferentis FMA:19240 FMA:TA vas deferen mucosa OBOL:automatic vas deferen mucosa of organ OBOL:automatic vas deferen mucous membrane OBOL:automatic vas deferen organ mucosa OBOL:automatic vas deferens mucosa OBOL:automatic vas deferens mucosa of organ OBOL:automatic vas deferens mucous membrane OBOL:automatic vas deferens organ mucosa OBOL:automatic A mucosa that is part of a hypopharynx [Automatically generated definition]. FMA:55030 hypopharynx mucosa hypopharynx mucosa of organ hypopharynx mucous membrane hypopharynx organ mucosa laryngeal pharynx mucosa laryngeal pharynx mucosa of organ laryngeal pharynx mucous membrane laryngeal pharynx organ mucosa laryngopharynx mucosa laryngopharynx mucosa of organ laryngopharynx mucous membrane laryngopharynx organ mucosa mucosa of hypopharynx mucosa of laryngeal pharynx mucosa of organ of hypopharynx mucosa of organ of laryngeal pharynx mucosa of organ of laryngopharynx mucous membrane of hypopharynx mucous membrane of laryngeal pharynx mucous membrane of laryngopharynx organ mucosa of hypopharynx organ mucosa of laryngeal pharynx organ mucosa of laryngopharynx uberon UBERON:0004987 mucosa of laryngopharynx A mucosa that is part of a hypopharynx [Automatically generated definition]. OBOL:automatic hypopharynx mucosa OBOL:automatic hypopharynx mucosa of organ OBOL:automatic hypopharynx mucous membrane OBOL:automatic hypopharynx organ mucosa OBOL:automatic laryngeal pharynx mucosa OBOL:automatic laryngeal pharynx mucosa of organ OBOL:automatic laryngeal pharynx mucous membrane OBOL:automatic laryngeal pharynx organ mucosa OBOL:automatic laryngopharynx mucosa OBOL:automatic laryngopharynx mucosa of organ OBOL:automatic laryngopharynx mucous membrane OBOL:automatic laryngopharynx organ mucosa OBOL:automatic mucosa of hypopharynx OBOL:automatic mucosa of laryngeal pharynx OBOL:automatic mucosa of organ of hypopharynx OBOL:automatic mucosa of organ of laryngeal pharynx OBOL:automatic mucosa of organ of laryngopharynx OBOL:automatic mucous membrane of hypopharynx OBOL:automatic mucous membrane of laryngeal pharynx OBOL:automatic mucous membrane of laryngopharynx OBOL:automatic organ mucosa of hypopharynx OBOL:automatic organ mucosa of laryngeal pharynx OBOL:automatic organ mucosa of laryngopharynx OBOL:automatic 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 an appendix [Automatically generated definition]. CALOHA:TS-2022 FMA:14991 appendiceal mucous membrane appendix mucosa appendix mucosa of organ appendix mucous membrane appendix organ mucosa caecal appendix mucosa caecal appendix mucosa of organ caecal appendix mucous membrane caecal appendix organ mucosa mucosa of caecal appendix mucosa of organ of appendix mucosa of organ of caecal appendix mucosa of organ of vermiform appendix mucosa of organ of vermix mucosa of vermiform appendix mucosa of vermix mucous membrane of appendix mucous membrane of caecal appendix mucous membrane of vermiform appendix mucous membrane of vermix organ mucosa of appendix organ mucosa of caecal appendix organ mucosa of vermiform appendix organ mucosa of vermix vermiform appendix mucosa vermiform appendix mucosa of organ vermiform appendix mucous membrane vermiform appendix organ mucosa vermix mucosa vermix mucosa of organ vermix mucous membrane vermix organ mucosa uberon UBERON:0004989 mucosa of appendix A mucosa that is part of an appendix [Automatically generated definition]. OBOL:automatic appendiceal mucous membrane FMA:14991 appendix mucosa OBOL:automatic appendix mucosa of organ OBOL:automatic appendix mucous membrane OBOL:automatic appendix organ mucosa OBOL:automatic caecal appendix mucosa OBOL:automatic caecal appendix mucosa of organ OBOL:automatic caecal appendix mucous membrane OBOL:automatic caecal appendix organ mucosa OBOL:automatic mucosa of caecal appendix OBOL:automatic mucosa of organ of appendix OBOL:automatic mucosa of organ of caecal appendix OBOL:automatic mucosa of organ of vermiform appendix OBOL:automatic mucosa of organ of vermix OBOL:automatic mucosa of vermiform appendix OBOL:automatic mucosa of vermix OBOL:automatic mucous membrane of appendix OBOL:automatic mucous membrane of caecal appendix OBOL:automatic mucous membrane of vermiform appendix OBOL:automatic mucous membrane of vermix OBOL:automatic organ mucosa of appendix OBOL:automatic organ mucosa of caecal appendix OBOL:automatic organ mucosa of vermiform appendix OBOL:automatic organ mucosa of vermix OBOL:automatic vermiform appendix mucosa OBOL:automatic vermiform appendix mucosa of organ OBOL:automatic vermiform appendix mucous membrane OBOL:automatic vermiform appendix organ mucosa OBOL:automatic vermix mucosa OBOL:automatic vermix mucosa of organ OBOL:automatic vermix mucous membrane OBOL:automatic vermix organ mucosa OBOL:automatic A mucosa that is part of an ascending colon [Automatically generated definition]. FMA:15005 ascending colon mucosa ascending colon mucosa of organ ascending colon mucous membrane ascending colon organ mucosa mucosa of organ of ascending colon mucous membrane of ascending colon organ mucosa of ascending colon uberon UBERON:0004990 mucosa of ascending colon A mucosa that is part of an ascending colon [Automatically generated definition]. OBOL:automatic ascending colon mucosa OBOL:automatic ascending colon mucosa of organ OBOL:automatic ascending colon mucous membrane OBOL:automatic ascending colon organ mucosa OBOL:automatic mucosa of organ of ascending colon OBOL:automatic mucous membrane of ascending colon OBOL:automatic organ mucosa of ascending colon OBOL:automatic A mucosa that is part of a transverse colon [Automatically generated definition]. FMA:15012 mucosa of organ of transverse colon mucous membrane of transverse colon organ mucosa of transverse colon transverse colon mucosa transverse colon mucosa of organ transverse colon mucous membrane transverse colon organ mucosa uberon UBERON:0004991 mucosa of transverse colon A mucosa that is part of a transverse colon [Automatically generated definition]. OBOL:automatic mucosa of organ of transverse colon OBOL:automatic mucous membrane of transverse colon OBOL:automatic organ mucosa of transverse colon OBOL:automatic transverse colon mucosa OBOL:automatic transverse colon mucosa of organ OBOL:automatic transverse colon mucous membrane OBOL:automatic transverse colon organ mucosa OBOL:automatic A mucosa that is part of a descending colon [Automatically generated definition]. FMA:15019 descending colon mucosa descending colon mucosa of organ descending colon mucous membrane descending colon organ mucosa mucosa of organ of descending colon mucous membrane of descending colon organ mucosa of descending colon uberon UBERON:0004992 mucosa of descending colon A mucosa that is part of a descending colon [Automatically generated definition]. OBOL:automatic descending colon mucosa OBOL:automatic descending colon mucosa of organ OBOL:automatic descending colon mucous membrane OBOL:automatic descending colon organ mucosa OBOL:automatic mucosa of organ of descending colon OBOL:automatic mucous membrane of descending colon OBOL:automatic organ mucosa of descending colon 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 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 right ureter [Automatically generated definition]. FMA:17806 mucosa of organ of right ureter mucous membrane of right ureter organ mucosa of right ureter right ureter mucosa right ureter mucosa of organ right ureter mucous membrane right ureter organ mucosa right ureteral mucosa uberon UBERON:0005004 mucosa of right ureter A mucosa that is part of a right ureter [Automatically generated definition]. OBOL:automatic mucosa of organ of right ureter OBOL:automatic mucous membrane of right ureter OBOL:automatic organ mucosa of right ureter OBOL:automatic right ureter mucosa OBOL:automatic right ureter mucosa of organ OBOL:automatic right ureter mucous membrane OBOL:automatic right ureter organ mucosa OBOL:automatic right ureteral mucosa FMA:17806 A mucosa that is part of a left ureter [Automatically generated definition]. FMA:17807 left ureter mucosa left ureter mucosa of organ left ureter mucous membrane left ureter organ mucosa left ureteral mucosa mucosa of organ of left ureter mucous membrane of left ureter organ mucosa of left ureter uberon UBERON:0005005 mucosa of left ureter A mucosa that is part of a left ureter [Automatically generated definition]. OBOL:automatic left ureter mucosa OBOL:automatic left ureter mucosa of organ OBOL:automatic left ureter mucous membrane OBOL:automatic left ureter organ mucosa OBOL:automatic left ureteral mucosa FMA:17807 mucosa of organ of left ureter OBOL:automatic mucous membrane of left ureter OBOL:automatic organ mucosa of left ureter OBOL:automatic A mucosa that is part of a renal pelvis [Automatically generated definition]. FMA:17931 kidney pelvis mucosa kidney pelvis mucosa of organ kidney pelvis mucous membrane kidney pelvis organ mucosa mucosa of kidney pelvis mucosa of organ of kidney pelvis mucosa of organ of pelvis of ureter mucosa of organ of renal pelvis mucosa of pelvis of ureter mucous membrane of kidney pelvis mucous membrane of pelvis of ureter mucous membrane of renal pelvis organ mucosa of kidney pelvis organ mucosa of pelvis of ureter organ mucosa of renal pelvis pelvis of ureter mucosa pelvis of ureter mucosa of organ pelvis of ureter mucous membrane pelvis of ureter organ mucosa renal pelvic mucosa renal pelvis mucosa renal pelvis mucosa of organ renal pelvis mucous membrane renal pelvis organ mucosa tunica mucosa pelvis renalis uberon UBERON:0005006 mucosa of renal pelvis A mucosa that is part of a renal pelvis [Automatically generated definition]. OBOL:automatic kidney pelvis mucosa OBOL:automatic kidney pelvis mucosa of organ OBOL:automatic kidney pelvis mucous membrane OBOL:automatic kidney pelvis organ mucosa OBOL:automatic mucosa of kidney pelvis OBOL:automatic mucosa of organ of kidney pelvis OBOL:automatic mucosa of organ of pelvis of ureter OBOL:automatic mucosa of organ of renal pelvis OBOL:automatic mucosa of pelvis of ureter OBOL:automatic mucous membrane of kidney pelvis OBOL:automatic mucous membrane of pelvis of ureter OBOL:automatic mucous membrane of renal pelvis OBOL:automatic organ mucosa of kidney pelvis OBOL:automatic organ mucosa of pelvis of ureter OBOL:automatic organ mucosa of renal pelvis OBOL:automatic pelvis of ureter mucosa OBOL:automatic pelvis of ureter mucosa of organ OBOL:automatic pelvis of ureter mucous membrane OBOL:automatic pelvis of ureter organ mucosa OBOL:automatic renal pelvic mucosa FMA:17931 renal pelvis mucosa OBOL:automatic renal pelvis mucosa of organ OBOL:automatic renal pelvis mucous membrane OBOL:automatic renal pelvis organ mucosa OBOL:automatic tunica mucosa pelvis renalis FMA:17931 FMA:TA A mucosa that is part of a neck of urinary bladder [Automatically generated definition]. FMA:17846 bladder neck mucosa bladder neck mucosa of organ bladder neck mucous membrane bladder neck organ mucosa mucosa of bladder neck mucosa of neck of bladder mucosa of organ of bladder neck mucosa of organ of neck of bladder mucosa of organ of neck of urinary bladder mucosa of organ of urinary bladder neck mucosa of organ of vesical neck mucosa of urinary bladder neck mucosa of vesical neck mucous membrane of bladder neck mucous membrane of neck of bladder mucous membrane of neck of urinary bladder mucous membrane of urinary bladder neck mucous membrane of vesical neck neck of bladder mucosa neck of bladder mucosa of organ neck of bladder mucous membrane neck of bladder organ mucosa neck of urinary bladder mucosa neck of urinary bladder mucosa of organ neck of urinary bladder mucous membrane neck of urinary bladder organ mucosa organ mucosa of bladder neck organ mucosa of neck of bladder organ mucosa of neck of urinary bladder organ mucosa of urinary bladder neck organ mucosa of vesical neck urinary bladder neck mucosa urinary bladder neck mucosa of organ urinary bladder neck mucous membrane vesical neck mucosa vesical neck mucosa of organ vesical neck mucous membrane vesical neck organ mucosa uberon UBERON:0005010 mucosa of neck of urinary bladder A mucosa that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck mucosa OBOL:automatic bladder neck mucosa of organ OBOL:automatic bladder neck mucous membrane OBOL:automatic bladder neck organ mucosa OBOL:automatic mucosa of bladder neck OBOL:automatic mucosa of neck of bladder OBOL:automatic mucosa of organ of bladder neck OBOL:automatic mucosa of organ of neck of bladder OBOL:automatic mucosa of organ of neck of urinary bladder OBOL:automatic mucosa of organ of urinary bladder neck OBOL:automatic mucosa of organ of vesical neck OBOL:automatic mucosa of urinary bladder neck OBOL:automatic mucosa of vesical neck OBOL:automatic mucous membrane of bladder neck OBOL:automatic mucous membrane of neck of bladder OBOL:automatic mucous membrane of neck of urinary bladder OBOL:automatic mucous membrane of urinary bladder neck OBOL:automatic mucous membrane of vesical neck OBOL:automatic neck of bladder mucosa OBOL:automatic neck of bladder mucosa of organ OBOL:automatic neck of bladder mucous membrane OBOL:automatic neck of bladder organ mucosa OBOL:automatic neck of urinary bladder mucosa OBOL:automatic neck of urinary bladder mucosa of organ OBOL:automatic neck of urinary bladder mucous membrane OBOL:automatic neck of urinary bladder organ mucosa OBOL:automatic organ mucosa of bladder neck OBOL:automatic organ mucosa of neck of bladder OBOL:automatic organ mucosa of neck of urinary bladder OBOL:automatic organ mucosa of urinary bladder neck OBOL:automatic organ mucosa of vesical neck OBOL:automatic urinary bladder neck mucosa OBOL:automatic urinary bladder neck mucosa of organ OBOL:automatic urinary bladder neck mucous membrane OBOL:automatic vesical neck mucosa OBOL:automatic vesical neck mucosa of organ OBOL:automatic vesical neck mucous membrane OBOL:automatic vesical neck organ mucosa OBOL:automatic A mucosa that is part of a right uterine tube [Automatically generated definition]. FMA:18452 mucosa of organ of right fallopian tube mucosa of organ of right oviduct mucosa of organ of right uterine tube mucosa of right fallopian tube mucosa of right oviduct mucous membrane of right fallopian tube mucous membrane of right oviduct mucous membrane of right uterine tube organ mucosa of right fallopian tube organ mucosa of right oviduct organ mucosa of right uterine tube right fallopian tube mucosa right fallopian tube mucosa of organ right fallopian tube mucous membrane right fallopian tube organ mucosa right oviduct mucosa right oviduct mucosa of organ right oviduct mucous membrane right oviduct organ mucosa right uterine tube mucosa right uterine tube mucosa of organ right uterine tube mucous membrane right uterine tube organ mucosa uberon UBERON:0005011 mucosa of right uterine tube A mucosa that is part of a right uterine tube [Automatically generated definition]. OBOL:automatic mucosa of organ of right fallopian tube OBOL:automatic mucosa of organ of right oviduct OBOL:automatic mucosa of organ of right uterine tube OBOL:automatic mucosa of right fallopian tube OBOL:automatic mucosa of right oviduct OBOL:automatic mucous membrane of right fallopian tube OBOL:automatic mucous membrane of right oviduct OBOL:automatic mucous membrane of right uterine tube OBOL:automatic organ mucosa of right fallopian tube OBOL:automatic organ mucosa of right oviduct OBOL:automatic organ mucosa of right uterine tube OBOL:automatic right fallopian tube mucosa OBOL:automatic right fallopian tube mucosa of organ OBOL:automatic right fallopian tube mucous membrane OBOL:automatic right fallopian tube organ mucosa OBOL:automatic right oviduct mucosa OBOL:automatic right oviduct mucosa of organ OBOL:automatic right oviduct mucous membrane OBOL:automatic right oviduct organ mucosa OBOL:automatic right uterine tube mucosa OBOL:automatic right uterine tube mucosa of organ OBOL:automatic right uterine tube mucous membrane OBOL:automatic right uterine tube organ mucosa OBOL:automatic A mucosa that is part of a left uterine tube [Automatically generated definition]. FMA:18453 left fallopian tube mucosa left fallopian tube mucosa of organ left fallopian tube mucous membrane left fallopian tube organ mucosa left oviduct mucosa left oviduct mucosa of organ left oviduct mucous membrane left oviduct organ mucosa left uterine tube mucosa left uterine tube mucosa of organ left uterine tube mucous membrane left uterine tube organ mucosa mucosa of left fallopian tube mucosa of left oviduct mucosa of organ of left fallopian tube mucosa of organ of left oviduct mucosa of organ of left uterine tube mucous membrane of left fallopian tube mucous membrane of left oviduct mucous membrane of left uterine tube organ mucosa of left fallopian tube organ mucosa of left oviduct organ mucosa of left uterine tube uberon UBERON:0005012 mucosa of left uterine tube A mucosa that is part of a left uterine tube [Automatically generated definition]. OBOL:automatic left fallopian tube mucosa OBOL:automatic left fallopian tube mucosa of organ OBOL:automatic left fallopian tube mucous membrane OBOL:automatic left fallopian tube organ mucosa OBOL:automatic left oviduct mucosa OBOL:automatic left oviduct mucosa of organ OBOL:automatic left oviduct mucous membrane OBOL:automatic left oviduct organ mucosa OBOL:automatic left uterine tube mucosa OBOL:automatic left uterine tube mucosa of organ OBOL:automatic left uterine tube mucous membrane OBOL:automatic left uterine tube organ mucosa OBOL:automatic mucosa of left fallopian tube OBOL:automatic mucosa of left oviduct OBOL:automatic mucosa of organ of left fallopian tube OBOL:automatic mucosa of organ of left oviduct OBOL:automatic mucosa of organ of left uterine tube OBOL:automatic mucous membrane of left fallopian tube OBOL:automatic mucous membrane of left oviduct OBOL:automatic mucous membrane of left uterine tube OBOL:automatic organ mucosa of left fallopian tube OBOL:automatic organ mucosa of left oviduct OBOL:automatic organ mucosa of left uterine tube OBOL:automatic A mucosa that is part of a male urethra [Automatically generated definition]. FMA:239937 male urethra mucosa male urethra mucosa of organ male urethra mucous membrane male urethra organ mucosa mucosa of organ of male urethra mucous membrane of male urethra organ mucosa of male urethra uberon UBERON:0005013 mucosa of male urethra A mucosa that is part of a male urethra [Automatically generated definition]. OBOL:automatic male urethra mucosa OBOL:automatic male urethra mucosa of organ OBOL:automatic male urethra mucous membrane OBOL:automatic male urethra organ mucosa OBOL:automatic mucosa of organ of male urethra OBOL:automatic mucous membrane of male urethra OBOL:automatic organ mucosa of male urethra OBOL:automatic A mucosa that is part of a female urethra [Automatically generated definition]. FMA:239940 female urethra mucosa female urethra mucosa of organ female urethra mucous membrane female urethra organ mucosa mucosa of organ of female urethra mucous membrane of female urethra organ mucosa of female urethra uberon UBERON:0005014 mucosa of female urethra A mucosa that is part of a female urethra [Automatically generated definition]. OBOL:automatic female urethra mucosa OBOL:automatic female urethra mucosa of organ OBOL:automatic female urethra mucous membrane OBOL:automatic female urethra organ mucosa OBOL:automatic mucosa of organ of female urethra OBOL:automatic mucous membrane of female urethra OBOL:automatic organ mucosa of female urethra OBOL:automatic A mucosa that is part of a lacrimal sac [Automatically generated definition]. FMA:72061 lacrimal sac mucosa lacrimal sac mucosa of organ lacrimal sac mucous membrane lacrimal sac organ mucosa mucosa of organ of lacrimal sac mucous membrane of lacrimal sac organ mucosa of lacrimal sac uberon UBERON:0005017 mucosa of lacrimal sac A mucosa that is part of a lacrimal sac [Automatically generated definition]. OBOL:automatic lacrimal sac mucosa OBOL:automatic lacrimal sac mucosa of organ OBOL:automatic lacrimal sac mucous membrane OBOL:automatic lacrimal sac organ mucosa OBOL:automatic mucosa of organ of lacrimal sac OBOL:automatic mucous membrane of lacrimal sac OBOL:automatic organ mucosa of lacrimal sac OBOL:automatic A mucosa that is part of a tongue [Automatically generated definition]. EFO:0002553 FMA:54807 lingual mucosa mucosa of organ of tongue mucous membrane of tongue organ mucosa of tongue tongue mucosa tongue mucosa of organ tongue mucous membrane tongue organ mucosa tunica mucosa linguae uberon UBERON:0005020 mucosa of tongue A mucosa that is part of a tongue [Automatically generated definition]. OBOL:automatic lingual mucosa FMA:54807 mucosa of organ of tongue OBOL:automatic mucous membrane of tongue OBOL:automatic organ mucosa of tongue OBOL:automatic tongue mucosa OBOL:automatic tongue mucosa of organ OBOL:automatic tongue mucous membrane OBOL:automatic tongue organ mucosa OBOL:automatic tunica mucosa linguae FMA:54807 FMA:TA A mucosa that is part of a nasopharynx [Automatically generated definition]. FMA:54971 mucosa of nasal part of pharynx mucosa of organ of nasal part of pharynx mucosa of organ of nasopharynx mucosa of organ of rhinopharynx mucosa of rhinopharynx mucous membrane of nasal part of pharynx mucous membrane of nasopharynx mucous membrane of rhinopharynx nasal part of pharynx mucosa nasal part of pharynx mucosa of organ nasal part of pharynx mucous membrane nasal part of pharynx organ mucosa nasopharynx mucosa nasopharynx mucosa of organ nasopharynx mucous membrane nasopharynx organ mucosa organ mucosa of nasal part of pharynx organ mucosa of nasopharynx organ mucosa of rhinopharynx rhinopharynx mucosa rhinopharynx mucosa of organ rhinopharynx mucous membrane rhinopharynx organ mucosa uberon UBERON:0005022 mucosa of nasopharynx A mucosa that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic mucosa of nasal part of pharynx OBOL:automatic mucosa of organ of nasal part of pharynx OBOL:automatic mucosa of organ of nasopharynx OBOL:automatic mucosa of organ of rhinopharynx OBOL:automatic mucosa of rhinopharynx OBOL:automatic mucous membrane of nasal part of pharynx OBOL:automatic mucous membrane of nasopharynx OBOL:automatic mucous membrane of rhinopharynx OBOL:automatic nasal part of pharynx mucosa OBOL:automatic nasal part of pharynx mucosa of organ OBOL:automatic nasal part of pharynx mucous membrane OBOL:automatic nasal part of pharynx organ mucosa OBOL:automatic nasopharynx mucosa OBOL:automatic nasopharynx mucosa of organ OBOL:automatic nasopharynx mucous membrane OBOL:automatic nasopharynx organ mucosa OBOL:automatic organ mucosa of nasal part of pharynx OBOL:automatic organ mucosa of nasopharynx OBOL:automatic organ mucosa of rhinopharynx OBOL:automatic rhinopharynx mucosa OBOL:automatic rhinopharynx mucosa of organ OBOL:automatic rhinopharynx mucous membrane OBOL:automatic rhinopharynx organ mucosa OBOL:automatic A mucosa that is part of a lower lip [Automatically generated definition]. FMA:59833 NCIT:C12225 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 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 A mucosa that is part of a bronchiole [Automatically generated definition]. FMA:263230 FMA:62774 bronchiole mucosa bronchiole mucosa of organ bronchiole mucous membrane bronchiole organ mucosa lobular bronchiole mucosa lobular bronchiole mucosa of organ lobular bronchiole mucous membrane lobular bronchiole organ mucosa mucosa of lobular bronchiole mucosa of organ of bronchiole mucosa of organ of lobular bronchiole mucous membrane of bronchiole mucous membrane of lobular bronchiole organ mucosa of bronchiole organ mucosa of lobular bronchiole uberon UBERON:0005039 mucosa of bronchiole A mucosa that is part of a bronchiole [Automatically generated definition]. OBOL:automatic bronchiole mucosa OBOL:automatic bronchiole mucosa of organ OBOL:automatic bronchiole mucous membrane OBOL:automatic bronchiole organ mucosa OBOL:automatic lobular bronchiole mucosa OBOL:automatic lobular bronchiole mucosa of organ OBOL:automatic lobular bronchiole mucous membrane OBOL:automatic lobular bronchiole organ mucosa OBOL:automatic mucosa of lobular bronchiole OBOL:automatic mucosa of organ of bronchiole OBOL:automatic mucosa of organ of lobular bronchiole OBOL:automatic mucous membrane of bronchiole OBOL:automatic mucous membrane of lobular bronchiole OBOL:automatic organ mucosa of bronchiole OBOL:automatic organ mucosa of lobular bronchiole OBOL:automatic A mucosa that is part of a terminal bronchiole [Automatically generated definition]. FMA:263232 bronchiolus terminalis mucosa bronchiolus terminalis mucosa of organ bronchiolus terminalis mucous membrane bronchiolus terminalis organ mucosa mucosa of bronchiolus terminalis mucosa of organ of bronchiolus terminalis mucosa of organ of terminal bronchiole mucous membrane of bronchiolus terminalis mucous membrane of terminal bronchiole organ mucosa of bronchiolus terminalis organ mucosa of terminal bronchiole terminal bronchiole mucosa terminal bronchiole mucosa of organ terminal bronchiole mucous membrane terminal bronchiole organ mucosa uberon UBERON:0005040 mucosa of terminal bronchiole A mucosa that is part of a terminal bronchiole [Automatically generated definition]. OBOL:automatic bronchiolus terminalis mucosa OBOL:automatic bronchiolus terminalis mucosa of organ OBOL:automatic bronchiolus terminalis mucous membrane OBOL:automatic bronchiolus terminalis organ mucosa OBOL:automatic mucosa of bronchiolus terminalis OBOL:automatic mucosa of organ of bronchiolus terminalis OBOL:automatic mucosa of organ of terminal bronchiole OBOL:automatic mucous membrane of bronchiolus terminalis OBOL:automatic mucous membrane of terminal bronchiole OBOL:automatic organ mucosa of bronchiolus terminalis OBOL:automatic organ mucosa of terminal bronchiole OBOL:automatic terminal bronchiole mucosa OBOL:automatic terminal bronchiole mucosa of organ OBOL:automatic terminal bronchiole mucous membrane OBOL:automatic terminal bronchiole organ mucosa OBOL:automatic A mucosa that is part of a nasolacrimal duct [Automatically generated definition]. FMA:59664 mucosa of organ of nasolacrimal duct mucous membrane of nasolacrimal duct nasolacrimal duct mucosa nasolacrimal duct mucosa of organ nasolacrimal duct mucous membrane nasolacrimal duct organ mucosa nasolacrimal ductal mucosa organ mucosa of nasolacrimal duct uberon UBERON:0005043 mucosa of nasolacrimal duct A mucosa that is part of a nasolacrimal duct [Automatically generated definition]. OBOL:automatic mucosa of organ of nasolacrimal duct OBOL:automatic mucous membrane of nasolacrimal duct OBOL:automatic nasolacrimal duct mucosa OBOL:automatic nasolacrimal duct mucosa of organ OBOL:automatic nasolacrimal duct mucous membrane OBOL:automatic nasolacrimal duct organ mucosa OBOL:automatic nasolacrimal ductal mucosa FMA:59664 organ mucosa of nasolacrimal duct OBOL:automatic A mucosa that is part of a fallopian tube [Automatically generated definition]. FMA:18319 fallopian tube mucosa fallopian tube mucosa of organ fallopian tube mucous membrane fallopian tube organ mucosa mucosa of fallopian tube mucosa of organ of fallopian tube mucosa of organ of uterine tube mucosa of oviduct mucous membrane of fallopian tube mucous membrane of uterine tube organ mucosa of fallopian tube organ mucosa of uterine tube tunica mucosa tubae uterinae uterine tubal mucosa uterine tube mucosa uterine tube mucosa of organ uterine tube mucous membrane uterine tube organ mucosa uberon UBERON:0005048 mucosa of uterine tube A mucosa that is part of a fallopian tube [Automatically generated definition]. OBOL:automatic fallopian tube mucosa OBOL:automatic fallopian tube mucosa of organ OBOL:automatic fallopian tube mucous membrane OBOL:automatic fallopian tube organ mucosa OBOL:automatic mucosa of fallopian tube OBOL:automatic mucosa of organ of fallopian tube OBOL:automatic mucosa of organ of uterine tube OBOL:automatic mucosa of oviduct FMA:18319 mucous membrane of fallopian tube OBOL:automatic mucous membrane of uterine tube OBOL:automatic organ mucosa of fallopian tube OBOL:automatic organ mucosa of uterine tube OBOL:automatic tunica mucosa tubae uterinae FMA:18319 FMA:TA uterine tubal mucosa FMA:18319 uterine tube mucosa OBOL:automatic uterine tube mucosa of organ OBOL:automatic uterine tube mucous membrane OBOL:automatic uterine tube organ mucosa OBOL:automatic A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]. FMA:18357 mucosa of infundibulum of fallopian tube mucosa of infundibulum of oviduct mucosa of organ of uterine tube infundibulum mucosa of uterine tube infundibulum mucous membrane of uterine tube infundibulum organ mucosa of uterine tube infundibulum uterine tube infundibulum mucosa uterine tube infundibulum mucosa of organ uterine tube infundibulum mucous membrane uterine tube infundibulum organ mucosa uberon UBERON:0005049 mucosa of infundibulum of uterine tube A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]. OBOL:automatic mucosa of infundibulum of fallopian tube FMA:18357 mucosa of infundibulum of oviduct FMA:18357 mucosa of organ of uterine tube infundibulum OBOL:automatic mucosa of uterine tube infundibulum OBOL:automatic mucous membrane of uterine tube infundibulum OBOL:automatic organ mucosa of uterine tube infundibulum OBOL:automatic uterine tube infundibulum mucosa OBOL:automatic uterine tube infundibulum mucosa of organ OBOL:automatic uterine tube infundibulum mucous membrane OBOL:automatic uterine tube infundibulum organ mucosa OBOL:automatic The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP] EMAPA:18331 FMA:19812 MA:0003240 body of highmore hilum of testicle mediastinum of testis testis mediastinum uberon UBERON:0005051 mediastinum testis The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP] body of highmore FMA:19812 mediastinum of testis FMA:19812 testis mediastinum FMA:19812 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 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 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 UMLS:C0814992 XAO:0000248 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 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]. 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 UMLS:C0814993 XAO:0004087 medullary fold uberon UBERON:0005062 neural fold One of the two elevated edges of the neural groove[GO,MP]. GO:0001842 MP:0011256 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]. UMLS:C0814993 ncithesaurus:Neural_Fold medullary fold MP:0011256 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 forebrain and adjacent_to a midbrain. The boundary between the diencephalon and the mesencephalon.[TAO] relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO] EMAPA:36449 TAO:0001367 ZFA:0001367 diencephalic-mesencephalic boundary forebrain midbrain boundary forebrain-midbrain boundary region uberon UBERON:0005075 forebrain-midbrain boundary definitional An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain. OBOL:automatic The boundary between the diencephalon and the mesencephalon.[TAO] 2012-08-14 TAO:0001367 TAO ZFIN:curator relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO] 2012-08-14 TAO:0001367 TAO diencephalic-mesencephalic boundary ZFA:0001367 forebrain midbrain boundary ZFA:0001367 forebrain-midbrain boundary region EMAPA:36449 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 The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. uberon UBERON:0005080 metanephric ureteric bud The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. GO:0035502 The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. uberon UBERON:0005081 ureter ureteric bud The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. GO:0035503 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 epithelial placode AEO:0000112 A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]. EMAPA:36479 hair placode vibrissa placode uberon hair gem hair germ hair peg UBERON:0005086 hair follicle placode Wikipathways:WP2062 A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]. GO:0060789 hair placode hair gem ISBN:9780878932504 hair germ hair peg ISBN:9780878932504 A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]. TODO - add bud uberon UBERON:0005088 sebaceous gland placode NCBIBook:NBK53175 Wikipathways:WP2062 A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]. GO:0060791 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 FBbt:00005073 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 . class added for consistency with GO - consider merging with kidney mesenchyme. uberon kidney anlage UBERON:0005095 kidney rudiment GO . GO:0072003 kidney anlage GOC:mtg_kidney_jan10 An epithelium that is part of a mesonephros [Automatically generated definition]. uberon UBERON:0005103 mesonephric epithelium An epithelium that is part of a mesonephros [Automatically generated definition]. OBOL:automatic A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] VHOG:0001526 uberon UBERON:0005106 metanephric tubule A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. GO:0072173 The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] 2012-09-17 VHOG:0001526 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. uberon UBERON:0005108 metanephric epithelium An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. GO:0072207 Any smooth muscle tissue that is part of a metanephros. uberon UBERON:0005109 metanephric smooth muscle tissue Any smooth muscle tissue that is part of a metanephros. GO:0072208 A metanephric nephron is the functional unit of the metanephros[GO]. The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG] UBERON:0005142 VHOG:0000719 uberon UBERON:0005110 metanephric nephron Wikipedia Bgee:AN A metanephric nephron is the functional unit of the metanephros[GO]. GO:0072273 The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG] 2012-09-17 VHOG:0000719 VHOG DOI:10.1093/icb/34.4.542 Ruppert EE, Evolutionary Origin of the Vertebrate Nephron. Integrative and Comparative Biology (1994) Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO]. uberon UBERON:0005111 metanephric pyramid Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO]. GO:0072211 EHDAA2:0001140 uberon UBERON:0005113 metanephric cortex mesenchyme EHDAA2 The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO]. uberon UBERON:0005115 metanephric cortical collecting duct true true The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO]. GO:0072219 The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO]. uberon UBERON:0005134 metanephric nephron epithelium true The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO]. GO:0072243 The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. UBERON:0005112 uberon UBERON:0005137 metanephric capsule The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. GO:0072213 A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]. UBERON:0005128 UBERON:0005152 uberon UBERON:0005146 metanephric nephron tubule ISBN:9780878932504 A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]. GO:0072282 The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. EHDAA2:0001245 EHDAA:9346 EMAPA:27678 metanephric vesicle uberon UBERON:0005147 metanephric renal vesicle EHDAA2 The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. GO:0072283 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 A cord of epithelial cells without a lumen and usually several cells thick. AEO:0000216 EHDAA2:0004052 uberon UBERON:0005154 epithelial cord AEO A cord of epithelial cells without a lumen and usually several cells thick. AEO:0000216 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. 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 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 FMA 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 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 OpenCyc:Mx4rvWo8WJwpEbGdrcN5Y29ycA 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). 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 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 abdomen organ uberon UBERON:0005172 abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. 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. 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. EMAPA:37274 MA:th back organ MA:0001901 An organ that is part of a chest [Automatically generated definition]. EMAPA:37272 MA:0000552 uberon UBERON:0005175 chest organ An organ that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37272 MA:th 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. 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. 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. 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. EMAPA:37271 MA:th upper body organ MA:0000563 Innermost layer of the hair shaft. BTO:0004671 EMAPA:35389 MA:0000158 uberon medulla of hair shaft UBERON:0005184 hair medulla Innermost layer of the hair shaft. medulla of hair shaft BTO:0004671 The portion of the collecting duct that resides in the renal medulla BTO:0004536 EMAPA:28061 EMAPA:35459 MA:0002935 kidney medulla collecting duct medullary collecting duct uberon UBERON:0005185 renal medulla collecting duct The portion of the collecting duct that resides in the renal medulla kidney medulla collecting duct MA:0002935 medullary collecting duct EMAPA:28061 An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP]. EMAPA:37513 FMA:18930 MA:0001940 arteria ductus deferentis artery of ductus deferens ductus deferens artery vas deferens artery uberon UBERON:0005192 deferent duct artery FMA Wikipedia An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP]. EMAPA:37513 MA:th arteria ductus deferentis artery of ductus deferens FMA:18930 ductus deferens artery FMA:18930 A vein that is part of a thorax [Automatically generated definition]. EMAPA:37197 MA:0002235 NCIT:C53142 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 A vein that is part of a vas deferens [Automatically generated definition]. EMAPA:37514 MA:0002100 uberon UBERON:0005195 deferent duct vein A vein that is part of a vas deferens [Automatically generated definition]. OBOL:automatic EMAPA:37514 MA:th A gland that is part of a larynx submucosa [Automatically generated definition]. EMAPA:35475 MA:0002729 uberon laryngeal submucosa gland UBERON:0005204 larynx submucosa gland A gland that is part of a larynx submucosa [Automatically generated definition]. OBOL:automatic laryngeal submucosa gland EMAPA:35475 EMAPA:35902 FMA:19979 MA:0002737 uberon vagina stroma UBERON:0005205 lamina propria of vagina vagina stroma MA:0002737 Stromal matrix surrounding blood vessels within the choroid plexus. EMAPA:36609 MA:0000825 choroid plexus stromal matrix uberon UBERON:0005206 choroid plexus stroma Stromal matrix surrounding blood vessels within the choroid plexus. PMCID:PMC3496674 choroid plexus stromal matrix PMCID:PMC3496674 A capsule that is part of a tonsil [Automatically generated definition]. FMA:294647 MA:0000776 uberon UBERON:0005207 tonsil capsule A capsule that is part of a tonsil [Automatically generated definition]. OBOL:automatic 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 An external ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic A subarachnoid space that is part of a midbrain [Automatically generated definition]. Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG] EMAPA:19055 VHOG:0001304 subarachnoid space midbrain uberon subarachnoid space mesencephalon UBERON:0005217 midbrain subarachnoid space A subarachnoid space that is part of a midbrain [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001304 VHOG subarachnoid space midbrain VHOG:0001304 subarachnoid space mesencephalon VHOG:0001304 A subarachnoid space that is part of a diencephalon [Automatically generated definition]. Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG] EMAPA:19053 VHOG:0001302 subarachnoid space diencephalon uberon UBERON:0005218 diencephalon subarachnoid space A subarachnoid space that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001302 VHOG subarachnoid space diencephalon VHOG:0001302 A subarachnoid space that is part of a hindbrain [Automatically generated definition]. Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG] EMAPA:18211 VHOG:0001303 subarachnoid space hindbrain uberon subarachnoid space rhombencephalon UBERON:0005219 hindbrain subarachnoid space A subarachnoid space that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001303 VHOG subarachnoid space hindbrain VHOG:0001303 subarachnoid space rhombencephalon VHOG:0001303 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 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 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 renal pelvis that is part of a metanephros. The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG] VHOG:0000945 metanephros pelvis uberon UBERON:0005249 metanephric renal pelvis A renal pelvis that is part of a metanephros. OBOL:automatic The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG] 2012-09-17 VHOG:0000945 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 metanephros pelvis VHOG:0000945 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 An artery that supplies the renal cortex. EMAPA:28147 MA:0002582 kidney cortex artery renal cortex artery uberon renal cortex arterial system UBERON:0005268 renal cortex artery MA An artery that supplies the renal cortex. kidney cortex artery MP:0011314 renal cortex artery MA:0002582 renal cortex arterial system MA:0002582 Artery that receives blood from the renal cortex[MP, modified] EMAPA:28152 MA:0002592 uberon kidney cortex vein renal cortex venous system UBERON:0005269 renal cortex vein MA Artery that receives blood from the renal cortex[MP, modified] MGI:csmith kidney cortex vein MP:0011322 renal cortex venous system MA:0002592 A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]. TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity' EFO:0003650 EHDAA2:0004362 EV:0100306 FMA:242675 MBA:73 TAO:0001261 ZFA:0001261 CNS ventricular system ventricular system ventricular system of neuraxis uberon ventricle system ventriculi cerebri UBERON:0005281 ventricular system of central nervous system ZFA A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]. CNS ventricular system EHDAA2:0004362 ventricular system ZFA:0001261 ventricular system of neuraxis FMA:242675 ventricle system ventriculi cerebri 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] CALOHA:TS-1295 EMAPA:37447 FMA:242787 VHOG:0000005 brain ventricular system uberon UBERON:0005282 ventricular system of brain 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:0000005 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 EMAPA:37447 MA:th brain ventricular system VHOG:0000005 A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]. Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]. Vascularized tela choroidea is choroid plexus. Note that the structure in ZFA may be different FMA:242849 TAO:0000447 ZFA:0000447 uberon tela chorioidea UBERON:0005283 tela choroidea FMA A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]. ISBN:0471888893 Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]. ZFA:0000447 Note that the structure in ZFA may be different ZFA tela chorioidea FMA:242849 Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP]. Tela chorioidea that lines the fourth ventricle.[TAO] tela choroidea BAMS:tc4v FMA:78493 TAO:0005158 ZFA:0005158 choroid membrane choroid membrane of fourth ventricle tela chorioidea fourth ventricle tela choroidea fourth ventricle tela choroidea of fourth ventricle tela choroidea ventriculi quarti uberon tela choroidea ventriculi quarti UBERON:0005287 tela choroidea of fourth ventricle Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP]. ZFIN:curator Tela chorioidea that lines the fourth ventricle.[TAO] 2012-08-14 TAO:0005158 TAO ZFIN:curator tela choroidea FMA:78493 FMA:TA choroid membrane FMA:78493 choroid membrane of fourth ventricle FMA:78493 tela choroidea ventriculi quarti FMA:78493 FMA:TA tela choroidea ventriculi quarti Tela chorioidea that lines the telencephalic ventricle. BAMS:tclv FMA:83712 TAO:0005160 ZFA:0005160 tela chorioidea of lateral ventricle tela chorioidea of telencephalic ventricle tela chorioidea telencephalic ventricle tela choroidea (ventriculi lateralis) tela choroidea of lateral ventricle tela choroidea telencephalic ventricle uberon UBERON:0005289 tela choroidea of telencephalic ventricle Tela chorioidea that lines the telencephalic ventricle. ZFIN:curator tela chorioidea telencephalic ventricle ZFA:0005160 tela choroidea (ventriculi lateralis) FMA:83712 FMA:TA tela choroidea of lateral ventricle FMA:83712 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 VHOG:0000456 uberon myelencephalon (medulla oblongata) UBERON:0005290 myelencephalon 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 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 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 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. the elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary TODO - check developmental relationships. merge with urogenital ridge? in eutherians, SRY transforms the indifferent gonad into testes AAO:0011047 BTO:0001402 EFO:0001414 EHDAA2:0004044 EMAPA:35899 FMA:321917 NCIT:C34184 NCIT:C34321 UMLS:C0231047 UMLS:C1512243 XAO:0000018 genital ridge gonadal ridge indifferent gonadal ridge uberon crista gonadalis genital cord UBERON:0005294 gonadal ridge the elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary MGI:anna MP:0011411 UMLS:C0231047 ncithesaurus:Urogenital_Ridge UMLS:C1512243 ncithesaurus:Gonadal_Ridge genital ridge MP:0011411 gonadal ridge indifferent gonadal ridge crista gonadalis genital cord MP:0011411 Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female. EHDAA2:0004051 NCIT:C34183 RETIRED_EHDAA2:0001523 UMLS:C1512242 uberon genital cord gonad cord gonadal cord primitive sex cord UBERON:0005295 sex cord EHDAA2 Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female. UMLS:C1512242 ncithesaurus:Gonadal_Cord structures that develop from sex cords in the female. After further development they become the ovarian follicles. TODO check secondary vs cortical vs ovary EHDAA2:0001363 EHDAA:8130 EMAPA:31058 NCIT:C34134 UMLS:C1511527 VHOG:0001339 ovigerous cord ovigerous cords uberon cortical cord cortical sex cord ovary primitive sex cord secondary cord UBERON:0005296 ovary sex cord structures that develop from sex cords in the female. After further development they become the ovarian follicles. UMLS:C1511527 ncithesaurus:Cortical_Cord ovigerous cords VHOG:0001339 The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]. TODO - check primary vs testis EHDAA2:0002011 EHDAA:8152 EMAPA:29098 VHOG:0001321 testis cord testis primary sex cords uberon primary sex cord testis primitive sex cord UBERON:0005297 testis sex cord Bgee:AN The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]. testis cord MP:0006424 testis primary sex cords EHDAA2:0002011 A zone of skin that is part of a clitoris [Automatically generated definition]. FMA:20168 clitoris skin uberon UBERON:0005298 skin of clitoris A zone of skin that is part of a clitoris [Automatically generated definition]. OBOL:automatic A pronephric nephron is the functional unit of the pronephros[GO]. The structure that is the basic functional unit of the pronephros.[AAO] AAO:0011091 XAO:0000285 uberon UBERON:0005309 pronephric nephron A pronephric nephron is the functional unit of the pronephros[GO]. GO:0039019 The structure that is the basic functional unit of the pronephros.[AAO] 2012-06-20 AAO:0011091 AAO UBERON:0005309 The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO]. Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO] TAO:0001558 XAO:0004105 ZFA:0001558 pronephric tubule uberon ciliated neck segment UBERON:0005310 pronephric nephron tubule GO The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO]. GO:0039020 ISBN:0073040584 Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO] 2012-08-14 TAO:0001558 TAO ZFIN:curator pronephric tubule ZFA:0001558 ciliated neck segment ZFA:0001558 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 The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO]. AAO:0010390 XAO:0000151 uberon UBERON:0005319 mesonephric collecting duct true The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO]. GO:0061211 . uberon UBERON:0005321 mesonephric smooth muscle tissue . GO:0061214 A nephron that is part of a mesonephros. The structure that is the basic functional unit of the kidney.[AAO] AAO:0010387 XAO:0000292 ZFA:0005592 nephron of mesonephros uberon stage IV nephron UBERON:0005322 mesonephric nephron XAO A nephron that is part of a mesonephros. The structure that is the basic functional unit of the kidney.[AAO] 2012-06-20 AAO:0010387 AAO stage IV nephron ZFA:0005592 Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. AAO:0011062 EHDAA2:0001132 EMAPA:16745 XAO:0000291 uberon UBERON:0005323 mesonephric mesenchyme Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. GO:0061219 The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO]. uberon UBERON:0005330 mesonephric nephron epithelium true The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO]. GO:0061241 The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. ZFA:0005586 mesonephric vesicle uberon UBERON:0005331 mesonephric renal vesicle ZFA The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. GO:0061243 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 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]. heart ventricle outflow tract MP:0010224 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 The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]. A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047] in humans develops into cortical layers II-VI CP CxP BAMS:CTXpl DHBA:10515 EMAPA:32711 MBA:695 PBA:294021914 cerebral cortex cortical plate future cortical layers II-VI neocortex cortical plate uberon future neocortex UBERON:0005343 cortical plate NCBIBook:NBK10047 The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]. MP:0008439 CP BRAINSPAN:BRAINSPAN CxP future cortical layers II-VI future neocortex The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP]. FMA:19937 GAID:395 MESH:D013085 NCIT:C12329 UMLS:C0037855 uberon funiculus spermaticus spermatic chord UBERON:0005352 spermatic cord The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP]. MP:0010145 UMLS:C0037855 ncithesaurus:Spermatic_Cord funiculus spermaticus A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord. EMAPA:35209 FMA:242770 ventricular layer uberon region of wall of ventricular system of neuraxis UBERON:0005358 ventricle of nervous system A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord. ventricular layer EMAPA:35209 region of wall of ventricular system of neuraxis FMA:242770 the group of sensory neuron cell bodies associated with the vagus nerve gX EMAPA:16798 FMA:53472 MA:0001081 TAO:0007067 VHOG:0000684 ZFA:0007067 ganglion of vagus nerve right glossopharyngeal ganglion vagal ganglion vagus ganglion vagus neural ganglion uberon vagus X UBERON:0005362 vagus X ganglion ZFA the group of sensory neuron cell bodies associated with the vagus nerve ISBN:0-683-40008-8 MP:0001100 gX ZFA:0007067 ganglion of vagus nerve FMA:53472 right glossopharyngeal ganglion FMA:53472 vagal ganglion ZFA:0007067 vagus neural ganglion FMA:53472 vagus X EMAPA:16798 An epithelium that lines the nasal cavity. this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism CALOHA:TS-0656 EHDAA2:0001227 EHDAA:6803 EMAPA:17605 FMA:63140 MA:0001324 NCIT:C49261 UMLS:C1709151 VHOG:0000501 nasal epithelium uberon nasal mucosa UBERON:0005384 nasal cavity epithelium An epithelium that lines the nasal cavity. UMLS:C1709151 ncithesaurus:Nasal_Cavity_Epithelium nasal epithelium FMA:63140 nasal mucosa MA:0001324 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. 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. 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 OpenCyc:Mx4rvg7rcJwpEbGdrcN5Y29ycA TAO:0000097 UMLS:C0007272 VHOG:0000266 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. 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 An arachnoid mater that surrounds a brain. The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32661 FMA:83981 MA:0000814 NCIT:C49331 VHOG:0000230 arachnoidea mater cranialis arachnoidea mater encephali brain arachnoid matter cranial arachnoid mater uberon UBERON:0005397 brain arachnoid mater An arachnoid mater that surrounds a brain. OBOL:automatic The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000230 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000230 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoidea mater cranialis FMA:83981 FMA:TA arachnoidea mater encephali FMA:83981 FMA:TA brain arachnoid matter MA:0000814 cranial arachnoid mater FMA:83981 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 A sex gland that is part of a male reproductive system. BTO:0000080 EMAPA:19285 MA:0000399 uberon accessory sex gland UBERON:0005399 male reproductive gland A sex gland that is part of a male reproductive system. OBOL:automatic accessory sex gland EMAPA:19285 An arachnoid mater that is part of a telencephalon. EMAPA:17775 MA:0000980 telencephalon arachnoid matter uberon UBERON:0005400 telencephalon arachnoid mater An arachnoid mater that is part of a telencephalon. OBOL:automatic telencephalon arachnoid matter MA:0000980 A gray matter that is part of a cerebral hemisphere. BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon BTO:0000823 CALOHA:TS-2361 EMAPA:37477 FMA:61821 MA:0000944 cerebral gray matter cerebral grey matter cerebral hemisphere grey matter uberon UBERON:0005401 cerebral hemisphere gray matter A gray matter that is part of a cerebral hemisphere. OBOL:automatic BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon BTO EMAPA:37477 MA:th cerebral gray matter BTO:0000823 cerebral grey matter MA:0000944 Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow. All vertebrates possess at least 4 circumventricular organs (including the hypothalamus) which can monitor the contents of the cerebrospinal fluid and secrete additional substances into it. (Butler, 1996, p. 330) CVOs contain neural tissue and are an integral part of neuroendocrine function; all of the CVOs, besides the subcommissural organ, contain extensive vasculature and fenestrated capillaries which leads to a leaky BBB at the site of the organs; the lack of a BBB allows CVOs to act as an alternative route for peptides and hormones in the neural tissue to the peripheral blood stream, while still protecting it from toxic substances EMAPA:35243 FMA:84081 MA:0002942 NLXANAT:20090312 CVO circumventricular organ circumventricular organ of neuraxis uberon UBERON:0005408 circumventricular organ Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow. MP:0013562 CVO NLXANAT:20090312 circumventricular organ NLXANAT:20090312 circumventricular organ of neuraxis FMA:84081 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:A03.492 NCIT:C12378 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. 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 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. AAO:0010381 BTO:0001645 EHDAA:1699 EMAPA:16406 FMA:296782 MIAA:0000065 RETIRED_EHDAA2:0003198 XAO:0003065 anterior limb bud limb bud - forelimb upper limb bud wing bud uberon arm bud UBERON:0005417 Genes: Tbx5 specifies forelimbs. Wnt2b restricts Fgf10 in chick // In tetrapods, the position of the forelimb is associated with the anterior expression border of Hoxc6 in the paraxial mesoderm (Burke et al., 1995) forelimb bud lexical A limb bud that develops into a forelimb. limb bud - forelimb MIAA:0000065 upper limb bud RETIRED_EHDAA2:0003198 wing bud NCBITaxon:8782 OBOL:automatic A limb bud that develops into a hindlimb. The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO] AAO:0010382 EHDAA:2358 EMAPA:16779 MIAA:0000256 RETIRED_EHDAA2:0003197 XAO:0003066 hind limb bud posterior limb bud uberon leg bud limb bud - hindlimb UBERON:0005418 Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. hindlimb bud lexical A limb bud that develops into a hindlimb. The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO] 2012-06-20 AAO:0010382 AAO XAO:curator hind limb bud XAO:0003066 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) 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 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 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 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 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 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 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 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 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 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 A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] 2012-09-17 VHOG:0001163 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] 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 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 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 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]. saccus aorticus FMA:24219 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 The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] AAO:0000249 EHDAA2:0000893 EHDAA:10631 EMAPA:18713 FMA:56432 NCIT:C12496 UMLS:C0222712 VHOG:0001113 Posterior lacerate foramen uberon foramen jugulare UBERON:0005456 jugular foramen The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] 2012-06-20 AAO:0000249 AAO AAO:LAP One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] 2012-09-17 VHOG:0001113 VHOG relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] 2012-06-20 AAO:0000249 AAO UMLS:C0222712 ncithesaurus:Jugular_Foramen Posterior lacerate foramen FMA:56432 foramen jugulare A thymus lobe that is in the left side of a thymus. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:71195 RETIRED_EHDAA2:0000964 left lobe of thymus left thymic lobe uberon UBERON:0005457 left thymus lobe A thymus lobe that is in the left side of a thymus. OBOL:automatic left lobe of thymus FMA:71195 left thymic lobe FMA:71195 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 uberon UBERON:0005460 left vitelline vein A vitelline vein that is in the left side of a multicellular organism. OBOL:automatic Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA]. lumbar lumbar region BTO:0001505 EMAPA:36623 FMA:61681 MA:0000027 NCIT:C34004 UMLS:C0024090 abdominal back back of abdomen dorsum of abdomen lower back lumbar part of back lumbar region of back posterior part of abdomen regio lumbalis uberon loin lombus lumbos UBERON:0005462 overlaps with region sometimes called 'loin' lower back MA Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA]. FMA:61681 lumbar region FMA:61681 UMLS:C0024090 ncithesaurus:Lumbar_Region abdominal back FMA:61681 back of abdomen FMA:61681 dorsum of abdomen FMA:61681 lower back MA:0000027 lumbar part of back FMA:61681 lumbar region of back posterior part of abdomen FMA:61681 regio lumbalis FMA:61681 FMA:TA loin BTO:0001505 A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae. marginal sinus EMAPA:37662 FMA:312355 MA:0003027 NCIT:C33033 NCIT:C33642 UMLS:C1518051 UMLS:C1518052 lymph node subcortical sinus uberon lymph path lymph sinus marginal sinus of lymph node subcapsular sinus UBERON:0005463 subcapsular sinus of lymph node A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae. marginal sinus EMAPA:37662 MA:th UMLS:C1518051 ncithesaurus:Lymph_Node_Sinus UMLS:C1518052 ncithesaurus:Lymph_Node_Subcapsular_Sinus lymph node subcortical sinus MA:0003027 lymph path lymph sinus marginal sinus of lymph node subcapsular sinus A thymus lobe that is in the right side of a thymus. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:71194 RETIRED_EHDAA2:0001758 right lobe of thymus right thymic lobe uberon UBERON:0005469 right thymus lobe A thymus lobe that is in the right side of a thymus. OBOL:automatic right lobe of thymus FMA:71194 right thymic lobe FMA:71194 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 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 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]. neural tube lateral wall sulcus limitans EHDAA2:0001265 Either of the two lateral lobes that constitute the thymus. each lobe of the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. Each lobe is composed of numerous lobules held together by delicate areolar tissue; the entire organ being enclosed in an investing capsule of a similar but denser structure. The primary lobules vary in size from that of a pin's head to that of a small pea, and are made up of a number of small nodules or follicles.[WP] FMA:71193 RETIRED_EHDAA2:0002021 lateral lobe of thymus lobe of thymus uberon UBERON:0005483 thymus lobe FMA-abduced-lr Either of the two lateral lobes that constitute the thymus. lateral lobe of thymus lobe of thymus FMA:71193 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 UMLS:C0231091 VHOG:0000401 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 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 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 omphalomesenteric vein EMAPA:16244 vitelline veins XAO:0004147 Cranial neural crest which gives rise to the glossopharyngeal ganglion. EHDAA2:0000714 EHDAA:660 TAO:0007066 ZFA:0007066 uberon UBERON:0005491 glossopharyngeal neural crest Cranial neural crest which gives rise to the glossopharyngeal ganglion. ZFA:0007066 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) non neural ectoderm ZFA:0001178 epidermal ectoderm epithelial ectoderm surface ectoderm ventral ectoderm ZFA:0001178 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16215 FMA:321916 TAO:0000149 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 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 A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]. we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO] variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals EFO:0003622 EHDAA2:0002023 EHDAA:2969 EMAPA:17523 TAO:0001077 ZFA:0001077 thymic primordium thymic rudiment uberon UBERON:0005562 thymus primordium ZFA EHDAA2 mesenchymal ZFA A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]. ZFA:0001077 we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. ISBN:0781714125 A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO] 2012-08-14 TAO:0001077 TAO ZFIN:curator variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals ISBN:0781714125 thymic primordium OBOL:automatic thymic rudiment ZFA:0001077 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 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 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 gonadal primordium ZFA:0001262 primitive gonad undifferentiated gonad ZFA:0001262 immature gonad Cranial neural crest that gives rise to the facio-acoustic ganglion. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0000492 EHDAA:658 EMAPA:16312 TAO:0000762 VHOG:0000268 ZFA:0000762 facio acoustic neural crest uberon UBERON:0005565 facio-acoustic neural crest EHDAA2 EHDAA2 Cranial neural crest that gives rise to the facio-acoustic ganglion. ZFA:0000762 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:0000268 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 facio acoustic neural crest ZFA:0000762 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 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 occipital somite 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. UBERON:3010717 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 uberon dorsal mesentery UBERON:0005602 dorsal mesogastrium MA 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. 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 UMLS:C1512038 ncithesaurus:Dorsal_Mesogastrium 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 Any of the three veins including the common, external and internal iliac veins. EHDAA2:0000811 EMAPA:37151 MA:0002142 MESH:D007084 NCIT:C12734 UMLS:C0020888 uberon pelvic vein UBERON:0005610 iliac vein Any of the three veins including the common, external and internal iliac veins. ncithesaurus:Iliac_Vein EMAPA:37151 MA:th UMLS:C0020888 ncithesaurus:Iliac_Vein 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 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 Contributes to the arch of aorta in humans 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 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. UMLS:C1182652 ncithesaurus:Subcapsular_Epithelium_of_the_Lens lens subcapsular epithelium 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 UMLS:C0025465 VHOG:0001117 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 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 UMLS:C0025473 uberon intestinal vein UBERON:0005617 mesenteric vein A vein that returns blood from the intestines. MESH:A07.231.908.670.385 UMLS:C0025473 ncithesaurus:Mesenteric_Vein intestinal vein 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 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 Normally regresses in humans Artery that supplies blood to the adrenal glands. EHDAA2:0001965 EHDAA:8596 EMAPA:37124 MA:0001914 NCIT:C33708 ncithesaurus:Adrenal_Artery uberon adrenal artery UBERON:0005624 suprarenal artery Artery that supplies blood to the adrenal glands. EMAPA:37124 MA:th adrenal artery MA:0001914 A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part. In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]. AEO:0000219 EHDAA2:0004112 EMAPA:35904 FMA:5900 XAO:0004143 plexus vasculosus uberon UBERON:0005629 vascular plexus A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part. In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]. plexus vasculosus 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 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 An epithelium that is part of a caecum. EHDAA2:0000209 uberon UBERON:0005636 caecum epithelium An epithelium that is part of a caecum. OBOL:automatic 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 2. 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] EHDAA2:0000055 EMAPA:16277 EMAPA:16397 EMAPA:16398 RETIRED_EHDAA2:0000064 VHOG:0001062 2nd pharyngeal arch ectoderm uberon UBERON:0005660 2nd arch ectoderm An ectoderm that is part of a pharyngeal arch 2. 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:0001062 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch ectoderm VHOG:0001062 An ectoderm that is part of a pharyngeal arch 3. 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] EHDAA2:0000072 EMAPA:16400 EMAPA:16582 EMAPA:16584 RETIRED_EHDAA2:0000079 VHOG:0000946 3rd pharyngeal arch ectoderm uberon UBERON:0005661 3rd arch ectoderm An ectoderm that is part of a pharyngeal arch 3. 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:0000946 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 3rd pharyngeal arch ectoderm VHOG:0000946 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) 4th pharyngeal arch ectoderm VHOG:0001095 An endoderm that is part of a pharyngeal arch 2. 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] EHDAA2:0000061 EMAPA:16274 EMAPA:16276 EMAPA:16278 RETIRED_EHDAA2:0000065 VHOG:0001108 2nd pharyngeal arch endoderm uberon UBERON:0005664 2nd arch endoderm An endoderm that is part of a pharyngeal arch 2. 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:0001108 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch endoderm VHOG:0001108 An endoderm that is part of a pharyngeal arch 3. 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] EHDAA2:0000075 EMAPA:16401 EMAPA:16585 EMAPA:16587 RETIRED_EHDAA2:0000080 VHOG:0001081 3rd pharyngeal arch endoderm uberon UBERON:0005665 3rd arch endoderm An endoderm that is part of a pharyngeal arch 3. 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:0001081 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 3rd pharyngeal arch endoderm VHOG:0001081 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) 4th pharyngeal arch endoderm VHOG:0001092 EHDAA2:0000314 uberon UBERON:0005667 connecting stalk mesoderm EHDAA2 EHDAA2 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 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 peritoneal mesothelium 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 mesentery that is part of a caecum. RETIRED_EHDAA2:0000210 uberon UBERON:0005677 caecum mesentery A mesentery that is part of a caecum. OBOL:automatic A dorsal mesentery that is part of a midgut. EMAPA:16722 EMAPA:17040 EMAPA:18671 RETIRED_EHDAA2:0001187 uberon UBERON:0005685 midgut dorsal mesentery A dorsal mesentery that is part of a midgut. OBOL:automatic A dorsal mesentery that is part of a caecum. RETIRED_EHDAA2:0000208 uberon UBERON:0005686 caecum dorsal mesentery A dorsal mesentery that is part of a caecum. 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 lens cavity EHDAA2:0000986 cavity of lens vesicle EMAPA:17164 Mesenchyme that is part of a pharyngeal arch 2. 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] EHDAA2:0000066 EHDAA:625 EMAPA:16279 FMA:295698 VHOG:0001102 2nd pharyngeal arch mesenchyme uberon 2nd branchial arch mesenchyme pharyngeal arch 2 mesenchyme UBERON:0005689 2nd arch mesenchyme Mesenchyme that is part of a pharyngeal arch 2. 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:0001102 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch mesenchyme VHOG:0001102 Mesenchyme that is part of a pharyngeal arch 3. 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] EHDAA2:0000081 EHDAA:1094 EMAPA:16402 FMA:295700 VHOG:0001083 3rd pharyngeal arch mesenchyme uberon 3rd branchial arch mesenchyme pharyngeal arch 3 mesenchyme UBERON:0005690 3rd arch mesenchyme Mesenchyme that is part of a pharyngeal arch 3. 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:0001083 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 3rd pharyngeal arch mesenchyme VHOG:0001083 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) 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 A mesoderm that has the potential to develop into a pronephros. Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] AAO:0011090 EFO:0003479 TAO:0000067 VHOG:0001239 XAO:0000264 ZFA:0000067 uberon pronephric anlage pronephric bulge pronephric mesenchyme pronephric primordium UBERON:0005721 the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm ZFA Bgee:AN A mesoderm that has the potential to develop into a pronephros. OBOL:automatic Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] 2012-06-20 AAO:0011090 AAO XAO:curator pronephric anlage XAO:0000264 pronephric bulge XAO:0000264 pronephric mesenchyme XAO:0000264 pronephric primordium XAO:0000264 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 A ring of cells capable of forming a limb. limb field of lateral plate mesoderm uberon UBERON:0005733 the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995) limb field A ring of cells capable of forming a limb. 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 UMLS:C0225342 adventitia externa tunica adventitia tunica adventitia of vessel uberon external coat tunica adventitia vasorum tunica externa vasorum UBERON:0005734 tunica adventitia of blood vessel cjm The outermost layer of a blood vessel, composed mainly of fibrous tissue. ISBN:0073040584 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)]. UMLS:C0225342 ncithesaurus:Tunica_Adventitia adventitia externa tunica adventitia tunica adventitia of vessel external coat tunica adventitia vasorum tunica externa vasorum A tunica intima that is part of a artery. EMAPA:36293 EV:0100028 FMA:14272 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 tunica advetitia tunica externa uberon UBERON:0005742 adventitia An outermost connective tissue covering of an organ, vessel, or other structure[WP]. tunica advetitia 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 foramens@fr foramina@fr uberon UBERON:0005744 bone foramen 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 foramens@fr TAO:0001736 foramina@fr TAO:0001736 The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. caudal portion of nephrogenic cord caudal region of nephrogenic cord rear part of nephrogenic cord rear portion of nephrogenic cord uberon UBERON:0005753 caudal part of nephrogenic cord The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. caudal portion of nephrogenic cord OBOL:automatic caudal region of nephrogenic cord OBOL:automatic rear part of nephrogenic cord OBOL:automatic rear portion of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. uberon UBERON:0005754 rostral part of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. A acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 uberon UBERON:0005764 acellular membrane A 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 UMLS:C0004799 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. UMLS:C0004799 ncithesaurus:Basement_Membrane basement membrane of connective tissue FMA:63872 membrana basalis basement membrane FMA:63872 Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. TODO - check ridge vs cord vs nephrogenic cord vs blastema EHDAA2:0001242 EHDAA:1015 EMAPA:16368 VHOG:0001240 uberon nephric cord UBERON:0005792 nephric ridge Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. nephric cord VHOG:0001240 FMA:72173 fetal uterus uberon UBERON:0005795 embryonic uterus fetal uterus FMA:72173 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 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 TAO:0000014 VHOG:0000264 XAO:0000051 ZFA:0000014 DA aorta dorsalis uberon aortae dorsales dorsal aorta root dorsal aortae dorsal aortic root dorsal aortæ UBERON:0005805 dorsal aorta 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 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] 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 DA ZFA:0000014 aorta dorsalis XAO:0000051 aortae dorsales dorsal aorta root VHOG:0000264 dorsal aortae dorsal aortic root VHOG:0000264 dorsal aortæ 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 UMLS:C0226727 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]. 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 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 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 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 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. 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 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 mandibular swelling prominentia mandibularis 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 UMLS:C1513037 embryonic maxillary process maxillary process maxillary process of embryo uberon prominentia maxilaris UBERON:0005868 maxillary 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 ISBN:0-683-40008-8 MP:0010940 UMLS:C1513037 ncithesaurus:Maxillary_Prominence maxillary process EHDAA2:0001070 prominentia maxilaris An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]. we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]. AAO:0011068 EFO:0003496 EHDAA2:0001295 EHDAA:4772 EMAPA:16800 FMA:295840 XAO:0000275 XAO:0004073 nasal pit uberon UBERON:0005870 olfactory pit EHDAA2 EMAPA EHDAA2 XAO:0000275 nasal pit An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]. GO:0060166 By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]. nasal pit XAO:0000275 the embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG] embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP] In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG] All amniotes studied to date initiate external genital development with the formation of paired genital swellings. In mammals, archosaurs, and turtles, these swellings merge to form a single genital tubercle, the precursor of the penis and clitoris[PMID:24960313] GT development is indistinguishable in male and female mouse embryos until approximately E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP:0011771] todo - add taxon constraints we assume the EMAPA class is the undifferentiated form based on TS timings EHDAA2:0000705 EHDAA:5925 EMAPA:17382 FMA:302888 VHOG:0000583 undifferentiated genital tubercle uberon genital tubercle phallic tubercle tuberculum genitale tuberculum phallicum UBERON:0005876 undifferentiated genital tubercle EHDAA2 the embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin MGI:anna MP:0011771 The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG] 2012-09-17 VHOG:0000583 VHOG embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP] MP In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG] 2012-09-17 VHOG:0000583 VHOG DOI:10.1242/dev.036830 Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development (2009) we assume the EMAPA class is the undifferentiated form based on TS timings EMAPA undifferentiated genital tubercle VHOG:0000583 genital tubercle EMAPA:17382 tuberculum genitale tuberculum phallicum A subdivision of skeleton that supports pharyngeal arch 2. it's not clear where AAO:'hyobranchial skeleton' belongs AAO:0000665 AAO:0010370 TAO:0001276 XAO:0003177 ZFA:0001276 hyal@fr hyocïde@fr hyoid arch skeleton pharyngeal arch 2 skeleton hyoid bars uberon hyoid arch visceral arch 2 UBERON:0005884 hyoid arch skeleton ZFA cjm A subdivision of skeleton that supports pharyngeal arch 2. OBOL:automatic it's not clear where AAO:'hyobranchial skeleton' belongs AAO hyal@fr TAO:0001276 hyocïde@fr TAO:0001276 hyoid arch skeleton ZFA:0001276 pharyngeal arch 2 skeleton ZFA:0001276 hyoid bars TAO:0001276 hyoid arch TAO:0001276 visceral arch 2 TAO:0001276 The epithelial lining of the surface of the coelom. EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium' XAO:0000329 celomic epithelium germinal epithelium of Waldeyer uberon UBERON:0005891 coelomic epithelium XAO XAO The epithelial lining of the surface of the coelom. XAO:0000329 EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium' EHDAA2 germinal epithelium of Waldeyer 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 TAO:0001414 XAO:0003173 ZFA:0001414 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 basicranial region ZFA:0001414 occipital part of head FMA:49187 occipital region of head FMA:49187 back of head FMA:49187 Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP]. EMAPA:29282 FMA:19473 ductus excretorius (vesicula seminalis) ductus excretorius glandulae vesiculosae excretory duct of seminal gland seminal vesicle duct uberon ductus excretorius glandulae vesiculosae UBERON:0005903 duct of seminal vesicle Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP]. ductus excretorius (vesicula seminalis) FMA:19473 ductus excretorius glandulae vesiculosae FMA:19473 FMA:TA excretory duct of seminal gland FMA:19473 seminal vesicle duct FMA:19473 ductus excretorius glandulae vesiculosae Any of the ducts that are part of a male reproductive system. this class groups the individual ducts in a variety of species uberon UBERON:0005904 duct of male reproductive system Any of the ducts that are part of a male reproductive system. Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] EMAPA:16060 FMA:9689 MA:0000005 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 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 UMLS:C0222645 VSAO:0000056 XAO:0004011 uberon skeleton axiale UBERON:0005944 axial skeleton plus cranial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. FMA:71221 VSAO:0000056 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 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 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 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 EMAPA:37926 MA:th UMLS:C1881209 ncithesaurus:Infundibulum RVOT MP:0010428 conus arteriosus (infundibulum) FMA:7216 infundibulum of right ventricle FMA:7216 infundibulum of right ventricle 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 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 aortic vestibule 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 A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]. EMAPA:16076 amnionic fold uberon UBERON:0005971 amniotic fold ISBN:0073040584 A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]. ISBN:0073040584 amnionic fold 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 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 paired arteries that carry blood to the yolk sac from the dorsal aorta EHDAA2:0002208 EMAPA:16207 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 ventral branch The paired arteries that carry blood to the yolk sac from the dorsal aorta MP:0010664 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 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. 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 skin adnexa 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 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. 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 post-anal tail region 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 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. 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 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. 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 lumbar subdivision of the body, containing the lumbar vertebrae. lumbar BTO:0004147 EHDAA2:0001037 EHDAA:5055 EMAPA:17393 FMA:16203 GAID:31 MA:0003156 NCIT:C69314 axial skeleton lumbar region lumbar skeleton lumbar spine lumbar vertebrae series lumbar vertebral column uberon UBERON:0006074 lumbar region of vertebral column Subdivision of vertebral column that corresponds to the lumbar subdivision of the body, containing the lumbar vertebrae. UBERONREF:0000006 axial skeleton lumbar region MA:0003156 lumbar skeleton EHDAA2:0001037 lumbar spine BTO:0004147 lumbar vertebral column FMA:16203 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 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. subdivision of vertebral skeleton vertebral column subdivision FMA:16201 The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. uberon UBERON:0006170 mesonephric capsule The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. GO:0061285 GOC:mtg_kidney_jan10 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 aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale uberon aortic septum spiral septum UBERON:0006207 aortico-pulmonary spiral septum 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 aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale aortic septum spiral 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 VHOG:0000380 uberon oral membrane oral plate oropharyngeal membrane pharyngeal membrane UBERON:0006211 buccopharyngeal membrane 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 pharyngeal membrane MP:0012521 the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO] UBERON:0013163 DHBA:10664 EHDAA2:0000231 EMAPA:17074 TAO:0001440 XAO:0004135 ZFA:0001440 uberon cerebellar anlage cerebellar primordium cerebellum primordium dorsal part of alar plate of metencephalon future cerebellum presumptive cerebellum rostral rhombic lip UBERON:0006215 rhombic lip EHDAA2 Wikipedia the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system MGI:anna MP:0012525 The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO] 2012-08-14 TAO:0001440 TAO ZFIN:curator cerebellar anlage MGI:anna cerebellar primordium EMAPA:17074 cerebellum primordium EHDAA2:0000231 EMAPA:17074 dorsal part of alar plate of metencephalon EMAPA:17074 future cerebellum presumptive cerebellum MGI:anna rostral rhombic lip MGI:anna The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] EHDAA2:0000257 EHDAA:214 EHDAA:2933 EMAPA:16832 FMA:295525 NCIT:C34128 UMLS:C0231056 VHOG:0001198 embryonic cloacal membrane uberon membrana cloacalis UBERON:0006217 cloacal membrane Wikipedia The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. MP:0011837 MP:anna A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0001198 VHOG In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] 2012-09-17 VHOG:0001198 VHOG PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002) UMLS:C0231056 ncithesaurus:Cloacal_Membrane membrana cloacalis The foremost region of the future forebrain that develops into the diencephalon. EFO:0003442 EHDAA2:0000600 EHDAA:844 EMAPA:16514 RETIRED_EHDAA2:0000386 TAO:0000574 ZFA:0000574 presumptive diencephalon uberon UBERON:0006222 future diencephalon EHDAA2 The foremost region of the future forebrain that develops into the diencephalon. UBERON:cjm presumptive diencephalon TAO:0000574 EHDAA:1477 EMAPA:16660 RETIRED_EHDAA2:0000496 VHOG:0000715 uberon facio-acoustic preganglion complex UBERON:0006232 facio-acoustic VII-VIII preganglion complex EHDAA2 facio-acoustic preganglion complex EMAPA:16660 A differentiated genital tubercle that is part of a female reproductive system. EHDAA:8118 EMAPA:18680 RETIRED_EHDAA2:0000500 VHOG:0000666 genital tubercle of female uberon UBERON:0006233 female genital tubercle true A differentiated genital tubercle that is part of a female reproductive system. OBOL:automatic genital tubercle of female EMAPA:18680 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 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) 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 cranial part of septum transversum A presumptive structure that has the potential to develop into a forebrain. TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate) BAMS:Pros EFO:0003423 EHDAA2:0000661 EHDAA:2643 EMAPA:16640 TAO:0000062 ZFA:0000062 future prosencephalon presumptive forebrain presumptive prosencephalon uberon prosencephalon UBERON:0006240 future forebrain A presumptive structure that has the potential to develop into a forebrain. OBOL:automatic presumptive forebrain ZFA:0000062 presumptive prosencephalon TAO:0000062 prosencephalon EHDAA2:0000661 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 uberon UBERON:0006242 gall bladder primordium cjm 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 Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG] Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] EHDAA2:0000996 EMAPA:17186 VHOG:0000449 uberon lingual swelling UBERON:0006260 the collection consisting of the two lateral swellings and the medial swelling lingual swellings EHDAA2 EHDAA2 Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG] 2012-09-17 VHOG:0000449 VHOG Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000449 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) lingual swelling EHDAA2:0000996 A differentiated genital tubercle that is part of a male reproductive system. EHDAA:8138 EMAPA:17969 RETIRED_EHDAA2:0001048 VHOG:0000667 genital tubercle of male uberon penis anlage UBERON:0006261 male genital tubercle true A differentiated genital tubercle that is part of a male reproductive system. OBOL:automatic genital tubercle of male EMAPA:17969 penis anlage EMAPA:17969 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 Groove between maxillary prominence and lateral nasal process. EHDAA2:0001238 EHDAA:4770 EMAPA:16679 FMA:300055 NCIT:C34218 UMLS:C1513875 VHOG:0001307 naso-lacrimal groove uberon s. lacrimalis maxillae UBERON:0006266 On the nasal surface of the body of the maxilla, in front of the opening of the sinus is a deep groove, the lacrimal groove (or lacrimal sulcus), which is converted into the nasolacrimal canal, by the lacrimal bone and inferior nasal concha; this canal opens into the inferior meatus of the nose and transmits the nasolacrimal duct[WP] See also: oblique facial cleft nasolacrimal groove EHDAA2 EHDAA2 EHDAA2 Groove between maxillary prominence and lateral nasal process. UMLS:C1513875 ncithesaurus:Nasolacrimal_Groove naso-lacrimal groove EMAPA:16679 s. lacrimalis maxillae 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 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 UMLS:C1518430 ncithesaurus:Notochordal_Process the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] UBERON:0009123 EHDAA2:0001336 EHDAA:929 EMAPA:16536 FMA:302911 NCIT:C34238 VHOG:0001147 otic cup uberon UBERON:0006273 otic pit EHDAA2 the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles ISBN:0-683-40008-8 MP:0011172 A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] 2012-09-17 VHOG:0001147 VHOG otic cup NCBIBook:NBK53175 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 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 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 TAO:0002231 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 future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle 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] DHBA:10595 EHDAA2:0001571 EHDAA:1356 EMAPA:16521 TAO:0001259 VHOG:0000644 ZFA:0001259 prosencephalic vesicle preevaginated forebrain vesicle uberon forebrain ventricle forebrain vesicle prosencephalic ventricle UBERON:0006284 early prosencephalic vesicle EHDAA2 future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle 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:0000644 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 prosencephalic vesicle EHDAA2:0001571 forebrain ventricle VHOG:0000644 forebrain vesicle VHOG:0000644 prosencephalic ventricle VHOG:0000644 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 splenic primordium EHDAA2:0001904 left spleen primordium XAO:0000326 A primordium that has the potential to develop into a submandibular gland. EHDAA2:0001939 EHDAA:9255 EMAPA:17755 uberon submaxillary gland primordium UBERON:0006298 submandibular gland primordium A primordium that has the potential to develop into a submandibular gland. OBOL:automatic submaxillary gland primordium EMAPA:17755 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 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 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. 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 fluid BIRNLEX:20 EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 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 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 A choroid plexus stroma that is part of a lateral ventricle. definitions should be fixed to use generic stroma class MA:0000963 uberon UBERON:0006338 lateral ventricle choroid plexus stroma A choroid plexus stroma that is part of a lateral ventricle. OBOL:automatic A choroid plexus stroma that is part of a fourth ventricle. MA:0000985 uberon UBERON:0006340 fourth ventricle choroid plexus stroma A choroid plexus stroma that is part of a fourth ventricle. OBOL:automatic 2 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 inferred from artery EMAPA:18646 MA:0002227 uberon UBERON:0006355 superior vesical vein true MA the unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species found in most mammals, with the exception of humans EMAPA:29769 MA:0000406 baculum os baculum penile bone penis bone uberon UBERON:0006435 os penis the unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species MGI:anna MP:0009103 baculum penile bone penile bone MP:0009104 penis bone The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals EMAPA:30823 MA:0000387 baubellum clitoral bone clitoris bone os clitoridis uberon UBERON:0006440 os clitoris The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals MP:0011849 baubellum clitoral bone MP:0011849 os clitoridis A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. this ontology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted) we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation seminal fluid may have a role in sperm capacitation, sperm motility BTO:0001232 CALOHA:TS-0918 EMAPA:36543 FMA:62967 MA:0002523 MAT:0000057 MIAA:0000057 seminal plasma uberon male genital fluid male genital secretion seminal fluid UBERON:0006530 seminal fluid A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation seminal plasma BTO:0001232 seminal fluid BTO:0001232 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 male reproductive gland. EMAPA:36541 MA:0002521 male reproductive system fluid/secretion uberon male reproductive system fluid male reproductive system secretion UBERON:0006536 male reproductive gland secretion A portion of organism substance that is secreted by a male reproductive gland. UBERON:cjm male reproductive system fluid/secretion MA:0002521 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 vasculature that is part of a kidney. EMAPA:28457 TAO:0005305 ZFA:0005305 uberon UBERON:0006544 kidney vasculature A vasculature that is part of a kidney. OBOL:automatic A tube in the kidney that collect and transport urine. in ZFA this is defined as part of mesonephros TAO:0005289 ZFA:0005289 uberon UBERON:0006553 renal duct A tube in the kidney that collect and transport urine. ZFIN:ZDB-PUB-071029-9 in ZFA this is defined as part of mesonephros ZFA 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 An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. consider merging with lymph vasculature Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] lymporeticular in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system AAO:0010522 CALOHA:TS-2024 EFO:0000870 EMAPA:18248 FMA:7162 MA:0002961 MESH:D008208 VHOG:0001761 lymphatic system lymphatic tree system uberon lymporeticular system UBERON:0006558 lymphatic part of lymphoid system AAO FMA MA An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] 2012-06-20 AAO:0010522 AAO AAO:BJB in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system FMA lymphatic system FMA:7162 MA:0002435 lymphatic tree system FMA:7162 lymporeticular system VHOG:0001761 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. branchial pharyngeal FBbt:00005380 MAT:0000049 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 urethral meatus that is part of a female urethra[Automatically generated definition]. The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts. EMAPA:36453 FMA:85266 MA:0002639 external orifice of female urethra external urethral orifice (female) female urethral meatus ostium urethrae externum (urethra feminina) urethral meatus of clitoral urethra uberon distal urethral opening of female urethral opening of clitoral urethra UBERON:0006565 female urethral meatus A urethral meatus that is part of a female urethra[Automatically generated definition]. OBOL:automatic The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts. external orifice of female urethra FMA:85266 external urethral orifice (female) FMA:85266 female urethral meatus FMA:85266 ostium urethrae externum (urethra feminina) FMA:85266 FMA:TA urethral meatus of clitoral urethra EMAPA:36453 distal urethral opening of female EMAPA:36453 urethral opening of clitoral urethra EMAPA:36453 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 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. 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 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. 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 nucleus of brain that is part of a hypothalamus. BTO:0002449 EMAPA:35417 FMA:258762 MA:0002426 nucleus of hypothalamus uberon UBERON:0006568 hypothalamic nucleus A nucleus of brain that is part of a hypothalamus. OBOL:automatic nucleus of hypothalamus FMA:258762 A nucleus of brain that is part of a diencephalon. TAO:0002191 ZFA:0001659 uberon UBERON:0006569 diencephalic nucleus A nucleus of brain that is part of a diencephalon. OBOL:automatic 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 UMLS:C0821671 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 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 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 linea anocutanea recto-anal junction site of anal membrane EMAPA:19159 An organ that is part of a vestibular system. BIRNLEX:2519 UMLS:C0682674 balance organ uberon UBERON:0006585 vestibular organ NIFSTD An organ that is part of a vestibular system. OBOL:automatic UMLS:C0682674 BIRNLEX:2519 balance organ 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. 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. 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. 2 2 A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified]. this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO] in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible AAO:0000277 FMA:75779 MA:0001490 TAO:0001851 ZFA:0005488 dentary symphysis inter-dentary joint inter-mandibular joint symphysis menti uberon mental symphysis symphysis mandibulae UBERON:0006606 mandibular symphysis FMA connects adjacent mandibles A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified]. TAO:wd ZFA:0005488 Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO] 2012-08-14 TAO:0001851 TAO TAO:wd in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible ISBN:0073040584 dentary symphysis TAO:0001851 inter-dentary joint TAO:0001851 inter-mandibular joint TAO:0001851 symphysis menti MA:0001490 mental symphysis symphysis mandibulae Exoskeleton or shell, including those of mollusks, turtles, insects and crustaceans. not to be confused with dermal skeleton exoskeletal BTO:0004659 lorica test uberon shell UBERON:0006611 exoskeleton Exoskeleton or shell, including those of mollusks, turtles, insects and crustaceans. lorica shell BTO:0004659 An artery with its origin in the lateral terminal branch of the internal thoracic artery, with distribution to the diaphragm and the intercostal muscles, and with anastomoses to the branches of the pericardiacophrenic and inferior phrenic. EMAPA:19215 FMA:10645 musculophrenic artery uberon UBERON:0006632 musculo-phrenic artery An artery with its origin in the lateral terminal branch of the internal thoracic artery, with distribution to the diaphragm and the intercostal muscles, and with anastomoses to the branches of the pericardiacophrenic and inferior phrenic. musculophrenic artery FMA:10645 A muscle layer that is part of a fallopian tube. EMAPA:29046 FMA:18318 muscle layer of fallopian tube muscle layer of oviduct muscle layer of uterine tube muscular coat of uterine tube muscular layer of uterine tube muscularis of uterine tube tunica muscularis (Tuba uterina) tunica muscularis tubae uterinae uterine tubal muscularis uberon UBERON:0006642 muscle layer of oviduct A muscle layer that is part of a fallopian tube. OBOL:automatic muscle layer of fallopian tube FMA:18318 muscle layer of oviduct FMA:18318 muscle layer of uterine tube FMA:18318 muscular coat of uterine tube FMA:18318 muscular layer of uterine tube FMA:18318 muscularis of uterine tube FMA:18318 tunica muscularis (Tuba uterina) FMA:18318 tunica muscularis tubae uterinae FMA:18318 FMA:TA uterine tubal muscularis FMA:18318 An adventitia that is part of a epididymis. EMAPA:30443 FMA:19136 epididymis adventitia uberon UBERON:0006645 adventitia of epididymis An adventitia that is part of a epididymis. OBOL:automatic epididymis adventitia FMA:19136 A muscle layer that is part of a epididymis. EMAPA:30747 FMA:19149 uberon UBERON:0006646 muscle layer of epididymis A muscle layer that is part of a epididymis. OBOL:automatic An adventitia that is part of a vas deferens. EMAPA:29767 FMA:19238 adventitia of deferent duct adventitia of ductus deferens adventitia of vas deferens deferent ductal adventitia tunica adventitia (ductus deferens) tunica adventitia ductus deferentis uberon UBERON:0006647 adventitia of ductus deferens An adventitia that is part of a vas deferens. OBOL:automatic adventitia of deferent duct FMA:19238 adventitia of ductus deferens FMA:19238 adventitia of vas deferens FMA:19238 deferent ductal adventitia FMA:19238 tunica adventitia (ductus deferens) FMA:19238 tunica adventitia ductus deferentis FMA:19238 FMA:TA An adventitia that is part of a seminal vesicle. EMAPA:29775 FMA:19403 adventitia of seminal gland seminal vesicle adventitia tunica adventitia (vesicula seminalis) tunica adventitia glandulae vesiculosae uberon UBERON:0006648 adventitia of seminal vesicle An adventitia that is part of a seminal vesicle. OBOL:automatic adventitia of seminal gland FMA:19403 seminal vesicle adventitia FMA:19403 tunica adventitia (vesicula seminalis) FMA:19403 tunica adventitia glandulae vesiculosae FMA:19403 FMA:TA EMAPA:30997 FMA:19976 muscular coat of vagina tunica muscularis vaginae vaginal muscularis uberon UBERON:0006652 muscular layer of vagina muscular coat of vagina FMA:19976 tunica muscularis vaginae FMA:19976 FMA:TA Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP]. BTO:0003117 EMAPA:19170 EMAPA:30829 FMA:19999 NCIT:C32681 UMLS:C0227769 clitoris glans glans of clitoris uberon glans clitoridis glans clitoris UBERON:0006653 glans clitoris cjm Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP]. BTO:0003117 UMLS:C0227769 ncithesaurus:Glans_Clitoris clitoris glans FMA:19999 glans of clitoris FMA:19999 glans clitoridis glans clitoris 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 UMLS:C0225358 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. 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 muscularis externa BTO:0004838 muscularis propria transverse muscular fibers tunica externa BTO:0004838 tunica muscularis On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]. EMAPA:18707 FMA:55805 uberon canalis caroticus UBERON:0006668 carotid canal On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]. canalis caroticus 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 UMLS:C0230162 VHOG:0001399 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 UMLS:C0230162 ncithesaurus:Central_Tendon_of_the_Diaphragm central tendon FMA:58279 centrum tendineum FMA:58279 centrum tendineum diaphragmatis FMA:58279 FMA:TA A valve that is part of a vein. FMA:68095 valve of vein uberon UBERON:0006675 venous valve A valve that is part of a vein. OBOL:automatic valve of vein FMA:68095 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 The hypoglossal canal is a bony canal in the occipital bone of the skull. EMAPA:19012 FMA:75370 uberon anterior condylar canal canalis nervi hypoglossi hyperglossal canal UBERON:0006682 hypoglossal canal The hypoglossal canal is a bony canal in the occipital bone of the skull. anterior condylar canal EMAPA:19012 canalis nervi hypoglossi hyperglossal canal A vein that is part of a vertebral column. EMAPA:18255 FMA:76735 MA:0002108 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 NCIT:C33869 NCIT:C34221 UMLS:C0037922 UMLS:C1522467 uberon c. vertebralis foramen vertebrale neural canal spinal canal spinal cavity vertebral canal UBERON:0006692 vertebral canal A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. 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 UMLS:C0037922 ncithesaurus:Vertebral_Canal UMLS:C1522467 ncithesaurus:Neural_Canal c. vertebralis foramen vertebrale AAO:0000693 neural canal AAO:0000693 spinal canal AAO:0000693 spinal cavity vertebral canal A vasculature that is part of a cerebellum. FMA:268519 uberon UBERON:0006694 cerebellum vasculature A vasculature that is part of a cerebellum. OBOL:automatic During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's]. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] EHDAA2:0001081 EMAPA:17187 FMA:312476 VHOG:0000730 median lingual swelling median tongue bud tuberculum impar tuberculum linguale mediale uberon UBERON:0006756 The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview] median lingual swelling EHDAA2 During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's]. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000730 VHOG median lingual swelling EHDAA2:0001081 median tongue bud tuberculum linguale mediale During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] paired EHDAA2:0000911 EMAPA:17189 FMA:313628 VHOG:0000731 uberon lateral lingual prominence lateral swellings tuberculum laterale tuberculum linguale laterale UBERON:0006757 lateral lingual swelling During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000731 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) lateral swellings tuberculum laterale tuberculum linguale laterale 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 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 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 corneal limbus GAID:896 corneal-scleral limbus corneoscleral junction GAID:896 limbus corneae sclerocorneal junction FMA:58342 sclerocorneal limbus GAID:896 limbus corneae 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. UMLS:C0682578 ncithesaurus:Glandular_Epithelium UMLS:C1708242 ncithesaurus:Glandular_Epithelial_Tissue Structural framework that provides support to the nasal sacs and ducts. AAO:0000320 FMA:60116 skeleton of nose uberon UBERON:0006813 nasal skeleton FMA FMA facial series Kardong-abduced Structural framework that provides support to the nasal sacs and ducts. AAO:0000320 skeleton of nose FMA:60116 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 loose areolar connective tissue uberon areolar tissue loose connective tissue UBERON:0006815 areolar connective tissue 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 An anatomical space that surrounded_by a trachea. FMA:7469 lumen of cartilaginous trachea tracheal lumen uberon UBERON:0006833 lumen of trachea An anatomical space that surrounded_by a trachea. OBOL:automatic lumen of cartilaginous trachea OBOL:automatic tracheal lumen FMA:7469 A furrow or an incomplete tube. AEO:0000161 EHDAA2_RETIRED:0003161 uberon groove UBERON:0006846 surface groove A furrow or an incomplete tube. AEO:0000161 AEO:JB groove AEO:0000161 A muscular coat that is part of a ureter. EMAPA:28811 FMA:15893 MA:0002654 muscular coat of ureter muscular layer of ureter muscularis of ureter tunica muscularis (ureter) tunica muscularis ureteris uberon ureteral smooth muscle layer UBERON:0006855 muscular coat of ureter FMA A muscular coat that is part of a ureter. OBOL:automatic muscular coat of ureter FMA:15893 muscular layer of ureter FMA:15893 muscularis of ureter FMA:15893 tunica muscularis (ureter) FMA:TA tunica muscularis ureteris FMA:TA ureteral smooth muscle layer EMAPA:28567 This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] keep this grouping class so long as it is required for GO All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] VHOG:0001141 adrenal gland - interrenal gland adrenal gland/interrenal tissue uberon adrenal - interrenal gland suprarenal gland - interrenal gland UBERON:0006858 adrenal/interrenal gland This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] GO:0030325 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 adrenal gland - interrenal gland VHOG:0001141 adrenal - interrenal gland VHOG:0001141 suprarenal gland - interrenal gland VHOG:0001141 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. rectum FBbt:00005756 A gland that secretes a seminal fluid. FBbt:00004958 WBbt:0006870 uberon UBERON:0006868 seminal fluid secreting gland A gland that secretes a seminal fluid. OBOL:automatic 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 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 gut cavity BTO:0000349 gut lumen FMA:45677 lumen of alimentary tract lumen of digestive tract 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 UMLS:C0221909 uberon UBERON:0006914 squamous epithelium 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 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 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 UMLS:C0836131 ncithesaurus:Stratified_Squamous_Epithelium epithelium stratificatum squamosum FMA:45563 A non-keratinized stratified squamous epithelium that is part of a tongue. FMA:62130 uberon UBERON:0006916 non-keratinized epithelium of tongue A non-keratinized stratified squamous epithelium that is part of a tongue. OBOL:automatic A squamous epithelium that is part of a tongue. this is a singleton subclass of tongue epithelium in MA MA:0002786 squamous epithelium of tongue uberon UBERON:0006919 tongue squamous epithelium A squamous epithelium that is part of a tongue. OBOL:automatic this is a singleton subclass of tongue epithelium in MA MA squamous epithelium of tongue OBOL:automatic 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 The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. MA:0001725 NCIT:C49219 UMLS:C1707351 cervical squamous epithelium uberon UBERON:0006922 cervix squamous epithelium The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. UMLS:C1707351 ncithesaurus:Cervix_Squamous_Epithelium A squamous epithelium that is part of a vagina. EMAPA:37794 MA:0001731 NCIT:C49314 UMLS:C1711259 vaginal squamous epithelium uberon UBERON:0006923 vagina squamous epithelium A squamous epithelium that is part of a vagina. OBOL:automatic EMAPA:37794 MA:th UMLS:C1711259 ncithesaurus:Vaginal_Squamous_Epithelium 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 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. 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 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 epithelial cells lining the capsule and trabeculae of the thymus TODO - check whether this is part of the thymus or borders it MA:0000769 uberon UBERON:0006936 thymus subcapsular epithelium the epithelial cells lining the capsule and trabeculae of the thymus ISBN:0-8153-1691-7 MGI:cwg MP:0002369 the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals EMAPA:32883 MA:0001189 uberon UBERON:0006937 inner ear epithelium the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals MGI:csmith MP:0003308 The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis. Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO] There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis Check EMAPA AAO:0010532 EMAPA:18993 FMA:19081 MA:0000398 NCIT:C32492 UMLS:C0228013 efferent ductule seminal duct uberon ductuli efferentes testis vasa efferentia UBERON:0006946 efferent duct FMA The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis. Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO] 2012-06-20 AAO:0010532 AAO AAO:BJB Check EMAPA EMAPA UMLS:C0228013 ncithesaurus:Efferent_Ductule efferent ductule efferent ductule FMA:19081 ductuli efferentes testis ductuli efferentes testis vasa efferentia AAO:0010532 A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra. we use this as a generic grouping class for a number of taxa in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct UBERON:0010140 FMA:55678 TAO:0001268 ZFA:0001268 sperm duct sperm ducts uberon UBERON:0006947 male genital duct FMA-abduced-lr A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra. in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct FMA sperm duct ZFA:0001268 sperm ducts TAO:0001268 An epithelium that is part of a efferent duct. EMAPA:29747 FMA:19195 MA:0001734 epithelium of efferent ductule of testis uberon UBERON:0006948 efferent duct epithelium An epithelium that is part of a efferent duct. OBOL:automatic epithelium of efferent ductule of testis FMA:19195 The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands. TODO - split off insect classes BTO:0002618 EMAPA:29786 uberon UBERON:0006953 ejaculatory duct epithelium The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands. An epithelium that is part of a uterus. BTO:0003082 uberon uterus epithelium UBERON:0006955 uterine epithelium An epithelium that is part of a uterus. OBOL:automatic uterus epithelium BTO:0003082 An epithelium that is part of a submandibular gland primordium. EHDAA2:0001940 EHDAA:9257 EMAPA:17756 uberon submaxillary gland primordium epithelium UBERON:0006957 submandibular gland primordium epithelium An epithelium that is part of a submandibular gland primordium. OBOL:automatic submaxillary gland primordium epithelium EMAPA:17756 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 UMLS:C0737271 interstitial tissue of ovary ovarian stroma ovary stroma stroma of the ovary stroma ovarica uberon stroma ovarii UBERON:0006960 ovary stroma 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. 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 stroma ovarica FMA:18626 stroma ovarii 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. 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 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 cardiogenic splanchnopleure EHDAA2:0000214 cardiac mesoderm XAO:0000235 cardiogenic mesoderm cardiogenic region heart primordia XAO:0000235 Organism at the cleavage stage. BILA:0000058 uberon UBERON:0007010 cleaving embryo Organism at the cleavage stage. OBOL:automatic A multicellular organism that is at the juvenile stage. Whole organism that is not fully grown or sexually mature.[TAO] juvenile BILA:0000076 TAO:0002047 juvenile organism juveniles uberon UBERON:0007021 sexually immature organism A multicellular organism that is at the juvenile stage. OBOL:automatic Whole organism that is not fully grown or sexually mature.[TAO] 2012-08-14 TAO:0002047 TAO TAO:wd juvenile organism BILA:0000076 juveniles TAO:0002047 A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. Whole organism that is fully grown or sexually mature.[TAO] adult BILA:0000078 FBbt:00003004 HAO:0000087 NCIT:C17600 TAO:0002046 UMLS:C0001675 galen:Adult adults uberon UBERON:0007023 adult organism A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. OBOL:automatic Whole organism that is fully grown or sexually mature.[TAO] 2012-08-14 TAO:0002046 TAO TAO:wd UMLS:C0001675 ncithesaurus:Adult adults TAO:0002046 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 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 Cranial neural crest that migrates into the hyoid arch. TAO:0007065 XAO:0000025 ZFA:0007065 hyoid crest uberon UBERON:0007099 hyoid neural crest ZFA ZFA Cranial neural crest that migrates into the hyoid arch. ZFA:0007065 hyoid crest XAO:0000025 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 FBbt:00003154 SPD:0000130 TADS:0000147 dorsal tube heart uberon adult heart UBERON:0007100 Gene notes: Bmp, Nkx, Gata primary circulatory organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. GO:0007507 dorsal tube heart GO:0007507 adult heart FBbt:00003154 A pharyngeal pouch that is between pharyngeal arches 1 and 2. . [][VHOG] In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery we use adjacency relations rather than part_of, as in EHDAA2. UBERON:0005718 AAO:0011114 EFO:0003631 EHDAA2:0000016 EMAPA:16124 EMAPA:16125 FMA:295668 NCIT:C34176 TAO:0001128 UMLS:C0231068 VHOG:0000555 VHOG:0000970 XAO:0000102 ZFA:0001128 1st arch branchial pouch 1st arch branchial pouch endoderm 1st arch pouch endoderm 1st branchial pouch 1st pharyngeal pouch endoderm first arch pharyngeal pouch first visceral pouch hyomandibular pouch pharyngeal pouches 1 visceral pouch 1 uberon first pharyngeal pouch UBERON:0007122 pharyngeal pouch 1 A pharyngeal pouch that is between pharyngeal arches 1 and 2. ISBN:0124020607 VHOG:0000970 . [][VHOG] 2012-09-17 VHOG:0000970 VHOG In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] 2012-09-17 VHOG:0000970 VHOG DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010) The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery WP we use adjacency relations rather than part_of, as in EHDAA2. EHDAA2 UMLS:C0231068 ncithesaurus:First_Pharyngeal_Pouch 1st arch branchial pouch EHDAA2:0000013 1st arch branchial pouch endoderm EHDAA2:0000016 1st arch pouch endoderm EHDAA2:0000016 1st pharyngeal pouch endoderm VHOG:0000555 first arch pharyngeal pouch OBOL:automatic first visceral pouch XAO:0000102 pharyngeal pouches 1 ZFA:0001128 visceral pouch 1 XAO:0000102 first pharyngeal pouch VHOG:0000970 A pharyngeal puch that is between the pharyngeal arches 2 and 3. A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG] Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[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] the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract. Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve UBERON:0005715 AAO:0011115 EFO:0003633 EHDAA2:0000058 EMAPA:16275 EMAPA:16276 FMA:295676 NCIT:C34289 RETIRED_EHDAA2:0000060 TAO:0001130 UMLS:C0231069 VHOG:0000561 VHOG:0000967 XAO:0000247 ZFA:0001130 2nd arch branchial pouch 2nd arch branchial pouch endoderm 2nd arch pouch endoderm 2nd branchial pouch 2nd pharyngeal pouch endoderm pharyngeal pouches 2 second arch pharyngeal pouch second visceral pouch visceral pouch 2 uberon second pharyngeal pouch UBERON:0007123 pharyngeal pouch 2 A pharyngeal puch that is between the pharyngeal arches 2 and 3. ISBN:0124020607 A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0000967 VHOG Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] 2012-06-20 AAO:0011115 AAO ISBN:0-226-55763-4 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:0000967 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) Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve WP UMLS:C0231069 ncithesaurus:Second_Pharyngeal_Pouch 2nd arch branchial pouch RETIRED_EHDAA2:0000060 2nd arch branchial pouch endoderm EHDAA2:0000061 2nd arch pouch endoderm EHDAA2:0000058 2nd pharyngeal pouch endoderm VHOG:0000561 pharyngeal pouches 2 ZFA:0001130 second arch pharyngeal pouch OBOL:automatic second visceral pouch XAO:0000247 visceral pouch 2 XAO:0000247 second pharyngeal pouch VHOG:0000967 A pharyngeal pouch that between pharyngeal arches 3 and 4. A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG] Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[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] The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve UBERON:0005716 AAO:0011116 EFO:0003634 EHDAA2:0000077 EMAPA:16586 FMA:295682 NCIT:C34311 RETIRED_EHDAA2:0000076 TAO:0001131 UMLS:C0231070 VHOG:0000966 VHOG:0001030 XAO:0000251 ZFA:0001131 3rd arch branchial pouch 3rd arch branchial pouch endoderm 3rd branchial pouch 3rd pharyngeal pouch endoderm pharyngeal pouches 3 third arch pharyngeal pouch third visceral pouch visceral pouch 3 uberon third pharyngeal pouch UBERON:0007124 pharyngeal pouch 3 A pharyngeal pouch that between pharyngeal arches 3 and 4. ISBN:0124020607 A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0000966 VHOG Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] 2012-06-20 AAO:0011116 AAO ISBN:0-226-55763-4 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:0000966 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) The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve WP UMLS:C0231070 ncithesaurus:Third_Pharyngeal_Pouch 3rd arch branchial pouch RETIRED_EHDAA2:0000076 3rd arch branchial pouch endoderm EHDAA2:0000077 3rd pharyngeal pouch endoderm VHOG:0001030 pharyngeal pouches 3 ZFA:0001131 third arch pharyngeal pouch OBOL:automatic third visceral pouch XAO:0000251 visceral pouch 3 XAO:0000251 third pharyngeal pouch VHOG:0000966 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 internal carotid artery that branching_part_of a left common carotid artery plus branches. EMAPA:16329 FMA:4062 arteria caritis interna sinistra uberon UBERON:0007142 left internal carotid artery An internal carotid artery that branching_part_of a left common carotid artery plus branches. OBOL:automatic arteria caritis interna sinistra FMA:4062 An internal carotid artery that branching_part_of a right common carotid artery plus branches. EMAPA:16330 FMA:3949 arteria carotis interna dextra uberon UBERON:0007143 right internal carotid artery An internal carotid artery that branching_part_of a right common carotid artery plus branches. OBOL:automatic arteria carotis interna dextra FMA:3949 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. 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 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 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 serous membrane that is part of a uterine tube infundibulum. EMAPA:29903 FMA:18324 serosa of infundibulum of fallopian tube serosa of infundibulum of oviduct uberon UBERON:0007181 serosa of infundibulum of uterine tube A serous membrane that is part of a uterine tube infundibulum. OBOL:automatic serosa of infundibulum of fallopian tube FMA:18324 serosa of infundibulum of oviduct FMA:18324 A muscle layer that is part of a uterine tube infundibulum. EMAPA:31264 FMA:18336 muscle layer of infundibulum of fallopian tube muscle layer of infundibulum of oviduct muscularis of infundibulum of uterine tube uberon UBERON:0007182 muscle layer of infundibulum of uterine tube A muscle layer that is part of a uterine tube infundibulum. OBOL:automatic muscle layer of infundibulum of fallopian tube FMA:18336 muscle layer of infundibulum of oviduct FMA:18336 muscularis of infundibulum of uterine tube FMA:18336 A mesothelium that is part of a serous pericardium. BTO:0003157 EMAPA:16133 FMA:18149 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 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. bone marrow stroma FMA:21426 The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. UBERON:0004102 FMA:7393 NCIT:C117875 arbor tracheobronchialis uberon tracheobronchial system UBERON:0007196 tracheobronchial tree Wikipedia The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. arbor tracheobronchialis FMA:7393 FMA:TA tracheobronchial system HP:0005607 multicellular organism that can produce both male and female gametes. AAO:0010035 BILA:0000029 CARO:0000029 HAO:0000029 TADS:0000601 WBbt:0007849 uberon dioecious organism hermaphrodite UBERON:0007197 hermaphroditic organism multicellular organism that can produce both male and female gametes. dioecious organism BILA:0000029 hermaphrodite WBbt:0007849 The vasculature consisting of brachiocephalic arteries and veins. uberon UBERON:0007204 brachiocephalic vasculature The vasculature consisting of brachiocephalic arteries and veins. 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 An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. EV:0300011 EVM:2990031 FBdv:00005333 FMA:63631 MIAA:0000399 MmusDv:0000031 OGES:000023 embryo late (growth) stage fetal stage fetus fetus stage uberon embryo late growth stage embryo late stage UBERON:0007220 late embryonic stage An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. BGEE:ANiknejad embryo late (growth) stage MIAA:0000399 fetal stage fetus MIAA:0000399 fetus stage embryo late growth stage BTO:0000449 embryo late stage BTO:0000449 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) 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) A tunica media that is part of a artery. EMAPA:36294 EV:0100029 FMA:14273 NCIT:C49321 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 arterial adventitia tunica externa (adventitia)(arteriae) uberon UBERON:0007240 tunica adventitia of artery 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 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 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 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. 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 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. superior olivary complex nucleus FMA:72246 A pre-cartilage condensation that is part of a trachea. EHDAA2:0002070 EHDAA:7082 uberon UBERON:0007267 trachea pre-cartilage rings A pre-cartilage condensation that is part of a trachea. OBOL:automatic 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. 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 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. 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 rhombencephalon EHDAA2:0001630 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 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 The part of the blastula that has the potential to develop into a paraxial mesoderm. UBERON:cjm future paraxial mesenchyme UBERON:cjm A presumptive structure that has the potential to develop into a forebrain-midbrain boundary. EFO:0003463 TAO:0001368 ZFA:0001368 uberon UBERON:0007288 presumptive forebrain midbrain boundary A presumptive structure that has the potential to develop into a forebrain-midbrain boundary. OBOL:automatic A presumptive structure that has the potential to develop into a pronephric mesoderm. EFO:0003619 TAO:0001070 ZFA:0001070 nephron primordium uberon UBERON:0007297 presumptive pronephric mesoderm A presumptive structure that has the potential to develop into a pronephric mesoderm. OBOL:automatic nephron primordium ZFA:0001070 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 TAO:0001372 VHOG:0000254 ZFA:0001372 duct of pancreas pancreas duct uberon ductus pancreaticus UBERON:0007329 pancreatic duct ZFA MA A duct that collects and carries secretions of the exocrine pancreas to the intestine. GOC:cvs GOC:ymb ORCiD:0000-0002-2244-7917 ORCiD: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 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) in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms EHDAA2 duct of pancreas OBOL:accepted pancreas duct OBOL:accepted ductus pancreaticus An anatomical surface that is part of a tongue. FMA:54647 tongue surface uberon UBERON:0007367 surface of tongue An anatomical surface that is part of a tongue. OBOL:automatic tongue surface FMA:54647 The upper (superior) side of the tongue. check superior/dorsal FMA:54646 dorsal surface of tongue uberon UBERON:0007371 superior surface of tongue The upper (superior) side of the tongue. dorsal surface of tongue FMA:54646 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 epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer uberon hypoderm hypodermis UBERON:0007376 outer epithelium 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 epidermis GO:0008544 hypoderm BTO:0000313 hypodermis GO:0008544 WBbt:0005733 Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO] relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO] connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis AAO:0010600 TAO:0001182 ZFA:0001182 dermal deep region stratum compactum uberon UBERON:0007377 stratum compactum of dermis Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. ISBN:0073040584 ZFIN:ZDB-PUB-040726-12 Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001182 TAO ZFIN:curator relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO] 2012-08-14 TAO:0001182 TAO dermal deep region ZFA:0001182 stratum compactum AAO:0010600 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. 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 lymphatic vessel that is part of a limb/fin. TAO:0005300 ZFA:0005300 uberon UBERON:0007384 appendage lymph vessel A lymphatic vessel that is part of a limb/fin. OBOL:automatic A lymphatic vessel that is part of a pectoral appendage. TAO:0005302 ZFA:0005302 uberon UBERON:0007385 pectoral appendage lymph vessel A lymphatic vessel that is part of a pectoral appendage. OBOL:automatic A lymphatic vessel that is part of a pelvic appendage. uberon UBERON:0007386 pelvic appendage lymph vessel A lymphatic vessel that is part of a pelvic appendage. OBOL:automatic 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. 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. EHDAA2:0003079 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 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 collection of connected epithelial tubes with a single portal. EHDAA2:0003117 AEO:0000117 EHDAA2:0003117 arborising epithelial duct system uberon UBERON:0007501 arborizing epithelial duct system AEO AEO A collection of connected epithelial tubes with a single portal. AEO:JB UBERONREF:0000001 arborising epithelial duct system AEO:0000117 A closed epithelium with a lumen. EHDAA2:0003119 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 uberon UBERON:0007521 smooth muscle sphincter A ring of smooth muscle cells whose contraction closes the opening of the ring. AEO:JB Mesenchyme with little extracellular matrix. EHDAA2:0003146 AEO:0000146 EHDAA2:0003146 uberon UBERON:0007524 dense mesenchyme tissue AEO Mesenchyme with little extracellular matrix. AEO:JB Mesenchymal cells that are migrating. this class will be an important part of the NC reorganization EHDAA2:0003152 AEO:0000152 EHDAA2:0003152 uberon UBERON:0007530 migrating mesenchyme population Mesenchymal cells that are migrating. AEO:JB A ciliated columnar epithelium that is part of a oviduct. in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA:62016 MA:0001719 uberon epithelium of uterine tube uterine tube epithelium UBERON:0007589 ciliated columnar oviduct epithelium MA FMA A ciliated columnar epithelium that is part of a oviduct. OBOL:automatic in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA epithelium of uterine tube FMA:62016 uterine tube epithelium FMA:62016 A cuboidal epithelium that is part of a oviduct. MA:0001720 uberon UBERON:0007590 cuboidal oviduct epithelium MA A cuboidal epithelium that is part of a oviduct. OBOL:automatic 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. Stratified columnar epithelia is a rare type of epithelial tissue composed of column shaped cells arranged in multiple layers. Stratified columnar epithelia are found in the ocular conjunctiva of the eye, in parts of the pharynx and anus, the female's uterus, the male urethra and vas deferens. Also found in intralobular ducts in salivary glands.[WP] FMA:45564 NCIT:C33620 UMLS:C0836132 epithelium stratificatum columnare uberon UBERON:0007602 stratified columnar epithelium FMA Stratified columnar epithelia is a rare type of epithelial tissue composed of column shaped cells arranged in multiple layers. Stratified columnar epithelia are found in the ocular conjunctiva of the eye, in parts of the pharynx and anus, the female's uterus, the male urethra and vas deferens. Also found in intralobular ducts in salivary glands.[WP] UMLS:C0836132 ncithesaurus:Stratified_Columnar_Epithelium epithelium stratificatum columnare FMA:45564 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 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 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 UMLS:C0040999 trigeminal nuclei uberon nuclei trigemini UBERON:0007641 trigeminal nuclear complex 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]. 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 UMLS:C0040999 BIRNLEX:4096 trigeminal nuclei FMA:71248 nuclei trigemini A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes FMA:12772 NCIT:C33769 UMLS:C0229745 lymph node of thorax uberon deep thoracic lymph node UBERON:0007644 thoracic lymph node A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes OBOL:automatic UMLS:C0229745 ncithesaurus:Thoracic_Lymph_Node lymph node of thorax FMA:12772 deep thoracic lymph node FMA:12772 A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx. decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d UBERON:0004065 EHDAA2:0004453 primary meninx uberon meninx primitiva primitive meninx primordial meninx UBERON:0007645 future meninx EHDAA2 ISBN:0073040584 A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx. the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d MP:0009726 primary meninx EHDAA2:0004453 meninx primitiva MP:0009726 The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx. future leptomeninges future leptomeninx uberon UBERON:0007646 endomeninx ISBN:9781607950325 The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx. ISBN:9781607950325 The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer). UBERON:0010115 EHDAA2:0004317 future dura mater uberon UBERON:0007647 ectomeninx ISBN:9781607950325 The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer). ISBN:9781607950325 future dura mater EHDAA2:0004317 2 An anatomical structure that connects two structures junction FMA:5898 anatomical junction uberon UBERON:0007651 anatomical junction FMA An anatomical structure that connects two structures 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 uberon UBERON:0007652 esophageal sphincter A sphincter that is part of an esophagus. functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule. FMA:17691 uberon UBERON:0007684 uriniferous tubule functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule. ISBN:0073040584 region of the embryo into the area in which the kidney rudiment will develop. uberon kidney anlage UBERON:0007687 kidney field region of the embryo into the area in which the kidney rudiment will develop. GO:0072004 GOC:mtg_kidney_jan10 kidney anlage GOC:mtg_kidney_jan10 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 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 JB:DEF endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]. uberon diverticulum thyroideum saccus thyroideus UBERON:0007689 thyroid diverticulum VHOG endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]. MP:0004662 diverticulum thyroideum saccus thyroideus . 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 cjm . early pharyngeal arch endoderm EHDAA2:0001457 pharyngeal endoderm ZFA:0001104 pharyngeal region endoderm EHDAA2:0001456 The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. FMA:63589 NCIT:C33738 UMLS:C0226971 porus gustatorius taste pore uberon UBERON:0007691 gustatory pore FMA FMA The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. UMLS:C0226971 ncithesaurus:Taste_Pore porus gustatorius taste pore FMA:63589 A nucleus of brain that is part of a thalamus. TODO - consider splitting nucleus and complex BTO:0002452 EMAPA:35859 FMA:256693 MA:0002992 thalamic nucleus uberon nuclear complex of thalamus UBERON:0007692 nucleus of thalamus A nucleus of brain that is part of a thalamus. OBOL:automatic thalamic nucleus MA:0002992 nuclear complex of thalamus FMA:256693 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 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 An endothelium that is part of a umbilical artery. BTO:0000857 uberon UBERON:0007778 umbilical artery endothelium BTO An endothelium that is part of a umbilical artery. OBOL:automatic 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 Any fluid produced by a serous gland. 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 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 Gefaesssystem@de UBERON:0007798 vascular system MA Anatomical system that consists of all blood and lymph vessels. 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 Gefaesssystem@de BTO:0001085 A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord. TODO - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels BTO:0004705 NCIT:C34132 UMLS:C1516792 uberon UBERON:0007806 connecting stalk EHDAA2 EHDAA2 A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord. UMLS:C1516792 ncithesaurus:Connecting_Stalk A vasculature that is part of a connecting stalk. EHDAA2:0000313 connecting stalk blood vessels uberon connecting stalk blood vessel vasculature of connecting stalk UBERON:0007807 connecting stalk vasculature EHDAA2 A vasculature that is part of a connecting stalk. OBOL:automatic connecting stalk blood vessels EHDAA2:0000313 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 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 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. UMLS:C0460004 ncithesaurus:Head_and_Neck cephalic area cephalic part of animal cephalic region 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 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] 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 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 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 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 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. 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 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 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] 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 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 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 skeleton of pectoral girdle cingulum pectorale 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 XAO:0003064 ZFA:0000565 galen:PelvicGirdle pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle uberon pelvic girdle UBERON:0007832 pelvic girdle skeleton 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 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 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 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 skeleton of pelvic girdle 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 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 TAO still mixes tissue and element TAO cartilage organ FMA:55107 cartilaginous element 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 UMLS:C0225333 VSAO:0000050 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 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 UMLS:C0502414 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. UMLS:C0502414 ncithesaurus:Irregular_Bone os irregulare 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 A anatomical surface that is part of a cartilage element. FMA:76668 cartilage surface uberon UBERON:0008115 surface of cartilage A 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 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]. 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 space of pelvic compartment uberon cavitas pelvis UBERON:0008203 pelvic cavity 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 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 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 lower back. EMAPA:37262 MA:0000502 uberon UBERON:0008242 lower back muscle MA MA A muscle of back that is part of a lower back. OBOL:automatic EMAPA:37262 MA:th A muscle of back that is part of a dorsal thoracic segment of trunk. EMAPA:37261 MA:0000508 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 A gland that is part of a nasopharynx. FMA:55076 uberon UBERON:0008310 nasopharyngeal gland A gland that is part of a nasopharynx. OBOL:automatic with numerous vascular spaces that may become engorged with blood uberon UBERON:0008324 Examples: corpus cavernosum or penis or clitoris erectile tissue with numerous vascular spaces that may become engorged with blood A smooth muscle tissue that is part of a clitoris. BTO:0005000 uberon clitoris smooth muscle UBERON:0008331 clitoral smooth muscle A smooth muscle tissue that is part of a clitoris. OBOL:automatic clitoris smooth muscle BTO:0005000 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 epithelium of duodenum uberon UBERON:0008346 duodenal epithelium FMA An epithelium that is part of a duodenum. OBOL:automatic epithelium of duodenum FMA:17231 An epithelium that is part of a breast. BTO:0001428 uberon UBERON:0008367 breast epithelium An epithelium that is part of a breast. OBOL:automatic A vertebral foramen that is part of a cervical vertebra. FMA:13480 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 lumbar vertebra. FMA:24826 uberon UBERON:0008430 lumbar vertebral foramen A vertebral foramen that is part of a lumbar vertebra. OBOL:automatic A vertebral foramen that is part of a thoracic vertebra. FMA:9143 uberon UBERON:0008432 thoracic vertebral foramen A vertebral foramen that is part of a thoracic vertebra. OBOL:automatic Any muscle organ that is part of an nose. FMA:73758 NCIT:C33158 UMLS:C0224219 muscle of nose uberon UBERON:0008522 nasal muscle FMA Any muscle organ that is part of an nose. OBOL:automatic UMLS:C0224219 ncithesaurus:Nasal_Muscle muscle of nose OBOL:automatic A muscle tissue that is part of a prostate gland. NCIT:C13100 UMLS:C1183911 prostate gland muscle tissue prostate muscle tissue prostatic muscle prostatic musclular tissue uberon UBERON:0008715 muscle tissue of prostate A muscle tissue that is part of a prostate gland. OBOL:automatic UMLS:C1183911 ncithesaurus:Prostatic_Muscular_Tissue prostate gland muscle tissue OBOL:automatic prostate muscle tissue 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 An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]. this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO] AAO:0010255 FBbt:00004850 HAO:0000091 TAO:0002036 TGMA:0000585 aedeagus penis uberon copulatory organ UBERON:0008811 intromittent organ An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]. Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO] 2012-08-14 TAO:0002036 TAO TAO:wd aedeagus FBbt:00004850 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 An endoderm that is part of a thymus primordium. uberon UBERON:0008817 thymus primordium endoderm An endoderm that is part of a thymus primordium. OBOL:automatic 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 ZFA FMA A brain that develops_from a neural tube. OBOL:automatic Any duct branching of of the main epididymis duct. EMAPA:36525 FMA:18297 MA:0001735 NCIT:C32484 UMLS:C0458632 epididymal duct epididymis duct uberon UBERON:0008824 duct of epididymis FMA Any duct branching of of the main epididymis duct. UMLS:C0458632 ncithesaurus:Duct_of_the_Epididymis epididymal duct MA:0001735 epididymis duct FMA:18297 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 XAO:0000101 liver diverticulum uberon diverticulum hepaticum UBERON:0008835 hepatic diverticulum 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 UMLS:C1512407 ncithesaurus:Hepatic_Diverticulum liver diverticulum XAO:0000101 diverticulum hepaticum BTO:0001642 uberon UBERON:0008836 liver bud cjm A ligament that does not connect two skeletal elements. Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625]. this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus. FMA:25625 MA:0003004 non-skeletal ligament uberon fibrous ligament UBERON:0008845 nonskeletal ligament cjm A ligament that does not connect two skeletal elements. Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625]. FMA:25625 this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus. FMA fibrous ligament Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified]. logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71 Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO] Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624]. ligament AAO:0010444 AEO:0000090 CALOHA:TS-2146 EHDAA2:0003232 EV:0100144 FMA:25624 GAID:118 MA:0003005 VSAO:0000072 articular larua articular ligament true ligament uberon UBERON:0008846 skeletal ligament bones or cartilage organs VSAO Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified]. GO_REF:0000034 Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO] 2012-08-14 VSAO:0000072 VSAO PSPUB:0000170 Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624]. FMA:25624 ligament VSAO:0000072 ZFA:0001675 articular larua articular ligament true ligament 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 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 canalis pyloricus uberon canalis pyloricus UBERON:0008858 pyloric canal FMA Wikipedia The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter MP:0010791 EMAPA:37944 MA:th canalis pyloricus canalis pyloricus 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 UMLS:C0227239 glandula pylorica pyloric antrum gland pyloric gland pyloric mucuous gland uberon UBERON:0008861 pyloric gastric gland MP 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 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 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 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 The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus. FMA:18933 NCIT:C32728 UMLS:C0226766 uberon haemorrhoidal plexus hemorrhoidal plexus plexus haemorrhoidalis plexus venosus rectalis UBERON:0008887 rectal venous plexus FMA The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus. UMLS:C0226766 ncithesaurus:Hemorrhoidal_Plexus haemorrhoidal plexus hemorrhoidal plexus plexus haemorrhoidalis plexus venosus rectalis 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 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 redundant Grays Subdivision of endoskeleton derived from pharyngeal arches ISBN:0073040584 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 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 VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. VSAO pharyngeal endoskeleton viscerocranium VHOG:0000315 ZFA:0001216 pharyngeal arch VSAO:0000149 pharyngeal arch skeleton ZFA:0001216 pharyngeal skeleton ZFA:0001216 visceral cranium visceral skeletal system visceral skeleton UBERONREF:0000007 A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher. Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO] AAO:0010362 BTO:0002152 EFO:0003694 TAO:0001597 XAO:0000099 ZFA:0001613 branchial arch branchial arches branchial bar branchial bars gill arch gill arches 1-5 pharyngeal arch 3-7 visceral arches 3-7 uberon gill bar UBERON:0008896 post-hyoid pharyngeal arch A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher. Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO] 2012-06-20 AAO:0010362 AAO AAO:EJS branchial arch ZFA:0001613 branchial arches ZFA:0001613 branchial bar ZFA:0001613 branchial bars ZFA:0001613 gill arch ZFA:0001613 gill arches 1-5 ZFA:0001613 pharyngeal arch 3-7 ZFA:0001613 visceral arches 3-7 ZFA:0001613 gill bar 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 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 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 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 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 bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder. GAID:178 MESH:D001133 NCIT:C12983 UMLS:C0003793 free forelimb bone wing bone uberon UBERON:0008962 forelimb bone A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder. UMLS:C0003793 ncithesaurus:Bone_of_the_Upper_Extremity free forelimb bone UBERONREF:0000003 wing bone Geisha:syn NCBITaxon:8782 wing bone NCBITaxon:8782 OBOL:automatic The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 parenchyma of kidney uberon kidney parenchyma UBERON:0008987 renal parenchyma FMA FMA The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 parenchyma of kidney FMA:15574 kidney parenchyma BTO:0003604 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 UMLS:C0227178 esophageal gland glandulae oesophageae mucous gland of submucosa of esophagus uberon UBERON:0008989 submocosal esophageal gland 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 UMLS:C0227178 ncithesaurus:Esophageal_Gland esophageal gland FMA:9404 glandulae oesophageae 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 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 Any portion of tissue that surrounds a urethra. BTO:0005081 uberon UBERON:0009010 periurethral tissue Any portion of tissue that surrounds a urethra. UBERON:cjm A zone of skin that is part of a lower back. EMAPA:37281 MA:0000504 uberon UBERON:0009014 lower back skin MA A zone of skin that is part of a lower back. OBOL:automatic EMAPA:37281 MA:th A zone of skin that is part of a dorsal thoracic segment of trunk. EMAPA:37280 MA:0000510 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 An artery that supplies blood to the urinary bladder. EMAPA:37131 MA:0002078 arteria vesicali vesical arteries uberon UBERON:0009027 vesical artery An artery that supplies blood to the urinary bladder. EMAPA:37131 MA:th arteria vesicali vesical arteries 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 UMLS:C0226670 uberon UBERON:0009030 left pulmonary vein 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]. 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 UMLS:C0226669 uberon UBERON:0009032 right 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]. ncithesaurus:Right_Pulmonary_Vein EMAPA:37379 MA:th UMLS:C0226669 ncithesaurus:Right_Pulmonary_Vein The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses. FMA:29711 uberon plexus venosus prostaticus pudendal venous plexus UBERON:0009042 prostatic venous plexus The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses. plexus venosus prostaticus pudendal venous plexus FMA:29711 An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 uberon gravid pregnant adult pregnant adult stage pregnant organism pregnant stage UBERON:0009097 gravid organism An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 gravid BTO:0004733 pregnant adult BTO:0004733 pregnant adult stage BTO:0004733 pregnant stage BTO:0004733 The uterus in pregnancy NCIT:C12406 UMLS:C1514389 ncithesaurus:Gravid_Uterus uberon womb UBERON:0009098 gravid uterus The uterus in pregnancy UMLS:C1514389 ncithesaurus:Pregnant_Uterus A mature thymus that is entirely part of the cervical region. A cervical thymus is a pathological structure in a human - it can form during the migration of the thymus to its location in the mediastinum. Some mice have a cervical thymus. There are examples of cervical thymi in marsupials and prosimians[ISBN:0781714125] uberon UBERON:0009114 cervical thymus A mature thymus that is entirely part of the cervical region. A mature thymus that is entirely part of thoracic region. uberon UBERON:0009115 thoracic thymus A mature thymus that is entirely part of thoracic region. 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. UMLS:C1512703 ncithesaurus:Indifferent_Gonad The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke's pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke's pouch, the anlage of the adenohypophysis. Rathke's pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009) EFO:0000229 TAO:0001198 XAO:0004208 ZFA:0001198 uberon pituitary placode UBERON:0009122 adenohypophyseal placode NCBIBook:NBK53175 ZFA The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary pituitary placode ZFA:0001198 Rostralmost epibranchial placode. Associated with 1st branchial cleft. EHDAA2:0004206 TAO:0001295 XAO:0004211 ZFA:0001295 epibranchial placode 1 facial epibranchial placode facial placode uberon facial VII placode hyoid VII placode hyoid placode UBERON:0009124 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to geniculate ganglion geniculate placode ZFA Rostralmost epibranchial placode. Associated with 1st branchial cleft. NCBIBook:NBK53175 epibranchial placode 1 EHDAA2:0004206 facial epibranchial placode XAO:0004211 facial placode ZFA:0001295 hyoid VII placode ISBN:0471888893 hyoid placode ISBN:0471888893 Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. EHDAA2:0004207 TAO:0001296 XAO:0004212 ZFA:0001296 epibranchial placode 2 glossopharyngeal IX placode glossopharyngeal epibranchial placode glossopharyngeal placode uberon UBERON:0009125 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion petrosal placode ZFA Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. NCBIBook:NBK53175 epibranchial placode 2 EHDAA2:0004207 glossopharyngeal IX placode ISBN:0471888893 glossopharyngeal epibranchial placode XAO:0004212 glossopharyngeal placode ISBN:0471888893 ZFA:0001296 Cranial ganglion which develops from an epibranchial placode. 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. ZFIN:curator epibranchial ganglia ZFA:0001555 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 UMLS:C1283968 VHOG:0000757 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. 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 UMLS:C1283968 ncithesaurus:Pleuroperitoneal_Membrane pleuroperitoneal fold VHOG:0000757 pleuroperitoneal membranes EHDAA2:0001483 A vein that is part of a craniocervical region. EHDAA2:0004542 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. EMAPA:16549 RETIRED_EHDAA2:0001454 pharyngeal region uberon UBERON:0009145 pharyngeal region of foregut EHDAA2 pharyngeal region EMAPA:16549 EHDAA2:0004021 uberon UBERON:0009196 indifferent external genitalia cjm 2 Any suture between cranial and/or facial bones. we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA joint of the skull bones uberon articulation of skull bones UBERON:0009198 craniofacial suture Any suture between cranial and/or facial bones. GO:0097094 joint of the skull bones OBOL:automatic articulation of skull bones OBOL:automatic 2 Any suture between facial bones. uberon UBERON:0009199 facial suture between two adjacent facial bones Any suture between facial bones. GO:0097096 The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium. EMAPA:32728 uberon UBERON:0009200 limb epidermis The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium. GOC:dph GOC:sdb_2009 GOC:tb A nephric duct is a tube that drains a primitive kidney[GO]. EMAPA:16577 uberon UBERON:0009201 pronephric duct or mesonephric duct nephric duct EHDAA2 A nephric duct is a tube that drains a primitive kidney[GO]. GO:0072176 Mesenchyme that is part of a lateral nasal prominence. EHDAA2:0000917 EMAPA:16807 FMA:312665 mesenchyme of latero-nasal process uberon UBERON:0009205 lateral nasal process mesenchyme Mesenchyme that is part of a lateral nasal prominence. OBOL:automatic mesenchyme of latero-nasal process EMAPA:16807 An ectoderm that is part of a lateral nasal prominence. EHDAA2:0000918 EMAPA:16806 ectoderm of latero-nasal process uberon UBERON:0009206 lateral nasal process surface ectoderm EHDAA2 An ectoderm that is part of a lateral nasal prominence. OBOL:automatic ectoderm of latero-nasal process EMAPA:16806 medial or lateral; in EHDAA2 also frontonasal or intermaxillary EHDAA2:0000581 EHDAA:4776 EMAPA:16680 FMA:293971 uberon nasal placode UBERON:0009292 embryonic nasal process medial or lateral; in EHDAA2 also frontonasal or intermaxillary EHDAA2 The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis). FMA:54651 NCIT:C32482 UMLS:C0226952 dorsal tongue dorsum linguae tongue dorsum uberon UBERON:0009471 dorsum of tongue FMA The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis). UMLS:C0226952 ncithesaurus:Dorsum_of_the_Tongue dorsal tongue FMA:54651 dorsum linguae tongue dorsum FMA:54651 Mesenchyme that is part of a otic placode. EHDAA2:0001340 EMAPA:16196 uberon UBERON:0009477 associated mesenchyme of otic placode Mesenchyme that is part of a otic placode. OBOL:automatic 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 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. 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 An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 uberon UBERON:0009497 epithelium of foregut-midgut junction EHDAA2 An epithelium that is part of a foregut-midgut junction. OBOL:automatic Anatomical region that surrounds the otic vesicle. EHDAA2:0001343 EMAPA:16670 XAO:0004474 otocyst associated mesenchyme otocyst mesenchyme uberon periotic region UBERON:0009500 periotic mesenchyme XAO EHDAA2 Anatomical region that surrounds the otic vesicle. XAO:0004474 XAO:curators otocyst associated mesenchyme EHDAA2:0001343 otocyst mesenchyme EMAPA:16670 periotic region XAO:0004474 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 Mesenchyme that is part of a developing trachea. EHDAA2:0002067 EMAPA:16854 trachea associated mesenchyme uberon UBERON:0009505 mesenchyme of trachea EHDAA2 Mesenchyme that is part of a developing trachea. OBOL:automatic trachea associated mesenchyme EHDAA2:0002067 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 An epithelium that is part of a lateral lingual swelling. EHDAA2:0000913 EMAPA:17190 FMA:313717 uberon UBERON:0009522 lateral lingual swelling epithelium An epithelium that is part of a lateral lingual swelling. 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 A vascular plexus that is part of a left lung. EHDAA2:0000963 EMAPA:17660 uberon UBERON:0009536 vascular element of left lung A vascular plexus that is part of a left lung. OBOL:automatic A vascular plexus that is part of a right lung. EHDAA2:0001757 EMAPA:17668 uberon UBERON:0009537 vascular element of right lung A vascular plexus that is part of a right lung. OBOL:automatic Mesenchyme that is part of a submandibular gland primordium. EHDAA2:0001941 EMAPA:17757 uberon submaxillary gland primordium mesenchyme UBERON:0009539 mesenchyme of submandibular gland primordium Mesenchyme that is part of a submandibular gland primordium. OBOL:automatic submaxillary gland primordium mesenchyme EMAPA:17757 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 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 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 EHDAA2:0000397 EMAPA:16906 VHOG:0000912 diencephalon lateral wall mantle layer mantle layer lateral wall diencephalon uberon UBERON:0009580 diencephalon mantle layer mantle layer lateral wall diencephalon VHOG:0000912 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 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 future forebrain. TAO:0007018 ZFA:0007018 uberon UBERON:0009610 forebrain neural plate ZFA ZFA A neural plate that develops_from a future forebrain. OBOL:automatic 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 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 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 future midbrain 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 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme EHDAA2:0000736 EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon trunk paraxial mesenchyme UBERON:0009618 trunk paraxial mesoderm trunk and cervical paraxial mesenchyme EHDAA2:0002094 trunk paraxial mesenchyme 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 The lumbar nerves are the five spinal nerves emerging from the lumbar vertebrae. They are divided into posterior and anterior divisions. FMA:5861 NCIT:C33015 UMLS:C0228897 lumbar spinal nerve nervus lumbalis uberon nervi lumbales UBERON:0009624 lumbar nerve The lumbar nerves are the five spinal nerves emerging from the lumbar vertebrae. They are divided into posterior and anterior divisions. UMLS:C0228897 ncithesaurus:Lumbar_Nerve lumbar spinal nerve FMA:5861 nervus lumbalis FMA:5861 FMA:TA nervi lumbales EMAPA:35878 MA:0001859 uberon UBERON:0009644 trachea non-cartilage connective tissue MA A basement membrane that is part of a nephron tubule. EMAPA:37490 MA:0001680 NCIT:C49273 UMLS:C1709901 kidney tubule basement membrane renal tubular basement membrane renal tubule basement membrane uberon UBERON:0009651 nephron tubule basement membrane true A basement membrane that is part of a nephron tubule. OBOL:automatic EMAPA:37490 MA:th UMLS:C1709901 ncithesaurus:Renal_Tubule_Basement_Membrane kidney tubule basement membrane MA:0001680 renal tubule basement membrane MA:0001680 A basement membrane that is part of a bronchus. MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108 EMAPA:37809 MA:0001832 NCIT:C49208 UMLS:C1707051 bronchial basement membrane uberon UBERON:0009652 bronchus basement membrane true A basement membrane that is part of a bronchus. OBOL:automatic MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108 MA EMAPA:37809 MA:th UMLS:C1707051 ncithesaurus:Bronchus_Basement_Membrane bronchial basement membrane A basement membrane that is part of a trachea. EMAPA:37552 MA:0001854 NCIT:C49302 UMLS:C1710455 uberon UBERON:0009653 trachea basement membrane true MA-modified A basement membrane that is part of a trachea. OBOL:automatic EMAPA:37552 MA:th UMLS:C1710455 ncithesaurus:Trachea_Basement_Membrane EMAPA:37092 MA:0001987 NCIT:C52947 UMLS:C1708633 labial artery uberon UBERON:0009657 artery of lip EMAPA:37092 MA:th UMLS:C1708633 ncithesaurus:Labial_Artery labial artery MA:0001987 Nucleus located in the midbrain. 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 A nucleus of brain that is part of a telencephalon. TAO:0002178 ZFA:0001660 uberon UBERON:0009663 telencephalic nucleus A nucleus of brain that is part of a telencephalon. OBOL:automatic EHDAA2:0004566 EMAPA:32911 MA:0003203 uberon peritoneal cavity mesentary peritoneal mesentary UBERON:0009664 gut mesentery EHDAA2 peritoneal cavity mesentary peritoneal mesentary 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 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 EFO:0003562 EHDAA2:0001981 EHDAA:1993 EHDAA:2671 EMAPA:16914 early telencephalic vesicle uberon early telencephalic ventricle UBERON:0009676 early telencephalic vesicle EHDAA2 EHDAA2 early telencephalic vesicle EHDAA2:0001981 A epithelium that is part of a hypopharynx. EHDAA2:0004575 FMA:62454 epithelium of laryngeal pharynx laryngopharynx epithelium uberon UBERON:0009695 epithelium of laryngopharynx EHDAA2 A epithelium that is part of a hypopharynx. OBOL:automatic epithelium of laryngeal pharynx FMA:62454 laryngopharynx epithelium FMA:62454 A epithelium that is part of a vermiform appendix. CALOHA:TS-2062 EHDAA2:0004561 FMA:63581 appendix epithelium epithelium of vermiform appendix uberon UBERON:0009697 epithelium of appendix A epithelium that is part of a vermiform appendix. OBOL:automatic appendix epithelium FMA:63581 epithelium of vermiform appendix FMA:63581 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 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. 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 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. 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 pharyngeal arch endoderm EHDAA2:0004621 The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels medullary sinus EMAPA:37898 FMA:312359 uberon lymph node medullary sinusoid UBERON:0009744 Lymph flows into the medullary sinuses from cortical sinuses, and into efferent lymphatic vessels. Medullary sinuses contain histiocytes (immobile macrophages) and reticular cells.[WP] lymph node medullary sinus The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels MP:0011222 EMAPA:37898 MA:th The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node medullary cord EMAPA:37897 uberon UBERON:0009745 lymph node medullary cord The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node MP:0011224 EMAPA:37897 MA:th The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. EMAPA mapping from TH EMAPA:32705 uberon limb mesoderm UBERON:0009749 limb mesenchyme The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. MP:0011261 EMAPA mapping from TH EMAPA limb mesoderm Geisha:syn NCBITaxon:8782 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. uberon UBERON:0009758 abdominal ganglion A ganglion that is part of a abdominal segment of trunk. OBOL:automatic A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules renal tubule (generic) tubule of excretory system uberon UBERON:0009773 renal tubule A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. GO:0061333 GOC:dph GOC:mtg_kidney_jan10 renal tubule (generic) tubule of excretory system 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 uberon UBERON:0009778 pleural sac FMA FMA-abduced-lr 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 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 uberon acini UBERON:0009842 glandular acinus The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinus FMA:55588 acini A solid cord of prostate epithelium. cord of prostate epithelium epithelial cord of prostate uberon UBERON:0009843 Complexity is conferred on the prostate during a postnatal development phase known as branching morphogenesis. Solid cords of prostate epithelium formed in utero elongate postnatally and their tips are bifurcated into primary, secondary, and tertiary branches in a pattern that is unique for each prostate lobe. Branching morphogenesis proceeds differentially for each of the three mouse prostate lobes (ventral, dorsolateral, and anterior) and is completed by about postnatal day 20 in mice, providing each lobe with unique glandular architecture [5]. It is important to note that the developing human prostate undergoes a similar series of morphogenetic events especially during prostatic bud formation, but gives rise to a mature glandular prostate that is unique from the rodent and features peripheral, central, and transitional zones[PMID:18977204] prostate epithelial cord A solid cord of prostate epithelium. GO:0060527 OBOL:automatic cord of prostate epithelium An anatomical space that surrounded_by a primitive urogenital sinus. EHDAA2:0002142 uberon UBERON:0009844 urogenital sinus lumen EHDAA2 An anatomical space that surrounded_by a primitive urogenital sinus. OBOL:automatic Mesenchyme that surrounds primitive urogenital sinus. Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth EMAPA:31500 UGM uberon UBERON:0009845 urogenital sinus mesenchyme Mesenchyme that surrounds primitive urogenital sinus. OBOL:automatic UGM An epithelium that is part of a embryonic cloaca. cloacal epithelium EHDAA2:0004585 uberon UBERON:0009846 embryonic cloacal epithelium EHDAA2 An epithelium that is part of a embryonic cloaca. OBOL:automatic cloacal epithelium EHDAA2:0004585 A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. uberon prostate primordium UBERON:0009847 prostate field A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. GO:0060515 GOC:dph The part of the uterus above the isthmus and below the orifices of the uterine tubes. CALOHA:TS-1265 EFO:0000382 FMA:17739 NCIT:C12316 UMLS:C0227813 corpus uteri uterine body uterine corpus uberon UBERON:0009853 body of uterus FMA The part of the uterus above the isthmus and below the orifices of the uterine tubes. UMLS:C0227813 ncithesaurus:Corpus_Uteri corpus uteri uterine body FMA:17739 uterine corpus FMA:17739 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. 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 gastric zone region of stomach section of stomach uberon UBERON:0009870 zone of stomach 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 gastric zone FMA:14558 outer portion of the renal cortex. Site of formation of medullary and cortical elements. see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish. EMAPA:27721 MA:0002996 uberon nephrogenic tissue UBERON:0009871 nephrogenic zone outer portion of the renal cortex. Site of formation of medullary and cortical elements. EFO:0003704 TAO:0005041 ZFA:0005041 ALPM uberon UBERON:0009881 anterior lateral plate mesoderm ZFA ALPM ZFA:0005041 A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla. FMA says parenchyma, MP says cortex Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla BTO:0001155 EMAPA:37906 FMA:74299 Ferrein's pyramid kidney medullary ray renal medullary ray uberon UBERON:0009883 medullary ray FMA MP A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla. MP:0011347 FMA says parenchyma, MP says cortex FMA EMAPA:37906 MA:th Ferrein's pyramid MP:0011347 kidney medullary ray MP:0011347 renal medullary ray MP:0011347 An artery that supplies a renal lobe. FMA only has the set term EMAPA:37091 FMA:71637 arteriae interlobares renis interlobar artery of kidney kidney interlobar artery renal interlobar artery uberon arteriae interlobares renis interlobar arteries of kidney set of interlobar arteries of kidney UBERON:0009885 interlobar artery An artery that supplies a renal lobe. FMA only has the set term FMA EMAPA:37091 MA:th arteriae interlobares renis FMA:TA interlobar artery of kidney FMA:71637 renal interlobar artery MP:0011355 arteriae interlobares renis interlobar arteries of kidney FMA:71637 set of interlobar arteries of kidney FMA:71637 The interlobar veins are veins of the renal circulation which drain the renal lobes. FMA only has the set term FMA:71631 interlobar vein of kidney venae interlobares renis uberon interlobar veins of kidney set of interlobar veins of kidney venae interlobares renis UBERON:0009887 interlobar vein The interlobar veins are veins of the renal circulation which drain the renal lobes. FMA only has the set term FMA interlobar vein of kidney FMA:71631 venae interlobares renis FMA:TA interlobar veins of kidney FMA:71631 set of interlobar veins of kidney FMA:71631 venae interlobares renis 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 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]. 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 anterior heart field 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 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 The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]. todo - add has_part relationships. human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys FMA:17881 NCIT:C32894 UMLS:C0736382 kidney lobe lobi renalis lobus renalis uberon lobi renales UBERON:0009913 renal lobe The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]. MP:0011381 human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys MP UMLS:C0736382 ncithesaurus:Kidney_Lower_Lobe kidney lobe MP:0011381 lobi renalis lobus renalis lobi renales The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys FMA:17670 kidney lobule lobulus renalis uberon cortical lobule cortical lobule of kidney lobuli corticales renis lobulus corticalis renalis renal cortical lobule renculus reniculus renunculus UBERON:0009914 Alternate definition: One of the subdivisions of the kidney, consisting of a medullary ray and that portion of the convoluted port (renal corpuscles and convoluted tubules) associated with its collecting duct. -http://www.mondofacto.com/facts/dictionary?lobulus+corticalis+renalis renal lobule FMA The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys MP:0011382 kidney lobule MP:0011382 cortical lobule MP:0011382 cortical lobule of kidney lobuli corticales renis lobulus corticalis renalis renal cortical lobule renculus reniculus renunculus An anatomical wall that is part of a ureter. FMA:15888 ureteral wall uberon UBERON:0009916 wall of ureter An anatomical wall that is part of a ureter. OBOL:automatic ureteral wall FMA:15888 The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary EMAPA:37886 uberon UBERON:0009917 kidney corticomedullary boundary MP The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary MP:0011376 EMAPA:37886 MA:th The smooth muscle tissue surrounding the epithelium of the ureter EMAPA:28811 ureteral smooth muscle ureteral smooth muscle layer uberon UBERON:0009919 ureter smooth muscle The smooth muscle tissue surrounding the epithelium of the ureter MP:0011426 ureteral smooth muscle MP:0011426 ureteral smooth muscle layer EMAPA:28844 EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest 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 A multicellular organism that existence_starts_with a post-embryonic stage. OBOL:automatic TS28 mouse MA:0002405 post-hatching organism post-natal organism 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 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. 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 A anatomical space that is enclosed by a urinary bladder. EHDAA2:0004058 FMA:15924 galen:UrinaryBladderCavity bladder cavity cavity of urinary bladder lumen of urinary bladder urinary bladder lumen uberon UBERON:0009958 bladder lumen FMA FMA EHDAA2 A anatomical space that is enclosed by a urinary bladder. OBOL:automatic bladder cavity FMA:15924 cavity of urinary bladder FMA:15924 lumen of urinary bladder FMA:15924 urinary bladder lumen FMA:15924 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 The junction between the ureter and the renal pelvis of the kidney EMAPA:37782 FMA:15898 MA:0003021 NCIT:C106203 pelviureteric junction pelvoureteric junction uberon UBERON:0009972 ureteropelvic junction MP The junction between the ureter and the renal pelvis of the kidney MP:0011487 EMAPA:37782 MA:th pelviureteric junction FMA:15898 The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney EMAPA:37783 FMA:15899 MA:0003020 NCIT:C106202 vesico-ureteral junction vesico-ureteric junction vesicoureteric junction uberon UBERON:0009973 ureterovesical junction MP The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney MP:0011488 EMAPA:37783 MA:th vesico-ureteral junction MA:0003020 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 multicellular structure FBbt:00100313 A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 FBbt:00007229 uberon UBERON:0010001 Examples include arthropod sensilla. cell cluster organ CARO CARO FBbt A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 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 The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch. The lateral lingual swellings grow and fuse with eachother, encompassing the tuberculum impar to provide the ectodermally derived mucosa of the anterior 2/3 of the tongue check NCIT EMAPA:37437 FMA:229084 NCIT:C32130 UMLS:C0226946 uberon anterior 2/3 of the tongue anterior 2/3 of tongue anterior two thirds of the tongue apex linguae apex of the tongue buccal part of the tongue front of the tongue oral part of the tongue pars anterior dorsi linguae UBERON:0010032 anterior part of tongue ISBN:1607950324 The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch. check NCIT NCIT EMAPA:37437 MA:th UMLS:C0226946 ncithesaurus:Apex_of_the_Tongue anterior 2/3 of the tongue anterior 2/3 of tongue anterior two thirds of the tongue apex linguae apex of the tongue buccal part of the tongue front of the tongue oral part of the tongue pars anterior dorsi linguae 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 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 associated mesenchyme of pharyngeal region EMAPA:16550 entire branchial arch associated mesenchyme 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 A mucosa that is part of a dorsum of tongue. check surface terms develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324 FMA:74871 mucosa of dorsal surface of tongue uberon UBERON:0010052 mucosa of dorsum of tongue A mucosa that is part of a dorsum of tongue. OBOL:automatic A compound organ that has the potential to develop into a tongue. EHDAA2:0000696 EHDAA:2951 uberon UBERON:0010056 future tongue EHDAA2 A compound organ that has the potential to develop into a tongue. OBOL:automatic EHDAA2:0004610 uberon UBERON:0010059 hypoglossal cord EHDAA2 EHDAA2 An anatomical space with at least one opening to another space or the exterior. AEO:0000221 EHDAA2:0004616 uberon UBERON:0010064 open anatomical space cjm An anatomical space with at least one opening to another space or the exterior. AEO:0000221 Organ system subdivision that consists primarily of chromaffin cells and their supporting structures. in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies FMA:79645 MESH:D002838 uberon argentaffin system chromaffin tissue UBERON:0010074 chromaffin system cjm Organ system subdivision that consists primarily of chromaffin cells and their supporting structures. argentaffin system MESH:A06.224 One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia. XAO:0004192 uberon UBERON:0010075 sacral neural crest One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia. XB:curator An epithelium consisting of cuboidal epithelial cells. TODO - coordinate with CL, add cuboidal cell in NCIT this is glandular NCIT:C32415 UMLS:C0682577 uberon UBERON:0010077 cuboidal epithelium An epithelium consisting of cuboidal epithelial cells. 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 A structure that will develop into a diaphragm. A multi-tissue structure that has the potential to develop into a meninx of hindbrain. EHDAA2:0000610 future hindbrain meninges uberon UBERON:0010091 future hindbrain meninx A multi-tissue structure that has the potential to develop into a meninx of hindbrain. OBOL:automatic future hindbrain meninges EHDAA2:0000610 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 facial nucleus. EHDAA2:0004639 uberon UBERON:0010123 future facial nucleus A gray matter that has the potential to develop into a facial nucleus. 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. specialized conducting tissue of heart FMA:83378 specialized muscle tissue of heart FMA:83378 any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli MA:0000720 neuroendocrine system gland uberon UBERON:0010133 neuroendocrine gland any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli ISBN:0-683-40008-8 MP:0000631 A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid. EMAPA:35759 MA:0002943 uberon UBERON:0010134 secretory circumventricular organ MA MA A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid. A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid. EMAPA:37741 MA:0002944 uberon humerosensory circumventricular organ humerosensory system humerosensory system organ sensitive circumventricular organs sensitive organs sensory CVOs sensory circumventricular organs UBERON:0010135 sensory circumventricular organ A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid. EMAPA:37741 MA:th humerosensory system NeuroNames:2856 sensitive circumventricular organs NeuroNames:2856 sensitive organs NeuroNames:2856 sensory CVOs NeuroNames:2856 sensory circumventricular organs NeuroNames:2856 A sex cord that is part of a indifferent gonad. note that this represents the indifferent structure. EHDAA2:0004051 indifferent sex cord primitive sex cords uberon UBERON:0010141 primitive sex cord of indifferent gonad EHDAA2 EHDAA2 A sex cord that is part of a indifferent gonad. OBOL:automatic primitive sex cords EHDAA2:0004051 A bodily secretion that is produced by a seminal vesicle. constitutes 60-70 % of the ejaculate in humans[MP] important for semen coagulation, sperm motility, and stability of sperm chromatin and suppression of the immune activity in the female reproductive tract[MP] in ncit, seminal fluid is a subtype of seminal vesicle secretion vesicular fluid BTO:0002053 FMA:62969 MA:0002526 NCIT:C33529 NCIT:C52552 UMLS:C0036614 UMLS:C0227987 secretion of seminal vesicle seminal vesicle secretion uberon seminal fluid UBERON:0010143 seminal vesicle fluid FMA A bodily secretion that is produced by a seminal vesicle. in ncit, seminal fluid is a subtype of seminal vesicle secretion ncit UMLS:C0036614 ncithesaurus:Seminal_Fluid UMLS:C0227987 ncithesaurus:Seminal_Vesicle_Secretion secretion of seminal vesicle FMA:62969 seminal vesicle secretion FMA:62969 seminal fluid Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. BTO:0004798 uberon male accessory gland male accessory reproductive gland UBERON:0010147 male accessory sex gland BTO Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. BTO:0004798 male accessory gland BTO:0004798 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. epidermal mucus BTO:0005082 An anatomical cavity that surrounded_by a lymphatic vessel. FMA:59681 lumen of lymphatic duct lymphatic vessel lumen uberon UBERON:0010160 lumen of lymphatic vessel An anatomical cavity that surrounded_by a lymphatic vessel. OBOL:automatic lumen of lymphatic duct FMA:59681 lymphatic vessel lumen FMA:59681 An anatomical cavity that surrounded_by a blood vessel. FMA:312610 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 EMAPA:37760 MA:th tail tip MA:0002848 end of tail MA:0002848 An anatomical cluster that composed_primarily_of a strand of hair. FMA:70752 hairs hairs set pili set of hairs uberon UBERON:0010164 collection of hairs An anatomical cluster that composed_primarily_of a strand of hair. OBOL:automatic hairs FMA:70752 hairs set FMA:70752 pili FMA:TA set of hairs FMA:70752 A collection of hairs that is part of a face. FMA:70741 facial hairs set set of facial hairs uberon facial hair UBERON:0010165 collection of hair on face A collection of hairs that is part of a face. OBOL:automatic facial hairs set FMA:70741 set of facial hairs FMA:70741 A strand of hair that is part of a face. FMA:54360 face hair face hair strand hair of face uberon facial hair UBERON:0010171 strand of hair of face A strand of hair that is part of a face. OBOL:automatic face hair FMA:54360 hair of face FMA:54360 facial hair FMA:54360 any of the numerous small mucous-secreting glands located in the wall of the penile urethra EMAPA:29645 FMA:21443 NCIT:C49311 UMLS:C1314737 Littre's gland gland of Littre gland of male urethra male urethra gland urethral gland (male) uberon glandulae urethrales urethrae masculinae UBERON:0010186 male urethral gland any of the numerous small mucous-secreting glands located in the wall of the penile urethra MGI:anna MP:0011794 UMLS:C1314737 ncithesaurus:Urethral_Gland Littre's gland FMA:21443 urethral gland (male) FMA:21443 glandulae urethrales urethrae masculinae An urethral gland that is part of a female urethra. EMAPA:29653 FMA:21444 female urethra gland gland of female urethra urethral gland (female) uberon UBERON:0010187 female urethral gland An urethral gland that is part of a female urethra. OBOL:automatic urethral gland (female) FMA:21444 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. gonadal artery uberon UBERON:0010192 genital artery One of the laterally paired arteries that supply the gonads. ISBN:0073040584 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 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton AAO:0000267 EHDAA2:0000904 laryngeal cartilage system uberon UBERON:0010212 laryngeal apparatus EHDAA2 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. AAO:0000267 laryngeal cartilage system EHDAA2:0000904 uberon UBERON:0010213 laryngeal pre-cartilage condensation EHDAA2-abstracted EHDAA2-abstracted EHDAA2:0004085 uberon UBERON:0010221 Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? laryngeal associated mesenchyme EHDAA2 EHDAA2 Wikipedia Wikipedia Wikipedia A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]. EHDAA2:0004469 FMA:258745 uberon UBERON:0010225 thalamic complex A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]. The core globe-shaped component of the camera-type eye. See notes for camera-type eye FMA:12513 MIAA:0000283 VHOG:0001616 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 The connective tissue that supports the lobules and follicles of the thyroid gland. FMA:86304 thyroid gland stroma thyroid stroma uberon UBERON:0010233 stroma of thyroid gland The connective tissue that supports the lobules and follicles of the thyroid gland. thyroid gland stroma FMA:86304 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 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 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 2nd arch mesenchyme. EHDAA2:0000068 EMAPA:16281 neural crest derived arch 2 mesenchyme pharyngeal arch 2 mesenchyme from neural crest uberon branchial arch 2 mesenchyme from neural crest UBERON:0010254 2nd arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 3rd 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] EHDAA2:0000083 EMAPA:16404 VHOG:0000571 3rd pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 3rd arch neural crest derived arch 3 mesenchyme pharyngeal arch 3 mesenchyme from neural crest uberon branchial arch 3 mesenchyme from neural crest UBERON:0010255 3rd arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 3rd 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:0000571 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 3rd pharyngeal arch mesenchyme derived from neural crest VHOG:0000571 mesenchyme derived from neural crest of mesenchyme of 3rd arch EMAPA:16404 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 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) 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 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 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 One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta. EMAPA:36493 allantoic vessel umbilical cord blood vessel umbilical vessel uberon umbilical cord blood vessels umbilical vasculature UBERON:0010260 umbilical blood vessel One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta. MP:0003230 allantoic vessel Hymans:Hymans umbilical cord blood vessels A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO] relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO] In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process). AAO:0000225 AAO:0000682 EMAPA:37600 MA:0003037 uberon apparatus hyobranchialis apparatus hyoideus hyobranchial apparatus hyolingual system UBERON:0010272 hyoid apparatus AAO A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO] 2012-06-20 AAO:0000225 AAO AAO:LAP relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO] 2012-06-20 AAO:0000225 AAO EMAPA:37600 MA:th apparatus hyobranchialis apparatus hyoideus hyobranchial apparatus AAO:0000225 hyolingual system AAO:0000225 A zone of bone organ that is part of a hyoid bone. FMA:59494 hyoid bone zone uberon UBERON:0010273 zone of hyoid bone A zone of bone organ that is part of a hyoid bone. OBOL:automatic hyoid bone zone FMA:59494 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 A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi. collect tears produced by the lacrimal glands FMA:59365 uberon lacrimal point lacrimal puncta puncta lacrimalia UBERON:0010284 lacrimal punctum FMA A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi. lacrimal point lacrimal puncta puncta lacrimalia 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 . 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 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. 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 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 epithelium stratificatum squamosum noncornificatum FMA:45569 nonkeratinizing stratified squamous epithelium FMA:45569 stratified squamous non-keratinized epithelium stratified squamous nonkeratinizing epithelium 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. 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. 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 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 bud. uberon UBERON:0010328 limb bud mesenchyme Mesenchyme that is part of a limb bud. OBOL:automatic Mesenchyme that is part of a limb/fin bud. uberon UBERON:0010329 paired limb/fin bud mesenchyme 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 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 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 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 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 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 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 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 2nd arch mesenchyme. EHDAA2:0000067 EMAPA:16280 head mesenchyme derived arch 2 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 2nd arch pharyngeal arch 2 mesenchyme from head mesenchyme uberon branchial arch 2 mesenchyme from head mesenchyme UBERON:0010343 2nd arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 2nd arch EMAPA:16280 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme. EHDAA2:0000082 EMAPA:16403 head mesenchyme derived arch 3 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 3rd arch pharyngeal arch 3 mesenchyme from head mesenchyme uberon branchial arch 3 mesenchyme from head mesenchyme UBERON:0010344 3rd arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 3rd arch EMAPA:16403 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 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 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 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 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 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 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 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 A anatomical space that is enclosed by a hypopharynx. FMA:55096 laryngopharynx lumen uberon UBERON:0010384 lumen of laryngopharynx FMA A anatomical space that is enclosed by a hypopharynx. OBOL:automatic laryngopharynx lumen FMA:55096 An organ cavity that is part of a urethra. FMA:19709 urethral lumen uberon UBERON:0010390 lumen of urethra An organ cavity that is part of a urethra. OBOL:automatic urethral lumen FMA:19709 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 An orifice that is part of a lower urinary tract. EMAPA:35965 MA:0002867 urethral orifice uberon UBERON:0010418 urethral opening An orifice that is part of a lower urinary tract. OBOL:automatic urethral orifice OBOL:automatic 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 ciliary processes ciliary processes set processus ciliares set of ciliary processes uberon ciliary process processus ciliares UBERON:0010427 ciliary processes 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. ciliary processes FMA:76551 ciliary processes set FMA:76551 processus ciliares FMA:TA set of ciliary processes FMA:76551 ciliary process processus ciliares 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 UMLS:C0222649 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. UMLS:C0222649 ncithesaurus:Flat_Bone os planum 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 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. 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 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 A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 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 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 . different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic. EHDAA2:0001143 EHDAA:7007 EHDAA:8105 EMAPA:17953 EMAPA:27621 MA:0002998 VHOG:0001241 induced blastemal cells nephrogenic interstitium of nephrogenic zone uberon cap mesenchyme of metanephros of urinary system nephrogenic interstitium peripheral blastema UBERON:0010531 metanephros induced blastemal cells EHDAA2 . different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic. EMAPA induced blastemal cells VHOG:0001241 nephrogenic interstitium of nephrogenic zone EMAPA:17953 cap mesenchyme of metanephros of urinary system EMAPA:17645 peripheral blastema EMAPA:17953 An epithelial tube that is fated to become a nephron. EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells developing nephron primitive nephron future nephron presumptive nephron uberon UBERON:0010532 primitive nephron EHDAA2-inferred EHDAA2 An epithelial tube that is fated to become a nephron. EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells EHDAA2 The metanephric cortex is the outer region of the metanephros[GO]. VHOG:0000714 uberon UBERON:0010533 metanephros cortex VHOG The metanephric cortex is the outer region of the metanephros[GO]. GO:0072214 Anatomical cluster which give rise to mature mesonephric nephrons. Zebrafish continously generate new mesonephric nephrons. ZFA:0005584 developing mesonephric nephron primitive mesonephric nephron uberon UBERON:0010534 primitive mesonephric nephron Anatomical cluster which give rise to mature mesonephric nephrons. Zebrafish continously generate new mesonephric nephrons. GOC:cvs ORCiD:0000-0002-2244-7917 ZFA:0005584 developing mesonephric nephron ZFA:0005584 A primitive nephron that is part of a metanephros. primitive nephron EHDAA2:0001516 developing metanephric nephron primitive metanephric nephron uberon UBERON:0010535 primitive metanephric nephron EHDAA2 A primitive nephron that is part of a metanephros. OBOL:automatic primitive nephron EHDAA2:0001516 uberon UBERON:0010536 nephron progenitor ZFA cjm Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells. ZFA:0005587 uberon UBERON:0010537 mesonephric nephron progenitor Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells. ZFA:0005587 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) haendel 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). 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 appendage-girdle complex appendage/girdle complex VSAO:0000214 girdle plus limb or fin 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 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 pectoral girdle plus pectoral limb or fin upper limb FMA:7183 upper limb and pectoral girdle upper limb and shoulder 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 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 pelvic girdle plus posterior limb or fin lower limb FMA:7184 lower limb and pelvic girdle lower limb and pelvis Skeletal subdivision that is a segment of the limb skeleton. note the distinction between this and skeleton of limb VSAO:0005018 uberon UBERON:0010712 limb skeleton subdivision VSAO Skeletal subdivision that is a segment of the limb skeleton. VSAO:0005018 VSAO:NI 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. 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 bone of extended limb/fin region UBERONREF:0000003 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 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 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 the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle MA hindlimb bone MA:0000660 UBERONREF:0000003 The collection of all meningeal layers that line a central nervous system. meningeal In some primitive organisms, the meningeal cluster includes only the primitive meninx EHDAA2:0004661 EMAPA:32660 FMA:231572 NCIT:C12349 cerebral meninges cluster of meninges meninges uberon UBERON:0010743 meningeal cluster The collection of all meningeal layers that line a central nervous system. cluster of meninges FMA:231572 meninges FMA:231572 A skeletal element that is part of a limb and composed of cartilage tissue. uberon UBERON:0010881 limb cartilage element A skeletal element that is part of a limb and composed of cartilage tissue. A skeletal element that is part of a limb and composed of pre-cartilage tissue. uberon UBERON:0010882 limb bone pre-cartilage condensation A skeletal element that is part of a limb and composed of pre-cartilage tissue. A cartilaginous condensation that has the potential to develop into a forelimb bone. EMAPA:32626 forelimb wing cartilaginous condensation wing cartilaginous condensation uberon UBERON:0010883 forelimb cartilage element A cartilaginous condensation that has the potential to develop into a forelimb bone. OBOL:automatic forelimb wing cartilaginous condensation NCBITaxon:8782 OBOL:automatic wing cartilaginous condensation NCBITaxon:8782 OBOL:automatic A pre-cartilage condensation that has the potential to develop into a forelimb bone. EMAPA:32625 wing bone pre-cartilage condensation uberon UBERON:0010884 forelimb bone pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a forelimb bone. OBOL:automatic wing bone pre-cartilage condensation NCBITaxon:8782 OBOL:automatic A cartilaginous condensation that has the potential to develop into a hindlimb bone. EMAPA:32632 hindlimb cartilage condensation uberon UBERON:0010885 hindlimb cartilage element A cartilaginous condensation that has the potential to develop into a hindlimb bone. OBOL:automatic hindlimb cartilage condensation EMAPA:32632 A pre-cartilage condensation that has the potential to develop into a hindlimb bone. EMAPA:32638 hindlimb pre-cartilage condensation uberon UBERON:0010886 hindlimb pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a hindlimb bone. OBOL:automatic hindlimb pre-cartilage condensation EMAPA:32638 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. 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 pelvic girdle or posterior limb muscle 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. 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 Hermaphroditic organism that produces both male and female gametes at the same time. AAO:0010046 BILA:0000046 CARO:0000046 HAO:0000046 TADS:0000609 uberon serially hermaphroditic organism simultaneous hermaphroditic organism UBERON:0010899 synchronous hermaphroditic organism CARO Hermaphroditic organism that produces both male and female gametes at the same time. CARO:0000046 serially hermaphroditic organism CARO:0000046 simultaneous hermaphroditic organism 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 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 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 VSAO cjm Skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 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) vertebra skeletal element vertebra element vertebra endochondral element vertebral endochondral element 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. UMLS:C0448281 ncithesaurus:Head_and_Neck_Muscle A cartilage element that is part of a splanchnocranium. 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 pharyngeal arch cartilages ZFA:0001460 splanchnocranium cartilage ZFA:0001460 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 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 vertebral pre-cartilage condensation VHOG:0000582 The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve. FMA:52628 NCIT:C32908 nervus lacrimalis uberon UBERON:0011096 lacrimal nerve FMA The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve. nervus lacrimalis 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 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 A skeletal joint that connects a laryngeal cartilage. FMA:55100 joint of larynx laryngeal articulation uberon UBERON:0011120 laryngeal joint FMA A skeletal joint that connects a laryngeal cartilage. OBOL:automatic joint of larynx FMA:55100 laryngeal articulation FMA:55100 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. 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. axial skeletal system Any synovial joint that is part of a (free) limb. FMA:258776 synovial joint of free limb segment uberon UBERON:0011139 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. synovial limb joint Any synovial joint that is part of a (free) limb. synovial joint of free limb segment FMA:258776 Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 NCIT:C61107 galen:UpperUrinaryTract uberon UBERON:0011143 upper urinary tract FMA FMA-abduced-lr Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 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 EMAPA:37970 MA:th Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 EMAPA:18022 FMA:53673 MA:0000318 facial skeleton uberon facial bone ossa facialia ossa faciei viscerocranium UBERON:0011156 facial skeleton FMA FMA Subdivision of skull that consists of the facial bones. MP:0005274 facial skeleton FMA:53673 facial bone MA:0000318 ossa facialia ossa faciei 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 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 chondrocranium bone uberon UBERON:0011164 neurocranium bone A bone that is part of a neurocranium [Automatically generated definition]. OBOL:automatic chondrocranium bone MA:0001478 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 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 uberon UBERON:0011216 organ system subdivision FBbt FBbt A subdivision of an anatomical system. 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 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 synovium BTO:0001823 FMA:40877 uberon UBERON:0011234 fibrous membrane of synovial tendon sheath 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. Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] 2012-08-14 VSAO:0000306 VSAO Scent glands are exocrine glands found in most mammals. They produce semi-viscous secretions which contain pheromones and other semiochemical compounds. These odor-messengers indicate information such as status, territory marking, mood, and sexual power. The odor may be subliminal-not consciously detectable. Though it is not their primary function, the salivary glands may also function as scent glands in some animals. Exocrine glands in animals which secrete scents which either repel or attract other animals, e.g. perianal glands of skunks, anal glands of weasels, musk glands of foxes, ventral glands of wood rats, and dorsal glands of peccaries[MESH:A13.820]. BTO:0002068 MESH:D012543 uberon UBERON:0011252 scent gland Scent glands are exocrine glands found in most mammals. They produce semi-viscous secretions which contain pheromones and other semiochemical compounds. These odor-messengers indicate information such as status, territory marking, mood, and sexual power. The odor may be subliminal-not consciously detectable. Though it is not their primary function, the salivary glands may also function as scent glands in some animals. Exocrine glands in animals which secrete scents which either repel or attract other animals, e.g. perianal glands of skunks, anal glands of weasels, musk glands of foxes, ventral glands of wood rats, and dorsal glands of peccaries[MESH:A13.820]. MESH:A13.820 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 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 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 The submucous layer of the wall of the uterine tube. BTO:0002116 submucosa of fallopian tube tela submucosa tubae uterinae uberon submucous layer of uterine tube uterine submucosa UBERON:0011298 submucosa of uterine tube The submucous layer of the wall of the uterine tube. BTO:0002116 tela submucosa tubae uterinae BTO:0002116 submucous layer of uterine tube BTO:0002116 A portion of gray matter that is part of a telencephalon. UBERON:0024186 BIRNLEX:1067 FMA:83911 predominantly gray regional part of telencephalon uberon UBERON:0011300 gray matter of telencephalon A portion of gray matter that is part of a telencephalon. OBOL:automatic predominantly gray regional part of telencephalon BIRNLEX:1067 EMAPA:17884 uberon UBERON:0011332 extrinsic tongue pre-muscle mass 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 A lymph vasculature that is part of a head. FMA:224562 TAO:0005298 ZFA:0005298 cranial lymph vessel cranial lymphatics set of lymphatic vessels of head uberon cranial lymph vessels set of cranial lymphatic vessels UBERON:0011363 cranial lymph vasculature A lymph vasculature that is part of a head. OBOL:automatic cranial lymph vessel ZFA:0005298 cranial lymphatics UBERON:cjm set of lymphatic vessels of head FMA:224562 cranial lymph vessels TAO:0005298 set of cranial lymphatic vessels FMA:224562 FMA:54364 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 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 A tube lumen that is part of a mesonephric duct. EHDAA2:0001244 nephric duct lumen uberon cavity of nephric duct UBERON:0011574 mesonephric duct lumen A tube lumen that is part of a mesonephric duct. OBOL:automatic nephric duct lumen EHDAA2:0001244 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. 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 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. EHDAA2:0001020 lower jaw future lip uberon UBERON:0011596 future lower lip EHDAA2 lower jaw future lip EHDAA2:0001020 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. 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 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 Paired structures in the embryo that represent the final stage of development of the caudal end of the external genitals before sexual differentiation. In both males and females the two swellings merge: in the female, they become the posterior labial commissure; In the male, they become the scrotum todo - add parthood relationships to tubercles EMAPA:30074 EMAPA:35377 VHOG:0000976 labioscrotal swelling uberon tuberculum labioscrotale UBERON:0011754 genital swelling EHDAA2 Paired structures in the embryo that represent the final stage of development of the caudal end of the external genitals before sexual differentiation. In both males and females the two swellings merge: in the female, they become the posterior labial commissure; In the male, they become the scrotum tuberculum labioscrotale A genital swelling that is part of a female reproductive system. labial swelling EHDAA2:0000501 EHDAA:9363 EMAPA:18329 EMAPA:30423 labioscrotal swelling of female uberon labial primordium UBERON:0011755 female labial swelling A genital swelling that is part of a female reproductive system. OBOL:automatic labial swelling EMAPA:18329 labioscrotal swelling of female EMAPA:30423 A genital swelling that is part of a male reproductive organ. EHDAA2:0001049 EMAPA:30509 labioscrotal swelling of male scrotal bulge scrotal primordium uberon UBERON:0011756 male genital swelling A genital swelling that is part of a male reproductive organ. OBOL:automatic labioscrotal swelling of male EMAPA:30509 . NCIT:C34274 UMLS:C1514448 uberon phallus phallus primordialis primordial phallus UBERON:0011757 differentiated genital tubercle . UMLS:C1514448 ncithesaurus:Primordial_Phallus phallus phallus primordialis primordial phallus The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP] EMAPA:25350 FMA:14469 MA:0001107 left recurrent laryngeal branch left recurrent laryngeal nerve vagus X nerve left recurrent laryngeal branch uberon UBERON:0011766 left recurrent laryngeal nerve left recurrent laryngeal branch EMAPA:25350 left recurrent laryngeal nerve FMA:14469 vagus X nerve left recurrent laryngeal branch MA:0001107 EMAPA:17275 FMA:14468 MA:0001108 right recurrent laryngeal branch right recurrent laryngeal nerve vagus X nerve right recurrent laryngeal branch uberon UBERON:0011767 right recurrent laryngeal nerve right recurrent laryngeal branch EMAPA:17275 right recurrent laryngeal nerve FMA:14468 vagus X nerve right recurrent laryngeal branch MA:0001108 Anatomical projection that is composed of cartilage tissue. FMA:284626 cartilage process cartilaginous process uberon UBERON:0011769 cartilaginous projection Anatomical projection that is composed of cartilage tissue. VSAO:wd 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 A cranial nerve nucleus that is associated with a vagus nerve. FMA:54573 nucleus of Xth nerve nucleus of vagal X nerve nucleus of vagal nerve nucleus of vagus nerve tenth cranial nerve nucleus vagal X nucleus vagal nucleus vagus nucleus uberon nodosal nucleus UBERON:0011775 vagus nerve nucleus A cranial nerve nucleus that is associated with a vagus nerve. OBOL:automatic nucleus of vagus nerve FMA:54573 tenth cranial nerve nucleus FMA:54573 vagal X nucleus vagal nucleus vagus nucleus nodosal nucleus 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. 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. An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales). cutaneous appendage follicle placode skin follicle placode uberon UBERON:0011817 skin appendage placode NCBIBook:NBK53175 An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales). 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 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 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 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 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 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 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 A duct that is part of a sebaceous gland. FMA:70947 NCIT:C33520 sebaceous gland duct uberon UBERON:0011845 duct of sebaceous gland A duct that is part of a sebaceous gland. OBOL:automatic sebaceous gland duct FMA:70947 An acinus that is part of a sebaceous gland. FMA:59657 sebaceous gland acinus uberon UBERON:0011846 acinus of sebaceous gland An acinus that is part of a sebaceous gland. OBOL:automatic sebaceous gland acinus FMA:59657 An acinus that is part of a salivary gland. FMA:59870 salivary gland acinus uberon UBERON:0011850 acinus of salivary gland An acinus that is part of a salivary gland. OBOL:automatic salivary gland acinus FMA:59870 An acinus that is part of a lacrimal gland. FMA:85250 lacrimal gland acinus uberon UBERON:0011857 acinus of lacrimal gland An acinus that is part of a lacrimal gland. OBOL:automatic lacrimal gland acinus FMA:85250 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 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 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 A organ cavity that is part of a vagina. FMA:19982 vaginal lumen uberon UBERON:0011894 lumen of vagina A organ cavity that is part of a vagina. OBOL:automatic vaginal lumen FMA:19982 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 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. UMLS:C0504096 ncithesaurus:Epimysium fascia of muscle organ FMA:9726 epimysia 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 in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels EHDAA2:0003242 blood island of umbilical vesicle insula sanguinea vesiculae umbilicalis uberon UBERON:0011921 connecting stalk blood islands EHDAA2 EHDAA2 EHDAA2 in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels EHDAA2 blood island of umbilical vesicle insula sanguinea vesiculae umbilicalis Hair in the nose FMA:53670 hair of nose hair of vestibular part of nose nose hair uberon UBERON:0011931 nasal hair Hair in the nose hair of nose FMA:53670 hair of vestibular part of nose FMA:53670 nose hair FMA:53670 An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle EMAPA:36582 FMA:70661 fabrica pilosebacea pilo-sebaceous apparatus pilo-sebaceous unit pilosebaceous apparatus uberon pilosebaceous gland UBERON:0011932 pilosebaceous unit ISBN:0123813611 An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle ISBN:0123813611 PMCID:PMC3130146 fabrica pilosebacea pilo-sebaceous apparatus FMA:70661 pilosebaceous gland FMA:70661 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 UMLS:C0227197 uberon glandular stomach UBERON:0011953 stomach glandular region A region of the stomach that is lined with glandular epithelium. UMLS:C0227197 ncithesaurus:Glandular_Stomach A hepatic vein that is part of a left lobe of liver. EMAPA:37164 FMA:14339 MA:0003032 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 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 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 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 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 FMA:62811 uberon UBERON:0012069 epithelium-associated lymphoid tissue FMA 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 An anatomical cavity that is part of a bronchus. FMA:62646 bronchial lumen lumen of bronchus uberon UBERON:0012082 bronchial lumen FMA FMA An anatomical cavity that is part of a bronchus. OBOL:automatic bronchial lumen FMA:62646 lumen of bronchus FMA:62646 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. dermatological system OBI:MC blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. BTO:0004053 CALOHA:TS-1079 EFO:0001942 MESH:D005312 uberon cord blood fetal blood umbilical cord blood UBERON:0012168 Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP] umbilical cord blood blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. cord blood BTO:0004053 fetal blood MESH:A12.207.152.200 umbilical cord blood MESH:A12.207.152.200 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 EHDAA2:0000494 EMAPA:16794 VHOG:0000715 acousticofacial ganglion facio-acoustic ganglion facio-acoustic ganglion complex VII-VIII uberon facio-acoustic VII-VIII ganglion complex facio-acoustic ganglion complex UBERON:0012175 acoustico-facial VII-VIII ganglion complex cjm EHDAA2 cjm facio-acoustic ganglion complex VII-VIII EMAPA:16794 facio-acoustic VII-VIII ganglion complex VHOG:0000715 facio-acoustic ganglion complex EMAPA:16794 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 network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP] EMAPA:28679 bladder vasculature blood vessels of bladder set of urinary bladder blood vessels uberon blood vessel of bladder UBERON:0012239 urinary bladder vasculature EMAPA network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP] MP:MP blood vessels of bladder EMAPA:28679 blood vessel of bladder EMAPA:28679 external opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]. EMAPA:37977 FMA:19650 external meatus of urethra external urethral orifice external urethral ostium external urinary meatus meatus urinarius orificium urethrae externum orificium urethræ externum urethral meatus uberon urinary meatus UBERON:0012240 urethral meatus external opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]. MP:MP EMAPA:37977 MA:th external meatus of urethra FMA:19650 external urethral orifice FMA:19650 external urethral ostium FMA:19650 external urinary meatus FMA:19650 meatus urinarius orificium urethrae externum orificium urethræ externum urethral meatus FMA:19650 A urethral meatus that is part of a male urethra[Automatically generated definition]. The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis. EMAPA:36434 FMA:85265 MA:0002642 external orifice of male urethra external urethral orifice (male) male urethra ostium ostium urethrae externum (urethra masculina) urethral meatus of penile urethra uberon distal urethral opening of male urethral opening of penile urethra UBERON:0012241 male urethral meatus A urethral meatus that is part of a male urethra[Automatically generated definition]. OBOL:automatic The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis. external orifice of male urethra FMA:85265 external urethral orifice (male) FMA:85265 male urethra ostium MA:0002642 ostium urethrae externum (urethra masculina) FMA:TA urethral meatus of penile urethra EMAPA:36434 distal urethral opening of male EMAPA:36434 urethral opening of penile urethra EMAPA:36434 the usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone FMA:85263 internal meatus of urethra internal urethral orifice of urinary bladder internal urethral ostium orificium urethrae internum ostium orificium internum ostium urethrae internum vesicourethral orifice uberon internal urethral ostium internal urinary meatus UBERON:0012242 internal urethral orifice the usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone MGI:anna MP:0011782 internal meatus of urethra FMA:85263 internal urethral orifice of urinary bladder FMA:85263 internal urethral ostium FMA:85263 orificium urethrae internum MP:0011782 ostium orificium internum ostium urethrae internum vesicourethral orifice FMA:85263 internal urethral ostium MP:0011782 internal urinary meatus MP:0011782 mucus-secreting glands in the mucosa of the uterine cervix NCIT:C32296 UMLS:C2724437 glandulae cervicales uberon UBERON:0012247 cervical gland mucus-secreting glands in the mucosa of the uterine cervix UMLS:C2724437 ncithesaurus:Cervical_Gland glandulae cervicales FMA:TA Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing. BTO:0000411 uberon UBERON:0012248 cervical mucosa Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing. BTO:0000411 The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium. distinction between two FMA classes not clear - we merge them here UBERON:0010182 BTO:0001850 CALOHA:TS-1098 FMA:77056 FMA:86484 NCIT:C12310 UMLS:C0227829 ectocervix portio vaginalis portio vaginalis cervicis uterine ectocervix vaginal part of cervix uberon exocervix UBERON:0012249 ectocervix BTO The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium. BTO:0001850 distinction between two FMA classes not clear - we merge them here FMA UMLS:C0227829 ncithesaurus:Ectocervix ectocervix BTO:0001850 ectocervix FMA:86484 portio vaginalis portio vaginalis cervicis BTO:0001850 uterine ectocervix CALOHA:TS-1098 vaginal part of cervix FMA:77056 exocervix BTO:0001850 A glandular epithelium that is part of a uterine cervix. The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. NCIT:C54414 UMLS:C1707350 uberon cervix columnar epithelium UBERON:0012250 cervix glandular epithelium A glandular epithelium that is part of a uterine cervix. OBOL:automatic The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. UMLS:C1707350 ncithesaurus:Cervix_Columnar_Epithelium A epithelium that is part of a ectocervix. exocervical epithelium uberon UBERON:0012251 ectocervical epithelium A epithelium that is part of a ectocervix. OBOL:automatic The glandular epithelium that lines the endocervix. NCIT:C96180 endocervical glandular epithelium uberon UBERON:0012252 endocervical epithelium The glandular epithelium that lines the endocervix. ncithesaurus:Endocervical_Glandular_Epithelium Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet squamocolumnar junction NCIT:C97148 squamo-columnar junction of uterine cervix squamocolumnar junction of uterine cervix uberon UBERON:0012253 Site of 90% of lower genital tract neoplasia. This junction is presumed, but not proven, to be the embryologic junction of the Müllerian and urogenital sinus epithelia. cervical squamo-columnar junction Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet An artery that originates from the abdominal aorta abdominal artery artery of abdomen uberon UBERON:0012254 abdominal aorta artery An artery that originates from the abdominal aorta 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] 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] 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 EMAPA:35308 FMA:86488 MA:0002732 glandular part of endometrium uterine glands uterine glands set uberon UBERON:0012276 endometrium glandular epithelium glandular part of endometrium FMA:86488 The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands. nasal gland EMAPA:37871 FMA:321518 NCIT:C22725 UMLS:C1522269 glandula nasalis glandulae nasales uberon UBERON:0012278 gland of nasal mucosa The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands. EMAPA:37871 MA:th UMLS:C1522269 ncithesaurus:Nose_Nasal_Cavity_Nasal_Gland_MMHCC glandula nasalis glandulae nasales A holocrine gland that is part of the pilosebaceous unit of a hair located in the area around the anus. EMAPA:37936 MESH:D010481 NCIT:C77620 uberon circumanal gland perianal gland UBERON:0012281 perianal sebaceous gland ISBN:0123813611 A holocrine gland that is part of the pilosebaceous unit of a hair located in the area around the anus. ISBN:0123813611 EMAPA:37936 MA:th circumanal gland MESH:A13.734 perianal gland MESH:A13.734 One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly cloacal fold EHDAA2:0004009 uberon UBERON:0012292 We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold EHDAA2 One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly MP:0011836 MP:anna cloacal fold EHDAA2:0004009 A mucosa that is part of a urethra. EMAPA:37912 FMA:76904 mucous membrane of urethra tunica mucosa urethrae urethral mucosa uberon UBERON:0012299 mucosa of urethra A mucosa that is part of a urethra. OBOL:automatic EMAPA:37912 MA:th mucous membrane of urethra FMA:76904 tunica mucosa urethrae FMA:TA urethral mucosa FMA:76904 EHDAA2:0000039 EMAPA:16389 ectoderm of maxillary component uberon UBERON:0012313 1st arch maxillary ectoderm EHDAA2 EHDAA2 EHDAA2 EHDAA2 ectoderm of maxillary component EMAPA:16389 One of five swellings formed during the development of the face FMA:293103 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 The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice introitus EMAPA:37983 FMA:19984 opening of vagina orifice of vagina ostium vaginae vagina opening vaginal orifice uberon introitus introitus of vagina vaginal introitus UBERON:0012317 vagina orifice The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice MGI:anna MGI:csmith MP:0001142 introitus FMA:19984 EMAPA:37983 MA:th orifice of vagina FMA:19984 ostium vaginae FMA:TA vagina opening MP:0001142 vaginal orifice FMA:19984 introitus FMA:19984 introitus of vagina MP:0001142 An artery of the neck EMAPA:37075 NCIT:C52850 UMLS:C1707349 uberon UBERON:0012320 cervical artery An artery of the neck EMAPA:37075 MA:th UMLS:C1707349 ncithesaurus:Cervical_Artery The deep cervical artery (Profunda cervicalis) is an artery of the neck. FMA:10659 uberon profunda cervicalis UBERON:0012321 deep cervical artery FMA The deep cervical artery (Profunda cervicalis) is an artery of the neck. profunda cervicalis The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals. FMA:79771 MA:0003030 NCIT:C77659 UMLS:C2698431 NALT naso-pharyngeal lymphoid tissue uberon UBERON:0012330 nasal-associated lymphoid tissue The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals. ncithesaurus:Nasal-Associated_Lymphoid_Tissue UMLS:C2698431 ncithesaurus:Nasal-Associated_Lymphoid_Tissue NALT naso-pharyngeal lymphoid tissue FMA:79771 A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis. FMA:16516 MESH:D001956 NCIT:C12318 UMLS:C0006205 broad uterine ligament uberon broad ligament ligamentum latum uteri UBERON:0012332 broad ligament of uterus MESH A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis. MESH:A02.513.170 UMLS:C0006205 ncithesaurus:Broad_Ligament broad uterine ligament FMA:16516 broad ligament MESH:A02.513.170 ligamentum latum uteri A zone of skin that is part of the area surrounding the anus. EMAPA:37715 FMA:29350 MA:0003046 skin of perianal area uberon UBERON:0012336 perianal skin A zone of skin that is part of the area surrounding the anus. EMAPA:37715 MA:th any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen. BTO:0002325 MA:0003042 uberon UBERON:0012344 holocrine gland MA MP any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen. MP:0013543 A bone element that is part of a jaw region. Do not manually classify under here - bones are automatically classified EMAPA:35453 MA:0003130 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 UMLS:C0225334 uberon UBERON:0012375 Contains nerves, blood vessels, lymphatics and lymph nodes subserosa A layer of tissue between the muscularis and serosa. UMLS:C0225334 ncithesaurus:Subserosa A muscular coat that is part of a urinary bladder. FMA:15930 NCIT:C32206 UMLS:C1288327 bladder muscular coat muscle layer of urinary bladder muscular coat of bladder muscular coat of urinary bladder muscular layer of bladder muscular layer of urinary bladder tunica musculari vesicae tunica muscularis (vesica urinaria) uberon UBERON:0012378 muscle layer of urinary bladder FMA A muscular coat that is part of a urinary bladder. OBOL:automatic UMLS:C1288327 ncithesaurus:Bladder_Muscular_Coat muscle layer of urinary bladder FMA:15930 muscular coat of bladder FMA:15930 muscular coat of urinary bladder FMA:15930 muscular layer of bladder FMA:15930 muscular layer of urinary bladder FMA:15930 tunica musculari vesicae FMA:TA tunica muscularis (vesica urinaria) FMA:TA 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 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 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. 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. 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 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. fibrous layer of eyeball FMA:58102 corneosclera fibrous tunic A 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 A 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. A 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 A 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. bones of upper limb FMA:24139 ossa membri superioris FMA:TA pectoral complex skeleton set of bones of upper limb FMA:24139 skeleton of anterior limb/fin and girdle 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. bones of lower limb FMA:24140 lower limb skeleton FMA:24140 ossa membri inferioris FMA:TA pelvic complex skeleton set of bones of lower limb FMA:24140 skeleton of posterior limb/fin and girdle The posterior region of the neck, including the suboccipital region. nuchal nape BTO:0000957 FMA:24189 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. 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 sphincter muscle that is part of a vagina. sphincter of vagina uberon UBERON:0012487 vaginal sphincter A sphincter muscle that is part of a vagina. OBOL:automatic A muscular coat that is part of a duodenum. FMA:14944 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 smooth muscle of duodenum A muscular coat that is part of a colon. EMAPA:27383 FMA:14986 MA:0003198 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 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 A serous membrane that is part of a vermiform appendix. FMA:14997 appendiceal serosa appendix serosa serosa of vermiform appendix visceral peritoneum of vermiform appendix uberon UBERON:0012498 serosa of appendix A serous membrane that is part of a vermiform appendix. OBOL:automatic appendiceal serosa FMA:14997 appendix serosa FMA:14997 serosa of vermiform appendix FMA:14997 visceral peritoneum of vermiform appendix FMA:14997 A serous membrane that is part of a fallopian tube. FMA:18316 serosa of fallopian tube serosa of oviduct serous coat of uterine tube tunica serosa (tuba uterina) tunica serosa tubae uterinae uterine tubal serosa uterine tube serosa uberon UBERON:0012499 serosa of uterine tube A serous membrane that is part of a fallopian tube. OBOL:automatic serosa of fallopian tube FMA:18316 serosa of oviduct FMA:18316 serous coat of uterine tube FMA:18316 tunica serosa (tuba uterina) FMA:18316 tunica serosa tubae uterinae FMA:TA uterine tubal serosa FMA:18316 uterine tube serosa FMA:18316 A adventitia that is part of a esophagus. FMA:63006 adventitia of oesophagus adventitious layer of esophagus esophageal adventitia esophagus adventitia tunica adventitia (esophagus) tunica adventitia oesophageae uberon UBERON:0012504 adventitia of esophagus A 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 A smooth muscle tissue that is part of a umbilical cord. BTO:0001847 uberon UBERON:0012615 umbilical smooth muscle A smooth muscle tissue that is part of a umbilical cord. OBOL:automatic A anatomical junction that connects a stomach and connects a duodenum. FMA:17046 uberon UBERON:0012650 gastroduodenal junction A 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 The subdivision of the digestive tract that consists of the colon and the rectum. colorectal BTO:0001613 CALOHA:TS-1298 NCIT:C54189 UMLS:C1711309 uberon UBERON:0012652 colorectum non-canonical cjm The subdivision of the digestive tract that consists of the colon and the rectum. UMLS:C1711309 ncithesaurus:Colorectal_Region A mucosa that is part of a colorectum. UBERON:0019041 BTO:0002435 uberon UBERON:0013067 colorectal mucosa A mucosa that is part of a colorectum. OBOL:automatic 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 abdominal vein uberon UBERON:0013126 vein of abdomen A vein that is part of a abdomen. OBOL:automatic A vein that drains a lip. 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 A nonskeletal ligament that is part of a liver. FMA:15820 NCIT:C32997 UMLS:C0230238 hepatic ligament liver ligament uberon UBERON:0013139 ligament of liver A nonskeletal ligament that is part of a liver. OBOL:automatic UMLS:C0230238 ncithesaurus:Liver_Ligament hepatic ligament FMA:15820 Any vein within the general circulation that transports blood back to the right atrium of the heart. FMA:66644 NCIT:C33719 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 EHDAA2:0000101 EMAPA:16917 rhombencephalic vesicle uberon UBERON:0013149 gives rise of 4th ventricle hindbrain vesicle EHDAA2 rhombencephalic vesicle EHDAA2:0000101 consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html). Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle' NCIT:C34259 early brain vesicle primitive brain vesicle primary brain vesicle secondary brain vesicle uberon brain vesicle UBERON:0013150 future brain vesicle EHDAA2 EHDAA2 One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions. NCIT:C32310 UMLS:C0226164 artery of choroid plexus choroid artery uberon UBERON:0013151 choroidal artery One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions. ncithesaurus:Choroidal_Artery UMLS:C0226164 ncithesaurus:Choroidal_Artery EHDAA2:0000033 EMAPA:16384 endoderm of mandibular component uberon UBERON:0013156 1st arch mandibular endoderm EHDAA2 EHDAA2 EHDAA2 endoderm of mandibular component EMAPA:16384 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 A telencephalic ventricle that is in_the_left_side_of a telencephalon. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:78450 left telencephalic ventricle uberon UBERON:0013161 left lateral ventricle FMA A telencephalic ventricle that is in_the_left_side_of a telencephalon. OBOL:automatic A telencephalic ventricle that is in_the_right_side_of a telencephalon. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:78449 right telencephalic ventricle uberon UBERON:0013162 right lateral ventricle FMA A telencephalic ventricle that is in_the_right_side_of a telencephalon. OBOL:automatic the layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles. EMAPA:37927 FMA:18613 NCIT:C33243 UMLS:C0227878 cortex of ovary cortex ovarii (zona parenchymatosa) uberon UBERON:0013191 ovarian cortex the layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles. MGI:anna EMAPA:37927 MA:th UMLS:C0227878 ncithesaurus:Ovarian_Cortex cortex of ovary FMA:18613 cortex ovarii (zona parenchymatosa) FMA:18613 highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles. composed of loose connective tissue that contains blood vessels, lymph vessels and nerves EMAPA:37928 FMA:18616 NCIT:C33245 UMLS:C0227879 medulla of ovary medulla ovarii (zona vasculosa) uberon zona vasculosa of Waldeyer UBERON:0013192 ovarian medulla highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles. MGI:anna composed of loose connective tissue that contains blood vessels, lymph vessels and nerves NCIT EMAPA:37928 MA:th UMLS:C0227879 ncithesaurus:Ovarian_Medulla medulla of ovary FMA:18616 medulla ovarii (zona vasculosa) FMA:18616 zona vasculosa of Waldeyer 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. uberon UBERON:0013238 future glans A future glans that is part of a male genital tubercle. EMAPA:29252 glans of male genital tubercle uberon UBERON:0013239 future glans penis EMAPA A future glans that is part of a male genital tubercle. OBOL:automatic A future glans that is part of a female genital tubercle. EMAPA:19170 glans of female genital tubercle uberon UBERON:0013240 future glans clitoris EMAPA A future glans that is part of a female genital tubercle. OBOL:automatic The precursor of the urethra In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week sulcus urethralis primarius urethral groove urethral sulcus uberon UBERON:0013241 embryonic urethral groove Wikipedia The precursor of the urethra In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week sulcus urethralis primarius A epithelial tube that develops from a Mullerian duct in a male. Later degenerates. consider separating the duct from the degenerating portion, as in EMAPA EHDAA2:0001052 EMAPA:29161 EMAPA:35661 uberon degenerating mesonephric portion of male paramesonephric duct UBERON:0013247 male paramesonephric duct EHDAA2 EHDAA2 A epithelial tube that develops from a Mullerian duct in a male. Later degenerates. degenerating mesonephric portion of male paramesonephric duct EMAPA:29161 Anatomical cavity that is the lumen of the skull and contains the brain. EMAPA:37497 FMA:9644 MA:0003061 NCIT:C77638 UMLS:C0230041 cavitas cranii uberon intracranial cavity intracranial space UBERON:0013411 cranial cavity 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 intracranial space The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type. NCIT:C12253 UMLS:C0227187 uberon proximal part of esophagus upper third of esophagus UBERON:0013472 upper esophagus The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type. ncithesaurus:Upper_Third_of_the_Esophagus UMLS:C0227187 ncithesaurus:Upper_Third_of_the_Esophagus A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus. In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil caecal tonsil uberon cecal GALT UBERON:0013478 cecal tonsil A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus. ISBN:0824754077 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 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 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 A lumbar vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001038 lumbar vertebral cartilage condensation group uberon UBERON:0013509 lumbar vertebra cartilage element A lumbar vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic lumbar vertebral cartilage condensation group EHDAA2:0001038 A lumbar vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013510 lumbar vertebra pre-cartilage condensation A lumbar 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. A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA:18302 subdivision of oviduct subdivision of uterine tube uterine tube zone zone of uterine tube subdivision of fallopian tube uberon UBERON:0013515 subdivision of oviduct A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA subdivision of oviduct FMA:18302 uterine tube zone FMA:18302 zone of uterine tube FMA:18302 subdivision of fallopian tube FMA:18302 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. 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 A anatomical cavity that is part of a ear vesicle. EHDAA2:0004121 EMAPA:25363 lumen of otocyst uberon UBERON:0013526 otocyst lumen EHDAA2 EHDAA2 EHDAA2 A anatomical cavity that is part of a ear vesicle. OBOL:automatic lumen of otocyst EMAPA:25363 A epithelium that is part of a intestinal villus. FMA:63587 intestinal villus epithelium uberon villous epithelium villus epithelium UBERON:0013636 epithelium of intestinal villus A epithelium that is part of a intestinal villus. OBOL:automatic intestinal villus epithelium FMA:63587 The prostate gland lobe that is located on the lateral side of the organ. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:29822 FMA:19577 MA:0003125 NCIT:C13092 lateral lobe of prostate lateral lobe of prostate gland uberon lateral prostate lateral ventral lobe of prostate gland UBERON:0013637 prostate gland lateral lobe The prostate gland lobe that is located on the lateral side of the organ. ncithesaurus:Lateral_Lobe_of_the_Prostate lateral lobe of prostate FMA:19577 lateral lobe of prostate gland FMA:19577 lateral ventral lobe of prostate gland MorphoBank:MorphoBank Anatomical space that is an opening in a bone of the skull. FMA:53165 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 foramen of skull cranial conduit FMA:53165 foramina of the skull 2 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 Lymphoid tissue located in the appendix. CALOHA:TS-1268 lymphatic tissue of appendix lymphatic tissue of vermiform appendix uberon appendix lymphoid UBERON:0013689 appendix lymphoid tissue Lymphoid tissue located in the appendix. CALOHA:TS-1268 lymphatic tissue of appendix OBOL:automatic lymphatic tissue of vermiform appendix OBOL:automatic appendix lymphoid CALOHA:TS-1268 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 The epithelium that forms the surface of the tonsil dips into the underlying connective tissue in numerous places, forming crypts kown as tonsillar crypts. Stratified squamous epithelium, that may be heavily infiltrated by lymphocytes. Epithelial cells are present in the germinal as well as in the periphery of the nodule. CALOHA:TS-2070 uberon epithelium of tonsil tonsil epithelial cell UBERON:0013696 tonsil epithelium The epithelium that forms the surface of the tonsil dips into the underlying connective tissue in numerous places, forming crypts kown as tonsillar crypts. Stratified squamous epithelium, that may be heavily infiltrated by lymphocytes. Epithelial cells are present in the germinal as well as in the periphery of the nodule. CALOHA:TS-2070 epithelium of tonsil CALOHA:TS-2070 tonsil epithelial cell CALOHA:TS-2070 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. 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 Anatomical projection that is part of the integumentl system. skin projection uberon UBERON:0013703 integumentary projection Anatomical projection that is part of the integumentl system. 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. 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 A organ component layer that is part of a integumental system. layer of skin skin layer uberon UBERON:0013754 integumentary system layer A organ component layer that is part of a integumental system. OBOL:automatic A blood that is part of a artery. 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 arterial blood FMA:83066 blood in artery FMA:83066 portion of arterial blood FMA:83066 A blood that is part of a vein. 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 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 One of two openings in the uterine cervix. FMA:20422 uberon cervical opening uterine cervix opening UBERON:0013758 cervical os One of two openings in the uterine cervix. Opening of uterine cervix into the body of the uterus. The internal orifice of the uterus (or internal orifice of the cervix uteri or internal os) is an interior narrowing of the uterine cavity. It corresponds to a slight constriction known as the isthmus that can be observed on the surface of the uterus about midway between the apex and base[Wikipedia:Internal_orifice_of_the_uterus]. FMA:17747 uberon internal orifice internal os UBERON:0013759 internal cervical os Opening of uterine cervix into the body of the uterus. The internal orifice of the uterus (or internal orifice of the cervix uteri or internal os) is an interior narrowing of the uterine cavity. It corresponds to a slight constriction known as the isthmus that can be observed on the surface of the uterus about midway between the apex and base[Wikipedia:Internal_orifice_of_the_uterus]. internal orifice internal os internal os FMA:17747 Opening of uterine cervix into the vagina. The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]. FMA:76836 NCIT:C32491 UMLS:C1512165 external os of uterus ostium uteri uberon external os ostium of uterus UBERON:0013760 external cervical os Opening of uterine cervix into the vagina. The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]. UMLS:C1512165 ncithesaurus:Ectocervical_Os external os of uterus FMA:76836 ostium uteri FMA:TA external os ostium of uterus The cavity formed by the walls of the cervix. BTO:0002249 FMA:17746 lumen of cervix of uterus uberon canal of the cervix cavity of cervix cervical canal cervical canal of uterus endocervical endocervical canal endocervix UBERON:0013761 cervical cavity The cavity formed by the walls of the cervix. lumen of cervix of uterus FMA:17746 canal of the cervix cavity of cervix BTO:0002249 cervical canal cervical canal of uterus BTO:0002249 endocervical endocervical canal endocervical canal BTO:0002249 endocervix 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 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. 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 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. A organ cavity that is part of a uterus. EMAPA:36273 FMA:17745 cavity of uterus uterine cavity uterine space uberon UBERON:0013769 uterine lumen A organ cavity that is part of a uterus. OBOL:automatic cavity of uterus FMA:17745 uterine cavity FMA:17745 Embryonic structure that gives rise to the telencephalon. EHDAA2:0004424 EMAPA:36024 TAO:0000571 ZFA:0000571 presumptive telencephalon uberon UBERON:0014371 paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP] future telencephalon definitional Embryonic structure that gives rise to the telencephalon. ZFA:0000571 ZFA:curator presumptive telencephalon ZFA:0000571 A collection of hairs that is part of a craniocervical region. uberon UBERON:0014382 collection of hairs on head or neck A collection of hairs that is part of a craniocervical region. OBOL:automatic 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 The simple cuboidal epithelium lining the lumen of kidney collecting ducts. In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis EMAPA:37885 collecting duct of renal tubule epithelium epithelium of collecting duct of renal tubule epithelium of renal collecting tubule uberon UBERON:0014388 kidney collecting duct epithelium The simple cuboidal epithelium lining the lumen of kidney collecting ducts. MGI:anna MP:0011843 EMAPA:37885 MA:th A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae. FMA:54822 gustatory papilla taste papilla uberon gustatory papillae taste papillae UBERON:0014389 gustatory papilla of tongue A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae. MGI:smb MP:0006256 gustatory papillae taste papillae A anatomical space that is enclosed by a sinusoid. FMA:63133 lumen of sinusoid sinusoid lumen uberon UBERON:0014399 sinusoidal space A 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 Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta EMAPA:31450 MA:0002591 kidney venous blood vessel venous blood vessel of kidney uberon kidney venous system UBERON:0014401 renal venous blood vessel Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. MGI:csmith we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta MA kidney venous blood vessel MA:0002591 kidney venous system EMAPA:31450 A taste bud that is located on the tongue, situated on a gustatory papilla. gustatory papilla taste bud gustatory papillae taste bud uberon UBERON:0014451 tongue taste bud A taste bud that is located on the tongue, situated on a gustatory papilla. gustatory papillae taste bud MP:0006260 A gustatory epithelium that is part of a tongue. BIRNLEX:4099 UMLS:C1179150 lingual gustatory epithelium uberon UBERON:0014452 gustatory epithelium of tongue A gustatory epithelium that is part of a tongue. OBOL:automatic UMLS:C1179150 BIRNLEX:4099 lingual gustatory epithelium 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 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 FMA:75136 uberon UBERON:0014466 subarachnoid fissure 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 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. thoracic skeleton EHDAA2:0002013 A gray matter of spinal cord that is part of a cervical spinal cord. BIRNLEX:1521 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 gray matter of spinal cord that is part of a thoracic spinal cord. BIRNLEX:980 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 A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component. EHDAA2:0000479 EMAPA:16374 VHOG:0000282 uberon UBERON:0014699 extraembryonic venous system VHOG A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component. OBOL:automatic A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component. EHDAA2:0000478 EMAPA:16370 VHOG:0001396 uberon UBERON:0014701 extraembryonic vascular system A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component. OBOL:automatic A epithelium that is part of a frontonasal prominence. EHDAA2:0004108 EMAPA:32918 uberon UBERON:0014702 frontonasal process epithelium EHDAA2 EHDAA2 A 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 A anatomical space that is enclosed by a pleuroperitoneal canal. EHDAA2:0004736 EMAPA:25034 pleuro-peritoneal canal cavity uberon UBERON:0014704 pleuroperitoneal canal lumen EHDAA2 A anatomical space that is enclosed by a pleuroperitoneal canal. OBOL:automatic pleuro-peritoneal canal cavity EMAPA:25034 A epithelium that is part of a median lingual swelling. EHDAA2:0001085 EMAPA:17188 uberon tuberculum impar epitheilium UBERON:0014705 median lingual swelling epithelium EHDAA2 EHDAA2 A epithelium that is part of a median lingual swelling. OBOL:automatic tuberculum impar epitheilium EMAPA:17188 EHDAA2:0001147 EMAPA:17646 metanephros primitive collecting ducts primitive collecting duct uberon UBERON:0014706 primitive renal collecting duct system EHDAA2 EHDAA2 metanephros primitive collecting ducts EHDAA2:0001147 primitive collecting duct EMAPA:17646 A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. NCIT:C32828 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. 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 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 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. The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. EHDAA2:0000597 EMAPA:17703 VHOG:0001546 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 The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. crural diaphragm crura of the diaphragm crus of the diaphragm diaphragm crura diaphragmatic crura 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 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 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 forebrain forebrain segment segment of forebrain FMA:61996 forebrain neuromere uberon future prosencephalon UBERON:0014775 prosomere A neuromere that is part of the presumptive forebrain 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 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 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 The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ. EMAPA:18274 FMA:54813 septum of tongue uberon median fibrous septum septum of tongue tongue septum UBERON:0014790 lingual septum The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ. septum of tongue FMA:54813 median fibrous septum septum of tongue tongue septum 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 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA TAO:0005277 VHOG:0000319 XAO:0000174 ZFA:0005277 uberon UBERON:0014892 skeletal muscle organ 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 The space between a blood vessel and the pia mater. VRS NCIT:C83196 Virchow-Robin space perivascular region uberon perivascular spaces UBERON:0014930 VRS belonging to the subarachnoid space are continuous with VRS of the subpial space. The direct communication between VRS of the subarachnoid space and the subpial space is unique to the brain's arteries, as no leptomeningeal layers surround the brain's veins[WP] perivascular space The space between a blood vessel and the pia mater. ncithesaurus:Perivascular_Space VRS Virchow-Robin space perivascular spaces these layers primarily refer to the mammalian future neocortex uberon UBERON:0014950 layer of developing cerebral cortex EMAPA 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. cervical vertebra skeletal element cervical vertebra element 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. thoracic vertebra skeletal element thoracic vertebra element A lumbar vertebra bone or its cartilage or pre-cartilage precursor. lumbar vertebra skeletal element lumbar vertebra element uberon UBERON:0015009 lumbar vertebra endochondral element A lumbar vertebra bone or its cartilage or pre-cartilage precursor. lumbar vertebra skeletal element lumbar vertebra element A forelimb bone or its cartilage or pre-cartilage precursor. forelimb skeletal element uberon UBERON:0015021 forelimb endochondral element A forelimb bone or its cartilage or pre-cartilage precursor. forelimb skeletal element A hindlimb bone or its cartilage or pre-cartilage precursor. hindlimb bone skeletal element uberon UBERON:0015022 hindlimb endochondral element A hindlimb bone or its cartilage or pre-cartilage precursor. hindlimb bone skeletal element A limb bone or its cartilage or pre-cartilage precursor. limb bone skeletal element limb bone endochondral element uberon UBERON:0015061 limb endochondral element A limb bone or its cartilage or pre-cartilage precursor. limb bone skeletal element limb bone endochondral element 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 epicardial adipose tissue pericardial adipose tissue uberon UBERON:0015129 epicardial fat Visceral intrapericardial fat contiguous with the myocardial surface. A portion of connective tissue that is part of a prostate gland. FMA:74165 connective tissue of prostate uberon UBERON:0015130 connective tissue of prostate gland FMA A portion of connective tissue that is part of a prostate gland. OBOL:automatic connective tissue of prostate FMA:74165 A strand of hair that is part of a tail. EMAPA:37971 uberon UBERON:0015148 tail hair A strand of hair that is part of a tail. OBOL:automatic EMAPA:37971 MA:th A strand of hair that is part of a dorsum. FMA:54320 uberon back hair dorsal coat hair hair of back UBERON:0015150 dorsal hair A strand of hair that is part of a dorsum. OBOL:automatic hair of back FMA:54320 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. A gland that is located in or around the ocular region, nearer the outer canthi. The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104 lateral ocular gland lateral orbital gland uberon UBERON:0015154 lateral gland of orbital region A gland that is located in or around the ocular region, nearer the outer canthi. An eye consisting of multiple light-sensing organs uberon UBERON:0015165 multi-unit eye An eye consisting of multiple light-sensing organs present on tentacular crown present on mantle edge in arcacean Bivalvia 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 A blood vessel that is part of a endometrium. blood vessel of endometrium uberon UBERON:0015172 endometrial blood vessel A blood vessel that is part of a endometrium. OBOL:automatic 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. 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 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. A ligament that is part of a diaphragm. EMAPA:19236 FMA:58280 uberon UBERON:0015214 arcuate ligament A ligament that is part of a diaphragm. OBOL:automatic 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. EMAPA:37680 MA:0003043 uberon UBERON:0015251 modified sebaceous gland MA EMAPA:37680 MA:th 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 A mesenchyme that is part of a urethra. EMAPA:37786 MA:0002648 uberon UBERON:0015418 urethra mesenchymal layer A mesenchyme that is part of a urethra. OBOL:automatic EMAPA:37786 MA:th A valve that is part of a ureter. EMAPA:37781 MA:0002658 ureteral valve valve or ureter uberon UBERON:0015420 ureteral valve A valve that is part of a ureter. OBOL:automatic EMAPA:37781 MA:th ureteral valve MA:0002658 A lymph node that is part of a hypodermis. MA:0003028 uberon UBERON:0015453 subcutaneous lymph node A lymph node that is part of a hypodermis. OBOL:automatic A zone of skin that is part of a scrotum. EMAPA:36411 FMA:20432 MA:0003093 scrotal skin skin of scrotum uberon UBERON:0015479 scrotum skin A zone of skin that is part of a scrotum. OBOL:automatic skin of scrotum FMA:20432 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. EMAPA:37478 MA:th choledochoduodenal junction MA:0003108 A 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 A epithelium that is part of a anal canal. OBOL:automatic anal canal epithelium FMA:17511 epithelium of anal canal FMA:17511 A smooth muscle tissue that is part of a ejaculatory duct. EMAPA:32289 FMA:19372 muscle layer of ejaculatory duct uberon UBERON:0015717 smooth muscle tissue layer of ejaculatory duct A smooth muscle tissue that is part of a ejaculatory duct. OBOL:automatic muscle layer of ejaculatory duct FMA:19372 FMA:62798 portion of heterogeneous tissue uberon UBERON:0015757 heterogeneous tissue FMA portion of heterogeneous tissue FMA:62798 A epithelium that is part of a duct of salivary gland. FMA:67682 epithelium of salivary duct salivary duct epithelium salivary ductal epithelium uberon UBERON:0015766 epithelium of duct of salivary gland FMA A epithelium that is part of a duct of salivary gland. OBOL:automatic epithelium of salivary duct FMA:67682 salivary duct epithelium FMA:67682 salivary ductal epithelium FMA:67682 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 Any anatomical conduit which is part of the upper respiratory tract Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]. FMA:265132 uberon respiratory conduit UBERON:0015787 upper respiratory conduit Any anatomical conduit which is part of the upper respiratory tract Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]. FMA:265132 respiratory conduit FMA:265132 An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. FMA:265136 uberon UBERON:0015788 olfactory apparatus chamber An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper EMAPA:25133 MA:0000579 cranial/facial muscle uberon cranial-facial muscle cranio-facial muscle craniofacial muscle UBERON:0015789 cranial or facial muscle cranial/facial muscle MA:0000579 cranial-facial muscle EMAPA:25133 cranio-facial muscle EMAPA:25133 craniofacial muscle EMAPA:25133 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 A epithelium that is part of a ear. EMAPA:32800 MA:0003161 uberon UBERON:0015807 ear epithelium A epithelium that is part of a ear. OBOL:automatic A epithelium that is part of a camera-type eye. EMAPA:35957 MA:0003162 uberon UBERON:0015808 eye epithelium A epithelium that is part of a camera-type eye. OBOL:automatic A epithelium that is part of a foregut. EMAPA:32922 MA:0003204 uberon UBERON:0015833 foregut epithelium A 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 FMA:66178 uberon UBERON:0015860 visceral abdominal lymph node FMA A lymph node that is part of a head. FMA:61212 uberon UBERON:0015870 lymph node of head A lymph node that is part of a head. OBOL:automatic Any of the lymph nodes that are part of a face. In humans, these comprise three groups: (a) infraorbital or maxillary, scattered over the infraorbital region from the groove between the nose and cheek to the zygomatic arch; (b) buccinator, one or more placed on the Buccinator opposite the angle of the mouth; (c) supramandibular, on the outer surface of the mandible, in front of the Masseter and in contact with the external maxillary artery and anterior facial vein. FMA:61222 buccal lymph node uberon UBERON:0015871 facial lymph node Any of the lymph nodes that are part of a face. buccal lymph node FMA:61222 A lymph node that is located close to the surface. FMA:12767 NCIT:C102716 uberon UBERON:0015917 superficial lymph node A lymph node that is located close to the surface. A lymph node that is located deeper within the organism, further from the surface. FMA:12768 uberon UBERON:0015918 deep lymph node A lymph node that is located deeper within the organism, further from the surface. A lymph node that is part of a hindlimb. FMA:44310 uberon UBERON:0016398 lymph node of lower limb A lymph node that is part of a hindlimb. OBOL:automatic A lymph node that is part of a forelimb. FMA:44311 uberon UBERON:0016399 lymph node of upper limb A lymph node that is part of a forelimb. OBOL:automatic 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 breast that is part of a male organism. FMA:19901 NCIT:C33048 mamma masculina uberon UBERON:0016410 male breast A breast that is part of a male organism. OBOL:automatic mamma masculina FMA:19901 Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall. EMAPA:37233 FMA:50060 NCIT:C62484 uberon UBERON:0016435 chest wall Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall. FMA:50060 EMAPA:37233 MA:th A strand of hair that is part of a head. FMA:54241 hair of scalp head hair uberon UBERON:0016446 hair of head A strand of hair that is part of a head. OBOL:automatic hair of scalp FMA:54241 head hair FMA:54241 A strand of hair that is part of a trunk. FMA:54250 trunk hair uberon UBERON:0016447 hair of trunk A strand of hair that is part of a trunk. OBOL:automatic trunk hair FMA:54250 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 A collagenous capsule covering the external surface of the liver. It consists of type III collagen and extends to the stroma of endothelial sinusoids. It is covered by a single layer of mesothelial cells. FMA:15813 capsula fibrosa perivascularis fibrous capsule of liver glisson's capsule hepatic capsule tunica fibrosa (hepar) tunica fibrosa hepatis uberon fibrous capsule of Glisson liver capsule UBERON:0016479 capsule of liver A collagenous capsule covering the external surface of the liver. capsula fibrosa perivascularis fibrous capsule of liver FMA:15813 glisson's capsule FMA:15813 hepatic capsule FMA:15813 tunica fibrosa (hepar) FMA:TA tunica fibrosa hepatis FMA:15813 FMA:TA fibrous capsule of Glisson liver capsule A lymph node that is part of a bronchus. MA:0003078 NCIT:C32232 uberon UBERON:0016481 bronchial lymph node A lymph node that is part of a bronchus. OBOL:automatic 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 OpenCyc:Mx4rvViwtJwpEbGdrcN5Y29ycA UMLS:C0587901 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. right ventricle lumen EMAPA:26047 right ventricular cavity FMA:FMA A epithelium that is part of a male urethra. EMAPA:30467 FMA:19684 male urethral epithelium urethral epithelium of male uberon UBERON:0016510 epithelium of male urethra A epithelium that is part of a male urethra. OBOL:automatic male urethral epithelium FMA:FMA urethral epithelium of male EMAPA:30467 A anatomical space that is part of a duodenum. EMAPA:19080 FMA:14589 doudenal lumen duodenal lumen uberon UBERON:0016512 lumen of duodenum A anatomical space that is part of a duodenum. OBOL:automatic doudenal lumen FMA:FMA duodenal lumen FMA:FMA 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. left ventricular cavity FMA:FMA A epithelium that is part of a female urethra. EMAPA:30470 FMA:19774 female urethral epithelium urethral epithelium of female uberon UBERON:0016520 epithelium of female urethra A epithelium that is part of a female urethra. OBOL:automatic female urethral epithelium FMA:FMA urethral epithelium of female EMAPA:30470 Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border. Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though frontal region regio frontalis BAMS:Frontal_lobe BIRNLEX:928 BM:Tel-Cx-FR CALOHA:TS-0389 DHBA:12113 EFO:0000913 EV:0100167 FMA:61824 HBA:4009 MAT:0000505 MESH:A08.186.211.730.885.213.270 NCIT:C12352 OpenCyc:Mx4rv3OJ8JwpEbGdrcN5Y29ycA UMLS:C0016733 UMLS:C1268977 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=56 lobi frontales lobus frontalis frontal cortex uberon UBERON:0016525 frontal lobe FMA Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border. FMA:61824 Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though MM frontal region FMA:61824 regio frontalis FMA:61824 FMA:TA regio frontalis FMA:TA UMLS:C0016733 BIRNLEX:928 UMLS:C0016733 ncithesaurus:Frontal_Lobe UMLS:C1268977 BIRNLEX:928 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=56 BIRNLEX:928 lobi frontales NeuroNames:56 lobus frontalis frontal cortex FMA:61824 Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. UBERON:0000322 BIRNLEX:922 BTO:0000445 FMA:61823 cerebral hemisphere lobe cerebral lobe lobe of cerebral cortex lobe parts of cerebral cortex lobi cerebri uberon cerebral cortical segment lobes of the brain regional organ part of cerebral cortex segment of cerebral cortex UBERON:0016526 We use the term lobe broadly as a rough regional area, encompassing homologous regions in smooth-brained mammals. We subdivide the lobes into white matter and neocortical parts. lobe of cerebral hemisphere Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. FMA:61823 cerebral hemisphere lobe FMA:61823 cerebral lobe BTO:0000445 lobe of cerebral cortex BIRNLEX:922 lobe parts of cerebral cortex BIRNLEX:922 lobi cerebri FMA:77800 FMA:TA cerebral cortical segment FMA:68603 lobes of the brain BIRNLEX:922 regional organ part of cerebral cortex FMA:68603 segment of cerebral cortex BIRNLEX:922 Grey matter neocortex region of a lobe of the cerebral hemisphere. FMA:242197 cortex of cerebral hemisphere lobe cortex of lobe of cerebral hemisphere uberon gray matter of lobe of cerebral hemisphere neocortical part of cerebral hemisphere UBERON:0016529 cortex of cerebral lobe Grey matter neocortex region of a lobe of the cerebral hemisphere. cortex of cerebral hemisphere lobe FMA:242197 cortex of lobe of cerebral hemisphere FMA:242197 gray matter of lobe of cerebral hemisphere FMA:242197 Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border. DHBA:10208 DMBA:16016 EMAPA:35667 FMA:242203 MA:0000916 NLX:79282 cortex of parietal lobe parietal lobe cortex parietal neocortex uberon gray matter of parietal lobe UBERON:0016530 parietal cortex Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border. NLX:79282 cortex of parietal lobe FMA:242203 parietal lobe cortex FMA:242203 parietal neocortex DHBA:10208 gray matter of parietal lobe FMA:242203 Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals BM:Tel-Cx-Te DHBA:10235 DMBA:16044 FMA:242201 MA:0000941 NLX:94939 cortex of temporal lobe temporal lobe cortex temporal neocortex uberon gray matter of temporal lobe UBERON:0016538 temporal cortex Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals NLX:94939 cortex of temporal lobe FMA:242201 temporal lobe cortex FMA:242201 temporal neocortex DHBA:10235 gray matter of temporal lobe FMA:242201 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. 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. gray matter layer of neuraxis FMA:83142 mucus produced in the respiratory tract. NCIT:C93171 uberon UBERON:0016552 phlegm mucus produced in the respiratory tract. 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). A blood vessel that is part of a cerebellum. uberon UBERON:0016565 cerebral blood vessel A blood vessel that is part of a cerebellum. OBOL:automatic 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 rexed lamina uberon UBERON:0016570 lamina of gray matter of spinal cord rexed lamina FMA:68861 A scent gland that is part of the skin cutaneous scent gland uberon UBERON:0016852 skin scent gland A scent gland that is part of the skin 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. dorsal optic cup dorsal region of optic cup 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 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 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. 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. 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 primordium that has the potential to develop into a saliva-secreting gland. uberon UBERON:0017651 salivary gland primordium A primordium that has the potential to develop into a saliva-secreting gland. OBOL:automatic 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 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 A renal pelvis that is part of a left ureter. FMA:15579 pelvis of left ureter renal pelvis of left kidney uberon UBERON:0018115 left renal pelvis A renal pelvis that is part of a left ureter. OBOL:automatic pelvis of left ureter FMA:15579 renal pelvis of left kidney FMA:15579 A renal pelvis that is part of a right ureter. FMA:15578 pelvis of right kidney pelvis of right ureter uberon UBERON:0018116 right renal pelvis A renal pelvis that is part of a right ureter. OBOL:automatic pelvis of right kidney FMA:15578 pelvis of right ureter FMA:15578 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). A zone of skin that is part of a lower lip. FMA:24767 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 An organ system subdivision that is the part of the lymphoid system that includes the pulmonary lymphatic vessels. FMA:67999 pulmonary lymphatic chain uberon pulmonary lymphatic vasculature UBERON:0018226 pulmonary part of lymphatic system An organ system subdivision that is the part of the lymphoid system that includes the pulmonary lymphatic vessels. pulmonary lymphatic chain FMA:67999 A lymphatic vessel that is part of a lung. FMA:234006 lymphatic vessel of lung uberon UBERON:0018227 pulmonary lymphatic vessel A lymphatic vessel that is part of a lung. OBOL:automatic 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 capsule that divides the parenchyma of the pancreas into lobes and lobules typically thin but can thicken with age pancreatic capsule uberon UBERON:0018235 capsule of pancreas A capsule that divides the parenchyma of the pancreas into lobes and lobules ISBN:0123813611 A boundary delimiting a rhombomere. rhombomere junction uberon UBERON:0018239 rhombomere boundary A boundary delimiting a rhombomere. GO:0021654 A vein that supplies blood to the thymus. FMA:10647 thymic branch of internal thoracic artery uberon thymic arteries UBERON:0018243 The arteries supplying the thymus are derived from the internal thoracic artery, and from the superior thyroid artery and inferior thyroids.[WP] thymic artery FMA A vein that supplies blood to the thymus. thymic branch of internal thoracic artery FMA:10647 thymic arteries A vein that drains a thyroid gland. EMAPA:18648 uberon UBERON:0018246 thyroid vein A vein that drains a thyroid gland. OBOL:automatic An artery that supplies a cervical thymus. uberon UBERON:0018247 cervical thymic artery An artery that supplies a cervical thymus. One of the veins draining a meninix. In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault. FMA:50839 uberon UBERON:0018251 meningeal vein One of the veins draining a meninix. 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 A vein that drains a lacrimal gland. FMA:51779 uberon UBERON:0018256 lacrimal vein A vein that drains a lacrimal gland. OBOL:automatic 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. Any organ component layer that consists of muscle tissue. NCITA class may refer to smooth muscle only FMA:45634 NCIT:C75444 uberon UBERON:0018260 layer of muscle tissue Any organ component layer that consists of muscle tissue. 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 Tissue that is part of some adrenal gland TODO - describe typology of adrenal gland tissue used in this ontology NCIT:C32051 UBERONTEMP:a7bf197b-0db2-467e-824e-be45b39e2672 adrenal gland tissue uberon UBERON:0018303 adrenal tissue Tissue that is part of some adrenal gland PHENOSCAPE:Alex adrenal gland tissue ncithesaurus:Adrenal_Gland_Tissue Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). UBERONTEMP:9ca0bda7-9111-4f59-bc72-5d47bc3d7d61 uberon UBERON:0018321 foramen for glossopharyngeal nerve Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). PHENOSCAPE:alex A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . FMA:54952 canalis nervi facialis facial canal uberon fallopian canal UBERON:0018413 facial nerve canal A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . canalis nervi facialis FMA:54952 FMA:TA facial canal FMA:54952 fallopian canal FMA:54952 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. 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 ventricular heart muscle ventricular muscle the neck region of a bone organ. bone neck neck of bone uberon UBERON:0018664 neck of bone element https://github.com/obophenotype/uberon/wiki/Hidden-GCIs the neck region of a bone organ. 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 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. EMAPA:35869 MA:0003178 uberon UBERON:0019206 tongue papilla epithelium The part of the eye that consists of both the retina and the optic choroid 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 DHBA:10654 FMA:268630 gray matter of the hindbrain uberon UBERON:0019263 gray matter of hindbrain gray matter of the hindbrain DHBA:HGM DHBA:10157 FMA:268608 uberon UBERON:0019264 gray matter of forebrain DHBA:10649 FMA:83913 uberon UBERON:0019267 gray matter of midbrain FMA:83912 uberon UBERON:0019269 gray matter of diencephalon EMAPA:35952 MA:0003174 uberon UBERON:0019304 sensory organ epithelium EMAPA:35958 MA:0003171 uberon UBERON:0019306 nose 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 integumental exocrine gland integumental system exocrine gland The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. EMAPA:37067 FMA:83965 MA:0001033 accessory neural nucleus uberon accessory nucleus of anterior column of spinal cord nucleus accessorius columnae anterioris medullae spinalis nucleus nervi accessorii nucleus of accessory nerve nucleus of the accessory nerve nucleus of the spinal accessory nerve spinal accessory nucleus UBERON:0020358 See also: Wikipedia:Spinal_accessory_nucleus accessory XI nerve nucleus FMA The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. EMAPA:37067 MA:th accessory neural nucleus FMA:83965 accessory nucleus of anterior column of spinal cord NeuroNames:2003 nucleus accessorius columnae anterioris medullae spinalis NeuroNames:2003 nucleus nervi accessorii NeuroNames:2003 nucleus of accessory nerve NeuroNames:2003 nucleus of the accessory nerve NeuroNames:2003 nucleus of the spinal accessory nerve NeuroNames:2003 spinal accessory nucleus A blood vessel that supplies or drains an ear. EMAPA:37386 MA:0001226 uberon UBERON:0020550 auricular blood vessel A blood vessel that supplies or drains an ear. EMAPA:37386 MA:th the single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland) in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe EMAPA:35464 uberon UBERON:0022284 lacrimal gland bud the single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland) MGI:anna 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 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. 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. cavity lining MA:0002448 parietal wall of serous membrane FMA:15859 The layer of endometrial epithelium adjacent to the uterine cavity. FMA:86492 NCIT:C32189 pars basalis of endometrium stratum basalis of endometrium uberon UBERON:0022355 basal layer of endometrium The layer of endometrial epithelium adjacent to the uterine cavity. stratum basalis of endometrium FMA:86492 A blood vessel of the placenta. placental vessel uberon UBERON:0022358 placenta blood vessel A blood vessel of the placenta. GO:0060674 A specific region of the foregut into the area in which the lung will develop. 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 BIRNLEX:1624 lumbar spinal cord gray matter uberon UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter BIRNLEX:1624 lumbar spinal cord gray matter BIRNLEX:1624 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 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 In the cerebellum, some neuronal precursors enter the marginal zone to form clusters of neurons called nuclei[NBK10047] DHBA:12695 EHDAA2:0001152 EMAPA:17789 marginal zone of cerebellum uberon MZCB UBERON:0034708 cerebellum marginal layer marginal zone of cerebellum DHBA:12695 MZCB DHBA:12695 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 The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate. EMAPA:35261 uberon UBERON:0034711 cortical preplate The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate. 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 cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. uberon UBERON:0034717 integumental taste bud A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. A taste bud that is located on a lip. uberon UBERON:0034719 lip taste bud A taste bud that is located on a lip. A taste bud that is located on the skin of the head. uberon UBERON:0034720 head taste bud A taste bud that is located on the skin of the head. A taste bud that is located in the pharynx. uberon UBERON:0034721 pharyngeal taste bud A taste bud that is located in the pharynx. A taste bud that is located in the esophagus. uberon UBERON:0034724 esophageal taste bud A taste bud that is located in the esophagus. A taste bud that is located on the skin of the trunk. uberon UBERON:0034726 trunk taste bud A taste bud that is located on the skin of the trunk. 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 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. EMAPA:37957 MA:th nervus visceralis FMA:5866 visceral nerve FMA:5866 EMAPA:37958 uberon UBERON:0034729 sympathetic nerve EMAPA:37958 MA:th A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. uberon UBERON:0034768 morphological feature A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. 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. 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. respiratory air FMA:84581 EHDAA2:0001472 EMAPA:32796 pituitary primordium uberon UBERON:0034875 future pituitary gland EMAPA Wikipedia pituitary primordium EHDAA2:0001472 the outgrowth of neuroectoderm located on the floor of the embryonic hypothalamus that gives rise to the neurohypophysis (posterior lobe) of the pituitary gland EMAPA:16647 EHDAA2:0004434 EMAPA:16647 uberon neurohypohysial region neurohypophyseal bud UBERON:0034876 future neurohypophysis EMAPA EMAPA the outgrowth of neuroectoderm located on the floor of the embryonic hypothalamus that gives rise to the neurohypophysis (posterior lobe) of the pituitary gland MP:0013339 neurohypohysial region EHDAA2:0004434 neurohypophyseal bud MP:0013339 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 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 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. FMA:19623 dorsum of penis dorsum penis uberon UBERON:0034928 dorsal surface of penis dorsum of penis FMA:19623 dorsum penis FMA:TA 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. 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 biliary system epithelium biliary epithelium BTO:0001513 biliary tract epithelium 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. 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 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. A population of lymphatic endothelial cell precursors that will form the lymph vessels. NCIT:C34262 uberon primary lymph sac UBERON:0034953 embryonic lymph sac VHOG A population of lymphatic endothelial cell precursors that will form the lymph vessels. NCIT:C25787 uberon duct epithelium ductal epithelium UBERON:0034969 epithelial layer of duct DHBA:12682 EMAPA:32917 hindbrain mantle layer uberon UBERON:0034994 hindbrain cortical intermediate zone hindbrain mantle layer EMAPA:32917 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 hemorrhoidal artery uberon UBERON:0035039 rectal artery Any of the interlobular excretory ducts of a salivary gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts[MP,generalized]. FMA:60052 uberon UBERON:0035049 excretory duct of salivary gland Any of the interlobular excretory ducts of a salivary gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts[MP,generalized]. MP:0013750 uberon UBERON:0035050 excretory duct FMA:60053 uberon UBERON:0035053 interlobular duct of salivary gland FMA:71193 uberon lobe or lobule of thymus UBERON:0035075 thymus subunit 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. 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. 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 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 The flattened aspect of the prostate with a slight furrow facing the rectum and anus. FMA:19592 NCIT:C13095 facies posterior (prostatae) facies posterior prostatae posterior surface of prostate gland uberon UBERON:0035165 posterior surface of prostate lexical The flattened aspect of the prostate with a slight furrow facing the rectum and anus. ncithesaurus:Posterior_Surface_of_the_Prostate facies posterior (prostatae) FMA:19592 facies posterior prostatae FMA:19592 FMA:TA posterior surface of prostate gland FMA:19592 The organ of hearing located on the right side of the head. FMA:53641 NCIT:C81285 uberon UBERON:0035174 right ear The organ of hearing located on the right side of the head. ncithesaurus:Right_Ear The tubules that carry lymph throughout the body that are just beneath the surface of the skin. FMA:52011 NCIT:C33663 superficial lymph vessel uberon UBERON:0035198 superficial lymphatic vessel The tubules that carry lymph throughout the body that are just beneath the surface of the skin. ncithesaurus:Superficial_Lymphatic_Vessel superficial lymph vessel FMA:52011 FMA:70506 NCIT:C32837 internal carotid arterial subdivision subdivision of internal carotid artery uberon UBERON:0035237 branch of internal carotid artery internal carotid arterial subdivision FMA:70506 subdivision of internal carotid artery FMA:70506 The narrowest portion of the gallbladder and distal to the cystic duct. FMA:14538 NCIT:C32649 cervix of gallbladder gallbladder neck uberon UBERON:0035267 neck of gallbladder The narrowest portion of the gallbladder and distal to the cystic duct. ncithesaurus:Gallbladder_Neck cervix of gallbladder FMA:14538 gallbladder neck FMA:14538 The organ of hearing located on the left side of the head[ncit,modified]. FMA:53642 NCIT:C81259 uberon UBERON:0035295 left ear The organ of hearing located on the left side of the head[ncit,modified]. ncithesaurus:Left_Ear FMA:55063 NCIT:C12249 posterior wall of hypopharynx uberon UBERON:0035313 posterior wall of laryngopharynx posterior wall of hypopharynx FMA:55063 The membrane the surrounds the prostate gland. FMA:19583 NCIT:C13086 capsule of prostate capsule of prostate gland uberon UBERON:0035316 prostatic capsule The membrane the surrounds the prostate gland. ncithesaurus:Capsule_of_the_Prostate capsule of prostate FMA:19583 capsule of prostate gland FMA:19583 FMA:54908 NCIT:C12244 lateral nasopharynx uberon UBERON:0035383 lateral wall of nasopharynx lateral nasopharynx FMA:54908 FMA:70505 NCIT:C32552 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 FMA:54907 NCIT:C12243 posterior nasopharynx uberon UBERON:0035401 posterior wall of nasopharynx posterior nasopharynx FMA:54907 An artery that supplies the pituitary gland. uberon UBERON:0035403 hypophysial artery An artery that supplies the pituitary gland. The parietal pleura that lines the mediastinum. FMA:9736 NCIT:C94820 mediastinal part of parietal pleura pars mediastinalis (pleurae) pars mediastinalis pleurae parietalis uberon UBERON:0035431 mediastinal pleura FMA FMA The parietal pleura that lines the mediastinum. ncithesaurus:Mediastinal_Pleura mediastinal part of parietal pleura FMA:9736 pars mediastinalis (pleurae) FMA:9736 pars mediastinalis pleurae parietalis FMA:9736 FMA:TA A vein that drains blood from the right adrenal gland into the inferior vena cava. FMA:14343 NCIT:C53131 vena suprarenalis (adrenalis) dextra uberon UBERON:0035435 right suprarenal vein A vein that drains blood from the right adrenal gland into the inferior vena cava. ncithesaurus:Right_Suprarenal_Vein vena suprarenalis (adrenalis) dextra FMA:14343 A space inside the uterus lined by a layer of mucus membranes called the endometrium. FMA:18076 NCIT:C32514 cavity of body of uterus endometrial cavity endometrial lumen intrauterine cavity uberon UBERON:0035465 endometrial cavity A space inside the uterus lined by a layer of mucus membranes called the endometrium. ncithesaurus:Endometrial_Cavity cavity of body of uterus FMA:18076 endometrial cavity FMA:18076 intrauterine cavity FMA:18076 FMA:15590 NCIT:C32895 facies posterior (Ren) facies posterior renis uberon UBERON:0035471 posterior surface of kidney facies posterior (Ren) FMA:15590 facies posterior renis FMA:15590 FMA:TA The external portion of the prostate including the anterior, inferolateral, lateral and posterior surfaces. FMA:19590 NCIT:C13091 prostatic surface surface of prostate gland uberon UBERON:0035480 surface of prostate The external portion of the prostate including the anterior, inferolateral, lateral and posterior surfaces. ncithesaurus:Surface_of_the_Prostate prostatic surface FMA:19590 surface of prostate gland FMA:19590 A vein that drains blood from the left adrenal gland into the left renal artery. FMA:14349 NCIT:C53138 uberon UBERON:0035483 left suprarenal vein A vein that drains blood from the left adrenal gland into the left renal artery. ncithesaurus:Left_Suprarenal_Vein The aspect of the prostate facing the pubic symphysis. FMA:19591 NCIT:C13089 anterior surface of prostate gland facies anterior (prostatae) facies anterior prostatae uberon UBERON:0035523 anterior surface of prostate lexical The aspect of the prostate facing the pubic symphysis. ncithesaurus:Anterior_Surface_of_the_Prostate anterior surface of prostate gland FMA:19591 facies anterior (prostatae) FMA:19591 facies anterior prostatae FMA:19591 FMA:TA Any of several arteries that arise from the aorta and supply blood to the esophagus. FMA:4149 NCIT:C32535 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 The tubules that carry lymph throughout the body that are in the interior of the body or limbs. FMA:52012 NCIT:C32439 deep lymph vessel uberon UBERON:0035545 deep lymphatic vessel The tubules that carry lymph throughout the body that are in the interior of the body or limbs. ncithesaurus:Deep_Lymphatic_Vessel deep lymph vessel FMA:52012 FMA:51797 ciliary vein uberon UBERON:0035546 uveal vein ciliary vein FMA:51797 uberon UBERON:0035548 colic artery 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. vasculature of skin FMA:225275 Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. FMA:76719 NCIT:C33666 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 superficial veins superficial vessels 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. A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. FMA:76718 NCIT:C32444 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 deep vessels Any chamber of the left side of the heart FMA:7166 uberon UBERON:0035553 left cardiac chamber Any chamber of the left side of the heart Any chamber of the right side of the heart FMA:7165 uberon UBERON:0035554 right cardiac chamber Any chamber of the right side of the heart An embryonic structure positioned halfway between the prospective eye and ear, adjacent to the future midbrain-hindbrain boundary. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. XAO:0004093 ophthalmic lobe of trigeminal placode ophthalmic lobe of trigeminal placode complex ophthalmic placode profundus placode uberon UBERON:0035597 profundal placode An embryonic structure positioned halfway between the prospective eye and ear, adjacent to the future midbrain-hindbrain boundary. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. XAO:0004093 ophthalmic lobe of trigeminal placode NCBIBook:NBK53171 ophthalmic lobe of trigeminal placode complex NCBIBook:NBK53171 ophthalmic placode profundus placode XAO:0004093 Any lymph vessel that is located in the dura mater of the brain. while Louveau et al (DOI:10.1038/nature14432) state this is within the CNS (thus overturning dogma about the presence of lymphatics in the CNS), in this ontology the dura dural lymph vessel uberon dural lymph vasculature UBERON:0035608 Louveau et al (DOI:10.1038/nature14432) claim the discovery of lymphatics in the cerebral dura mater, but this is disputed by Bucchieri et al (DOI:10.1111/joa.12381) dura mater lymph vessel Any lymph vessel that is located in the dura mater of the brain. 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 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 adnexa oculi accessory visual structures accessory visual structures FMA:76554 accessory visual structures set FMA:76554 appendage of eye appendages of the eye set of accessory visual structures FMA:76554 structurae oculi accessoriae Any nerve that innervates the larynx. MESH:A08.800.050.050.925.450 uberon UBERON:0035642 laryngeal nerve Any nerve that innervates the larynx. UBERON:cjm Any nerve that innervates the penis. EMAPA:35057 penile nerve penis nerve uberon UBERON:0035649 nerve of penis Any nerve that innervates the penis. UBERON:cjm Any nerve that innervates the clitoris. EMAPA:35044 clitoral nerve clitoris nerve uberon UBERON:0035650 nerve of clitoris Any nerve that innervates the clitoris. UBERON:cjm uberon UBERON:0035651 glans 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 FMA:5968 intrapulmonary lymph node pulmonary node uberon UBERON:0035764 pulmonary lymph node intrapulmonary lymph node FMA:5968 pulmonary node FMA:5968 FMA:223208 NCIT:C12930 uberon UBERON:0035767 intrapulmonary bronchus 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 muscularis externa of sigmoid colon FMA:15028 FMA:12241 uberon UBERON:0035809 serous cavity The sum of epicardial and paracardial fat deposits. ZFA:0005765 uberon UBERON:0035814 pericardial fat The sum of epicardial and paracardial fat deposits. 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 . intrathoracic fat 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 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 MA:0000054 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. peritoneal component EMAPA:16137 the thick outer layer of the adrenal gland that is in the left side of the abdomen FMA:69089 cortex of left adrenal gland cortex of left suprarenal gland left adrenal cortex uberon UBERON:0035825 left adrenal gland cortex true the thick outer layer of the adrenal gland that is in the left side of the abdomen cortex of left adrenal gland FMA:69089 cortex of left suprarenal gland FMA:69089 left adrenal cortex FMA:69089 the adrenal gland medulla that is in the left side of the abdomen FMA:69092 left adrenal medulla medulla of left adrenal gland medulla of left suprarenal gland uberon UBERON:0035826 left adrenal gland medulla true the adrenal gland medulla that is in the left side of the abdomen left adrenal medulla FMA:69092 medulla of left adrenal gland FMA:69092 medulla of left suprarenal gland FMA:69092 the thick outer layer of the adrenal gland that is in the right side of the abdomen FMA:69088 cortex of right adrenal gland cortex of right suprarenal gland right adrenal cortex uberon UBERON:0035827 right adrenal gland cortex true the thick outer layer of the adrenal gland that is in the right side of the abdomen cortex of right adrenal gland FMA:69088 cortex of right suprarenal gland FMA:69088 right adrenal cortex FMA:69088 the adrenal gland medulla that is in the right side of the abdomen FMA:69091 medulla of right adrenal gland medulla of right suprarenal gland right adrenal medulla uberon UBERON:0035828 right adrenal gland medulla true the adrenal gland medulla that is in the right side of the abdomen medulla of right adrenal gland FMA:69091 medulla of right suprarenal gland FMA:69091 right adrenal medulla FMA:69091 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 costal part of diaphragm pars costalis diaphragmatis uberon UBERON:0035831 costal diaphragm 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. costal part of diaphragm FMA:58277 pars costalis diaphragmatis FMA:TA The lumen of the epididymis FMA:18274 epididymis lumen lumen of epididymis uberon UBERON:0035956 epididymal lumen FMA The lumen of the epididymis GOC:DOS epididymis lumen FMA:18274 lumen of epididymis FMA:18274 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 The lower portion of the larynx, extending from just beneath the vocal cords down to the top of the trachea. the structures in the subglottis are implicated in the regulation of the temperature of the breath EMAPA:37969 FMA:55477 NCIT:C12280 infraglottic part of larynx subglottic larynx subglottic region uberon UBERON:0036068 subglottis The lower portion of the larynx, extending from just beneath the vocal cords down to the top of the trachea. MP:0030000 ORCID:orcid.org/0000-0002-6490-7723 EMAPA:37969 MA:th infraglottic part of larynx FMA:55477 subglottic larynx FMA:55477 subglottic region MP:0030000 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. BGEE:ann An organ subunit in the skin that gives rise to cutaneous appendage. follicle cutaneous appendage follicle skin follicle uberon UBERON:0036150 skin appendage follicle An organ subunit in the skin that gives rise to cutaneous appendage. UBERON:cjm An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 uberon rectosigmoid region UBERON:0036214 rectosigmoid junction An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 rectosigmoid region NCIT:C54188 Material anatomical entity that forms the outermost boundary of an anatomical structure. AAO:0010270 AEO:0000154 ZFA:0005594 uberon UBERON:0036215 anatomical surface region Material anatomical entity that forms the outermost boundary of an anatomical structure. 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. 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 Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. uberon vaginal discharge vaginal secretion UBERON:0036243 vaginal fluid Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. 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 Any of the eight ligaments pertaining to the uterus including the anterior, posterior, lateral, sacro-uterine and round ligaments. NCIT:C61360 uberon UBERON:0036262 uterine ligament Any of the eight ligaments pertaining to the uterus including the anterior, posterior, lateral, sacro-uterine and round ligaments. NCIT:C61360 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 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. ramus zygomaticotemporalis (Nervus zygomaticus) FMA:52972 ramus zygomaticotemporalis nervus zygomatici FMA:TA zygomaticotemporal branch of zygomatic nerve FMA:52972 zygomaticotemporal zygomaticotemporal branch uberon UBERON:0036267 vulval vein uberon UBERON:0036268 pelvic vein EMAPA:30807 uberon penis vasculature vasculature of penis UBERON:0036269 penis blood vessel vasculature of penis EMAPA:30807 Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall pared del ventrC-culo izquierdo@es 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 pared del ventrC-culo izquierdo@es FMA:9556 Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 pared del ventrC-culo derecho@es 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 pared del ventrC-culo derecho@es FMA:9533 right ventricular wall FMA:9533 FMA:9560 uberon UBERON:0036288 anterior wall of left ventricle 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 The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 renal pelvis and ureter renal pelvis plus ureter uberon UBERON:0036295 renal pelvis/ureter NCIT The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 FMA:225251 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 A zone of skin that is part of the face. eriks 2012-02-05T05:23:01Z EMAPA:36657 FMA:24758 NCIT:C33561 UMLS:C0222084 face skin uberon facial skin UBERON:1000021 skin of face A zone of skin that is part of the face. UBERON:EJS 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 EFO:0003612 TAO:0001053 ZFA:0001053 PICA primitive internal carotid artery uberon UBERON:2001053 future internal carotid artery EHDAA2 PICA TAO:0001053 primitive internal carotid artery ZFA:0001053 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 teleost_anatomy_curators ZFA:0001073 uberon/phenoscape-anatomy axial vasculature 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 teleost_anatomy_curators ZFA:0001457 uberon/phenoscape-anatomy postcranial axial cartilage Cartilage which is part of the axial skeleton. ZFIN:curator 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 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 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 teleost_anatomy_curators ZFA:0007013 uberon/phenoscape-anatomy preplacodal ectoderm Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. ZFIN:curator 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 amphibian_anatomy_curators uberon/phenoscape-anatomy 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 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 amphibian_anatomy_curators uberon/phenoscape-anatomy head external integument structure Dermal, epidermal, glandular and pigment structures of the external head integument. AAO:EJS 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 amphibian_anatomy_curators uberon/phenoscape-anatomy body external integument structure Dermal, epidermal, glandular and pigment structures of the body integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the limb 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 amphibian_anatomy_curators uberon/phenoscape-anatomy limb external integument structure Dermal, epidermal, glandular and pigment structures of the limb integument. AAO:EJS 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 amphibian_anatomy_curators uberon/phenoscape-anatomy tail external integument structure Dermal, epidermal, glandular and pigment structures of the tail integument. AAO:EJS Blood vessels in respiratory skin. Modified from the original AAO source amphibian_anatomy_curators uberon/phenoscape-anatomy vasculature of respiratory integument Blood vessels in respiratory skin. AAO:EJS Anatomical projection that is composed of bone or cartilage tissue. none skeletal element projection An anatomical surface that is part of a bone bone surface surface of bone Mesenchyme that is part of a forelimb bud. WD forelimb bud mesenchyme Mesenchyme that is part of a hindlimb bud. WD hindlimb bud mesenchyme example to be eventually removed 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 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 term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term 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 Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated 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 Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged 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 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 This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other true 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 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 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 Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term 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 ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times 2019-07-12T14:23:27Z avoided excessive intake of food 2 2 1 2 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 From ligand activity to has_ligand This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" 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 From has_ligand to ligand activity 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).